From 99c8e2243b7c37f2284189984e37a26742a21b3b Mon Sep 17 00:00:00 2001 From: Samuel Nichols Date: Fri, 6 May 2022 10:59:05 -0600 Subject: [PATCH 01/33] Adding files --- CRISPRessoReport.py | 636 +++++++++++++++++++++++ templates/CRISPResso_justcup.png | Bin 0 -> 42782 bytes templates/favicon.ico | Bin 0 -> 1150 bytes templates/layout.html | 104 ++++ templates/multiReport.html | 285 +++++++++++ templates/report.html | 854 +++++++++++++++++++++++++++++++ 6 files changed, 1879 insertions(+) create mode 100644 CRISPRessoReport.py create mode 100644 templates/CRISPResso_justcup.png create mode 100644 templates/favicon.ico create mode 100644 templates/layout.html create mode 100644 templates/multiReport.html create mode 100644 templates/report.html diff --git a/CRISPRessoReport.py b/CRISPRessoReport.py new file mode 100644 index 00000000..a49f2584 --- /dev/null +++ b/CRISPRessoReport.py @@ -0,0 +1,636 @@ +''' +CRISPResso2 - Kendell Clement and Luca Pinello 2018 +Software pipeline for the analysis of genome editing outcomes from deep sequencing data +(c) 2020 The General Hospital Corporation. All Rights Reserved. +''' + +import os +from jinja2 import Environment, FileSystemLoader +from CRISPResso2 import CRISPRessoShared + + +def make_report_from_folder(crispresso_report_file, crispresso_folder, _ROOT): + """ + Makes an html report for a crispresso run + + Parameters: + crispresso_report_file (string): name of the html file to create + crispresso_folder (string): path to the crispresso output + _ROOT (string): path to crispresso executables (for templates) + + Returns: + Nothin + """ + run_data = CRISPRessoShared.load_crispresso_info(crispresso_folder) + make_report(run_data, crispresso_report_file, crispresso_folder, _ROOT) + + +def make_report(run_data, crispresso_report_file, crispresso_folder, _ROOT): + # dicts for each amplicon fig_names[amp_name] = [list of fig names] + # fig_locs[amp_name][fig_name] = figure location + # print('crispresso_report file: ' + crispresso_report_file + ' crispresso_folder : ' + crispresso_folder + ' root: ' + _ROOT) + figures = {'names': {}, 'locs': {}, 'titles': {}, 'captions': {}, 'datas': {}, 'htmls': {}, 'sgRNA_based_names': {}} + + def add_fig_if_exists(fig_name, fig_root, fig_title, fig_caption, fig_data, + amplicon_fig_names, amplicon_figures): + """ + Helper function to add figure if the file exists + if fig at filename exists, + amplicon_figs[figname] is set to that file + """ + # fullpath=os.path.join(crispresso_folder,fig_root+'.png') + pngfullpath = os.path.join(crispresso_folder, fig_root + '.png') + htmlfullpath = os.path.join(crispresso_folder, fig_root + '.html') + # print('adding file ' + fig_root + ' at ' + fullpath) + if os.path.exists(pngfullpath) or os.path.exists(htmlfullpath): + amplicon_fig_names.append(fig_name) + # amplicon_fig_locs[fig_name]=os.path.basename(fig_root+'.png') + amplicon_figures['locs'][fig_name] = os.path.basename(fig_root) + amplicon_figures['titles'][fig_name] = fig_title + amplicon_figures['captions'][fig_name] = fig_caption + amplicon_figures['datas'][fig_name] = [] + for (data_caption, data_file) in fig_data: + if os.path.exists(os.path.join(crispresso_folder, data_file)): + amplicon_figures['datas'][fig_name].append((data_caption, data_file)) + if os.path.exists(htmlfullpath): + with open(htmlfullpath) as html: + html_string = "
" + html_string += html.read() + html_string += "
" + amplicon_figures['htmls'][fig_name] = html_string + + global_fig_names = [] + for fig in ['1a', '1b', '1c', '1d', '5a', '6a', '8a', '11c']: + fig_name = 'plot_' + fig + if fig_name + '_root' in run_data['results']['general_plots']: + add_fig_if_exists(fig_name, run_data['results']['general_plots'][fig_name + '_root'], 'Figure ' + fig, + run_data['results']['general_plots'][fig_name + '_caption'], + run_data['results']['general_plots'][fig_name + '_data'], + global_fig_names, figures) + + amplicons = [] + for amplicon_name in run_data['results']['ref_names']: + amplicons.append(amplicon_name) + amplicon_figures = {'names': [], 'locs': {}, 'titles': {}, 'captions': {}, 'datas': {}} + + for fig in ['2a', '3a', '3b', '4a', '4b', '4c', '4d', '4e', '4f', '4g', '5', '6', '7', '8', '10a', '10b', '10c', + '11a']: + fig_name = 'plot_' + fig + if fig_name + '_root' in run_data['results']['refs'][amplicon_name]: + add_fig_if_exists(fig_name, run_data['results']['refs'][amplicon_name][fig_name + '_root'], + 'Figure ' + fig_name, + run_data['results']['refs'][amplicon_name][fig_name + '_caption'], + run_data['results']['refs'][amplicon_name][fig_name + '_data'], + global_fig_names, amplicon_figures) + + this_sgRNA_based_fig_names = {} + for fig in ['2b', '9', '10d', '10e', '10f', '10g', '11b']: + # fig 2b's + this_fig_names = [] + if 'plot_' + fig + '_roots' in run_data['results']['refs'][amplicon_name]: + for idx, plot_root in enumerate(run_data['results']['refs'][amplicon_name]['plot_' + fig + '_roots']): + fig_name = "plot_" + fig + "_" + str(idx) + add_fig_if_exists(fig_name, plot_root, 'Figure ' + fig_name + ' sgRNA ' + str(idx + 1), + run_data['results']['refs'][amplicon_name]['plot_' + fig + '_captions'][idx], + run_data['results']['refs'][amplicon_name]['plot_' + fig + '_datas'][idx], + this_fig_names, amplicon_figures) + this_sgRNA_based_fig_names[fig] = this_fig_names + + figures['names'][amplicon_name] = amplicon_figures['names'] + figures['sgRNA_based_names'][amplicon_name] = this_sgRNA_based_fig_names + + figures['locs'][amplicon_name] = amplicon_figures['locs'] + figures['titles'][amplicon_name] = amplicon_figures['titles'] + figures['captions'][amplicon_name] = amplicon_figures['captions'] + figures['datas'][amplicon_name] = amplicon_figures['datas'] + + report_display_name = "" + if run_data['running_info']['args'].name != "": + report_display_name = run_data['running_info']['args'].name + + # find path between the report and the data (if the report is in another directory vs in the same directory as the data) + crispresso_data_path = os.path.relpath(crispresso_folder, os.path.dirname(crispresso_report_file)) + if crispresso_data_path == ".": + crispresso_data_path = "" + else: + crispresso_data_path += "/" + + report_data = { + 'amplicons': amplicons, + 'figures': figures, + 'run_data': run_data, + 'report_display_name': report_display_name, + 'crispresso_data_path': crispresso_data_path, + } + + j2_env = Environment(loader=FileSystemLoader(os.path.join(_ROOT, 'templates'))) + template = j2_env.get_template('report.html') + + # dest_dir = os.path.dirname(crispresso_report_file) + # shutil.copy2(os.path.join(_ROOT,'templates','CRISPResso_justcup.png'),dest_dir) + # shutil.copy2(os.path.join(_ROOT,'templates','favicon.ico'),dest_dir) + + outfile = open(crispresso_report_file, 'w') + outfile.write(template.render(report_data=report_data)) + outfile.close() + + +def make_batch_report_from_folder(crispressoBatch_report_file, crispresso2_info, batch_folder, _ROOT): + batch_names = crispresso2_info['results']['completed_batch_arr'] + display_names = crispresso2_info['results']['batch_input_names'] + + window_nuc_pct_quilts = crispresso2_info['results']['general_plots']['window_nuc_pct_quilt_plot_names'] + nuc_pct_quilts = crispresso2_info['results']['general_plots']['nuc_pct_quilt_plot_names'] + + window_nuc_conv_plots = crispresso2_info['results']['general_plots']['window_nuc_conv_plot_names'] + nuc_conv_plots = crispresso2_info['results']['general_plots']['nuc_conv_plot_names'] + + summary_plot_names = [] + if 'summary_plot_names' in crispresso2_info['results']['general_plots']: + summary_plot_names = crispresso2_info['results']['general_plots']['summary_plot_names'] + summary_plot_titles = {} + if 'summary_plot_titles' in crispresso2_info['results']['general_plots']: + summary_plot_titles = crispresso2_info['results']['general_plots']['summary_plot_titles'] + summary_plot_labels = {} + if 'summary_plot_labels' in crispresso2_info['results']['general_plots']: + summary_plot_labels = crispresso2_info['results']['general_plots']['summary_plot_labels'] + summary_plot_datas = {} + if 'summary_plot_datas' in crispresso2_info['results']['general_plots']: + summary_plot_datas = crispresso2_info['results']['general_plots']['summary_plot_datas'] + + allele_modification_heatmap_plot = {} + if 'allele_modification_heatmap_plot_names' in crispresso2_info['results']['general_plots']: + allele_modification_heatmap_plot['names'] = crispresso2_info['results']['general_plots']['allele_modification_heatmap_plot_names'] + else: + allele_modification_heatmap_plot['names'] = [] + if 'allele_modification_heatmap_plot_paths' in crispresso2_info['results']['general_plots']: + allele_modification_heatmap_plot['paths'] = crispresso2_info['results']['general_plots']['allele_modification_heatmap_plot_paths'] + else: + allele_modification_heatmap_plot['paths'] = {} + if 'allele_modification_heatmap_plot_titles' in crispresso2_info['results']['general_plots']: + allele_modification_heatmap_plot['titles'] = crispresso2_info['results']['general_plots']['allele_modification_heatmap_plot_titles'] + else: + allele_modification_heatmap_plot['titles'] = [] + if 'allele_modification_heatmap_plot_labels' in crispresso2_info['results']['general_plots']: + allele_modification_heatmap_plot['labels'] = crispresso2_info['results']['general_plots']['allele_modification_heatmap_plot_labels'] + else: + allele_modification_heatmap_plot['labels'] = {} + if 'allele_modification_heatmap_plot_datas' in crispresso2_info['results']['general_plots']: + allele_modification_heatmap_plot['datas'] = crispresso2_info['results']['general_plots']['allele_modification_heatmap_plot_datas'] + else: + allele_modification_heatmap_plot['datas'] = {} + + allele_modification_line_plot = {} + if 'allele_modification_line_plot_names' in crispresso2_info['results']['general_plots']: + allele_modification_line_plot['names'] = crispresso2_info['results']['general_plots']['allele_modification_line_plot_names'] + else: + allele_modification_line_plot['names'] = [] + if 'allele_modification_line_plot_paths' in crispresso2_info['results']['general_plots']: + allele_modification_line_plot['paths'] = crispresso2_info['results']['general_plots']['allele_modification_line_plot_paths'] + else: + allele_modification_line_plot['paths'] = {} + if 'allele_modification_line_plot_titles' in crispresso2_info['results']['general_plots']: + allele_modification_line_plot['titles'] = crispresso2_info['results']['general_plots']['allele_modification_line_plot_titles'] + else: + allele_modification_line_plot['titles'] = [] + if 'allele_modification_line_plot_labels' in crispresso2_info['results']['general_plots']: + allele_modification_line_plot['labels'] = crispresso2_info['results']['general_plots']['allele_modification_line_plot_labels'] + else: + allele_modification_line_plot['labels'] = {} + if 'allele_modification_line_plot_datas' in crispresso2_info['results']['general_plots']: + allele_modification_line_plot['datas'] = crispresso2_info['results']['general_plots']['allele_modification_line_plot_datas'] + else: + allele_modification_line_plot['datas'] = {} + + allele_modification_heatmap_plot['htmls'] = {} + for heatmap_plot_name, heatmap_plot_path in allele_modification_heatmap_plot['paths'].items(): + with open(heatmap_plot_path) as fh: + allele_modification_heatmap_plot['htmls'][heatmap_plot_name] = fh.read() + + allele_modification_line_plot['htmls'] = {} + for line_plot_name, line_plot_path in allele_modification_line_plot['paths'].items(): + with open(line_plot_path) as fh: + allele_modification_line_plot['htmls'][line_plot_name] = fh.read() + + #find path between the report and the data (if the report is in another directory vs in the same directory as the data) + crispresso_data_path = os.path.relpath(batch_folder, os.path.dirname(crispressoBatch_report_file)) + if crispresso_data_path == ".": + crispresso_data_path = "" + else: + crispresso_data_path += "/"; + + sub_html_files = {} + run_names = [] + for name in batch_names: + display_name = display_names[name] + sub_folder = 'CRISPResso_on_' + name + crispresso_folder = os.path.join(batch_folder, sub_folder) + run_data = CRISPRessoShared.load_crispresso_info(crispresso_folder) + if 'running_info' not in run_data: + raise Exception('CRISPResso run %s has no report. Cannot add to batch report.' % sub_folder) + + this_sub_html_file = sub_folder + ".html" + if run_data['running_info']['args'].place_report_in_output_folder: + this_sub_html_file = os.path.join(sub_folder, run_data['running_info']['report_filename']) + sub_html_files[display_name] = this_sub_html_file + + run_names.append(display_name) + + output_title = 'CRISPResso Batch Output' + if crispresso2_info['running_info']['args'].name != '': + output_title += '
{0}'.format(crispresso2_info['running_info']['args'].name) + + make_multi_report( + run_names, + sub_html_files, + crispressoBatch_report_file, + batch_folder, + _ROOT, + output_title, + summary_plots={ + 'names': summary_plot_names, + 'titles': summary_plot_titles, + 'labels': summary_plot_labels, + 'datas': summary_plot_datas, + }, + window_nuc_pct_quilts=window_nuc_pct_quilts, + nuc_pct_quilts=nuc_pct_quilts, + window_nuc_conv_plots=window_nuc_conv_plots, + nuc_conv_plots=nuc_conv_plots, + allele_modification_heatmap_plot=allele_modification_heatmap_plot, + allele_modification_line_plot=allele_modification_line_plot, + ) + + +def make_pooled_report_from_folder(crispresso_report_file, crispresso2_info, folder, _ROOT): + names_arr = crispresso2_info['results']['good_region_names'] + output_title = 'CRISPResso Pooled Output' + if crispresso2_info['running_info']['args'].name != '': + output_title += '
{0}'.format(crispresso2_info['running_info']['args'].name) + make_multi_report_from_folder(crispresso2_info, names_arr, output_title, crispresso_report_file, folder, _ROOT) + + +def make_compare_report_from_folder(crispresso_report_file, crispresso2_info, folder, _ROOT): + names_arr = [] + output_title = 'CRISPResso Compare Output' + if crispresso2_info['running_info']['args'].name != '': + output_title += '
{0}'.format(crispresso2_info['running_info']['args'].name) + make_multi_report_from_folder(crispresso2_info, names_arr, output_title, crispresso_report_file, folder, _ROOT) + + +def make_meta_report_from_folder(crispresso_report_file, crispresso2_info, folder, _ROOT): + names_arr = crispresso2_info['meta_names_arr'] + input_names = crispresso2_info['meta_input_names'] + output_title = 'CRISPresso Meta Output' + if crispresso2_info['running_info']['args'].name != '': + output_title += '
{0}'.format(crispresso2_info['running_info']['args'].name) + make_multi_report_from_folder(crispresso2_info, names_arr, output_title, crispresso_report_file, folder, _ROOT, + display_names=input_names) + + +def make_wgs_report_from_folder(crispresso_report_file, crispresso2_info, folder, _ROOT): + names_arr = crispresso2_info['results']['good_region_names'] + output_title = 'CRISPResso WGS Output' + if crispresso2_info['running_info']['args'].name != '': + output_title += '
{0}'.format(crispresso2_info['running_info']['args'].name) + make_multi_report_from_folder(crispresso2_info, names_arr, output_title, crispresso_report_file, folder, _ROOT) + + +def make_multi_report_from_folder(crispresso2_info, names_arr, report_name, crispresso_report_file, folder, _ROOT, + display_names=None): + """ + Prepares information to make a report of multiple CRISPResso runs - like CRISPRessoWGS or CRISPRessoPooled + + Parameters: + crispresso2_info (dict): information from the crispresso multi run + names_arr (arr of strings): Names of the crispresso runs + report_name (string): text to be shown at top of report + crispresso_report_file (string): path to write report to + folder (string): folder containing crispresso runs + _ROOT (string): location of crispresso assets (images, templates, etc) + display_names (dict): report_name->display_name; Titles to be shown for crispresso runs (if different from names_arr, e.g. if display_names have spaces or bad chars, they won't be the same as names_arr) + + Returns: + Nothin + """ + + summary_plot_names = [] + if 'summary_plot_names' in crispresso2_info['results']['general_plots']: + summary_plot_names = crispresso2_info['results']['general_plots']['summary_plot_names'] + summary_plot_titles = {} + if 'summary_plot_titles' in crispresso2_info['results']['general_plots']: + summary_plot_titles = crispresso2_info['results']['general_plots']['summary_plot_titles'] + summary_plot_labels = {} + if 'summary_plot_labels' in crispresso2_info['results']['general_plots']: + summary_plot_labels = crispresso2_info['results']['general_plots']['summary_plot_labels'] + summary_plot_datas = {} + if 'summary_plot_datas' in crispresso2_info['results']['general_plots']: + summary_plot_datas = crispresso2_info['results']['general_plots']['summary_plot_datas'] + + run_names = [] + sub_html_files = {} + sub_2a_labels = {} + sub_2a_pdfs = {} + + for name in names_arr: + display_name = name + if display_names is not None: + display_name = display_names[name] + + folder_name = 'CRISPResso_on_%s' % name + sub_folder = os.path.join(folder, folder_name) + run_data = CRISPRessoShared.load_crispresso_info(sub_folder) + if 'running_info' not in run_data: + raise Exception('CRISPResso run %s has no report. Cannot add to report.' % sub_folder) + + run_names.append(display_name) + + this_sub_html_file = os.path.basename(folder_name) + ".html" + if run_data['running_info']['args'].place_report_in_output_folder: + this_sub_html_file = os.path.join(os.path.basename(sub_folder), run_data['running_info']['report_filename']) + sub_html_files[display_name] = this_sub_html_file + + this_sub_2a_labels = [] + this_sub_2a_pdfs = [] + for ref_name in run_data['results']['ref_names']: + if 'plot_2a_root' in run_data['results']['refs'][ref_name]: + pdf_file = run_data['results']['refs'][ref_name]['plot_2a_root'] + ".pdf" + if os.path.exists(pdf_file): + this_sub_2a_pdfs.append(run_data['results']['refs'][ref_name]['plot_2a_root'] + ".pdf") + this_sub_2a_labels.append("Nucleotide distribution across " + ref_name) + + sub_2a_labels[display_name] = this_sub_2a_labels + sub_2a_pdfs[display_name] = this_sub_2a_pdfs + + make_multi_report( + run_names, + sub_html_files, + crispresso_report_file, + folder, + _ROOT, + report_name, + summary_plots={ + 'names': summary_plot_names, + 'titles': summary_plot_titles, + 'labels': summary_plot_labels, + 'datas': summary_plot_datas, + }, + ) + + +def make_multi_report( + run_names, + sub_html_files, + crispresso_multi_report_file, + crispresso_folder, + _ROOT, + report_name, + window_nuc_pct_quilts=[], + nuc_pct_quilts=[], + window_nuc_conv_plots=[], + nuc_conv_plots=[], + summary_plots={ + 'names': [], + 'titles': [], + 'labels': [], + 'datas': [], + }, + compact_plots_to_show={}, + allele_modification_heatmap_plot={}, + allele_modification_line_plot={}, +): + """ + Makes an HTML report for a run containing multiple crispresso runs + + Parameters: + run_names (arr of strings): names of runs + sub_html_files (dict): dict of run_name->file_loc + crispresso_multi_report_file (string): path of file to write to + report_name (string): description of report type to be shown at top of report + crispresso_folder (string): absolute path to the crispresso output + _ROOT (string): absolute path to the crispresso executable + +<<<<<<< HEAD + summary_plot (dict): a dict with the following keys: +======= + summary_plots (dict): a dict with the following keys: +>>>>>>> origin/master + names (list): list of plot names - keys for following dicts + titles (dict): dict of plot_name->plot_title + labels (dict): dict of plot_name->plot_label + datas (dict): dict of plot_name->[(datafile_description, data_filename), ...] + compact_plots_to_show (dict): name=>{'href': path to target(report) when user clicks on image, 'img': path to png image to show} + allele_modification_heatmap_plot (dict): a dict with the following keys: + names (list): list of plot names for heatmaps, keys for dicts below + htmls (dict): dict of plot_name->HTML for the plot + titles (dict): dict of plot_name->plot_title + labels (dict): dict of plot_name->plot_label + datas (dict): dict of plot_name->[(datafile_description, data_filename), ...] + """ + + def dirname(path): + return os.path.basename(os.path.dirname(path)) + + def fill_default(dictionary, key, default_type=list): + if key not in dictionary: + dictionary[key] = default_type() + + j2_env = Environment( + loader=FileSystemLoader(os.path.join(_ROOT, 'templates')), + ) + j2_env.filters['dirname'] = dirname + template = j2_env.get_template('multiReport.html') + + crispresso_data_path = os.path.relpath( + crispresso_folder, os.path.dirname(crispresso_multi_report_file), + ) + if crispresso_data_path == ".": + crispresso_data_path = "" + else: + crispresso_data_path += "/" + + dictionaries = [ + allele_modification_heatmap_plot, allele_modification_line_plot, + ] + keys_and_default_types = [ + ('names', list), + ('htmls', dict), + ('titles', list), + ('labels', dict), + ('datas', dict), + ] + for dictionary in dictionaries: + for key, default_type in keys_and_default_types: + fill_default( + dictionary, + key, + default_type, + ) + + with open(crispresso_multi_report_file, 'w') as outfile: + outfile.write(template.render( + window_nuc_pct_quilts=window_nuc_pct_quilts, + nuc_pct_quilts=nuc_pct_quilts, + window_nuc_conv_plots=window_nuc_conv_plots, + nuc_conv_plots=nuc_conv_plots, + crispresso_data_path=crispresso_data_path, + summary_plot_names=summary_plots['names'], + summary_plot_titles=summary_plots['titles'], + summary_plot_labels=summary_plots['labels'], + summary_plot_datas=summary_plots['datas'], + run_names=run_names, + sub_html_files=sub_html_files, + report_name=report_name, + compact_plots_to_show=compact_plots_to_show, + allele_modification_heatmap_plot_names=allele_modification_heatmap_plot['names'], + allele_modification_heatmap_plot_htmls=allele_modification_heatmap_plot['htmls'], + allele_modification_heatmap_plot_titles=allele_modification_heatmap_plot['titles'], + allele_modification_heatmap_plot_labels=allele_modification_heatmap_plot['labels'], + allele_modification_heatmap_plot_datas=allele_modification_heatmap_plot['datas'], + allele_modification_line_plot_names=allele_modification_line_plot['names'], + allele_modification_line_plot_htmls=allele_modification_line_plot['htmls'], + allele_modification_line_plot_titles=allele_modification_line_plot['titles'], + allele_modification_line_plot_labels=allele_modification_line_plot['labels'], + allele_modification_line_plot_datas=allele_modification_line_plot['datas'], + )) + + +def make_aggregate_report( + crispresso2_info, + report_name, + crispresso_report_file, + crispresso_report_folder, + _ROOT, + folder_arr, + crispresso_html_reports, + compact_plots_to_show={}, + display_names=None, +): + """ + Prepares information to make a report of a CRISPRessoAggregate run + + Parameters: + crispresso2_info (dict): information from the crispresso aggregate run + report_name (string): text to be shown at top of report + crispresso_report_file (string): path to write report to + crispresso_report_folder (string): path containing aggregated plots, etc. + _ROOT (string): location of crispresso assets (images, templates, etc) + folder_arr (arr of strings): paths to the aggregated crispresso folders + crispresso_html_reports (dict): folder->html_path; Paths to the aggregated crispresso run html reports + compact_plots_to_show (dict): name=>{'href': path to target(report) when user clicks on image, 'img': path to png image to show} + display_names (dict): folder->display_name; Titles to be shown for crispresso runs (if different from names_arr, e.g. if display_names have spaces or bad chars, they won't be the same as names_arr) + + Returns: + Nothin + """ + summary_plots = {} + if 'summary_plot_names' in crispresso2_info['results']['general_plots']: + summary_plots['names'] = crispresso2_info['results']['general_plots']['summary_plot_names'] + else: + summary_plots['names'] = [] + if 'summary_plot_titles' in crispresso2_info['results']['general_plots']: + summary_plots['titles'] = crispresso2_info['results']['general_plots']['summary_plot_titles'] + else: + summary_plots['titles'] = {} + if 'summary_plot_labels' in crispresso2_info['results']['general_plots']: + summary_plots['labels'] = crispresso2_info['results']['general_plots']['summary_plot_labels'] + else: + summary_plots['labels'] = {} + if 'summary_plot_datas' in crispresso2_info['results']['general_plots']: + summary_plots['datas'] = crispresso2_info['results']['general_plots']['summary_plot_datas'] + else: + summary_plots['datas'] = {} + + allele_modification_heatmap_plot = {} + if 'allele_modification_heatmap_plot_names' in crispresso2_info['results']['general_plots']: + allele_modification_heatmap_plot['names'] = crispresso2_info['results']['general_plots']['allele_modification_heatmap_plot_names'] + else: + allele_modification_heatmap_plot['names'] = [] + if 'allele_modification_heatmap_plot_paths' in crispresso2_info['results']['general_plots']: + allele_modification_heatmap_plot['paths'] = crispresso2_info['results']['general_plots']['allele_modification_heatmap_plot_paths'] + else: + allele_modification_heatmap_plot['paths'] = {} + if 'allele_modification_heatmap_plot_titles' in crispresso2_info['results']['general_plots']: + allele_modification_heatmap_plot['titles'] = crispresso2_info['results']['general_plots']['allele_modification_heatmap_plot_titles'] + else: + allele_modification_heatmap_plot['titles'] = {} + if 'allele_modification_heatmap_plot_labels' in crispresso2_info['results']['general_plots']: + allele_modification_heatmap_plot['labels'] = crispresso2_info['results']['general_plots']['allele_modification_heatmap_plot_labels'] + else: + allele_modification_heatmap_plot['labels'] = {} + if 'allele_modification_heatmap_plot_datas' in crispresso2_info['results']['general_plots']: + allele_modification_heatmap_plot['datas'] = crispresso2_info['results']['general_plots']['allele_modification_heatmap_plot_datas'] + else: + allele_modification_heatmap_plot['datas'] = {} + + allele_modification_line_plot = {} + if 'allele_modification_line_plot_names' in crispresso2_info['results']['general_plots']: + allele_modification_line_plot['names'] = crispresso2_info['results']['general_plots']['allele_modification_line_plot_names'] + else: + allele_modification_line_plot['names'] = [] + if 'allele_modification_line_plot_paths' in crispresso2_info['results']['general_plots']: + allele_modification_line_plot['paths'] = crispresso2_info['results']['general_plots']['allele_modification_line_plot_paths'] + else: + allele_modification_line_plot['paths'] = {} + if 'allele_modification_line_plot_titles' in crispresso2_info['results']['general_plots']: + allele_modification_line_plot['titles'] = crispresso2_info['results']['general_plots']['allele_modification_line_plot_titles'] + else: + allele_modification_line_plot['titles'] = {} + if 'allele_modification_line_plot_labels' in crispresso2_info['results']['general_plots']: + allele_modification_line_plot['labels'] = crispresso2_info['results']['general_plots']['allele_modification_line_plot_labels'] + else: + allele_modification_line_plot['labels'] = {} + if 'allele_modification_line_plot_datas' in crispresso2_info['results']['general_plots']: + allele_modification_line_plot['datas'] = crispresso2_info['results']['general_plots']['allele_modification_line_plot_datas'] + else: + allele_modification_line_plot['datas'] = {} + + window_nuc_pct_quilts = [] + if 'window_nuc_pct_quilt_plot_names' in crispresso2_info['results']['general_plots']: + window_nuc_pct_quilts = crispresso2_info['results']['general_plots']['window_nuc_pct_quilt_plot_names'] + nuc_pct_quilts = [] + if 'nuc_pct_quilt_plot_names' in crispresso2_info['results']['general_plots']: + nuc_pct_quilts = crispresso2_info['results']['general_plots']['nuc_pct_quilt_plot_names'] + + run_names = [] + sub_html_files = {} + + for idx, folder in enumerate(folder_arr): + display_name = folder + if display_names is not None: + display_name = display_names[folder] + + run_names.append(display_name) + sub_html_file = os.path.relpath(crispresso_html_reports[folder], crispresso_report_folder) + sub_html_files[display_name] = sub_html_file + + for compact_plot in compact_plots_to_show: + old_href = compact_plots_to_show[compact_plot]['href'] + compact_plots_to_show[compact_plot]['href'] = os.path.relpath(old_href, crispresso_report_folder) + old_img = compact_plots_to_show[compact_plot]['img'] + compact_plots_to_show[compact_plot]['img'] = os.path.relpath(old_img, crispresso_report_folder) + + allele_modification_heatmap_plot['htmls'] = {} + for heatmap_plot_name, heatmap_plot_path in allele_modification_heatmap_plot['paths'].items(): + with open(heatmap_plot_path) as fh: + allele_modification_heatmap_plot['htmls'][heatmap_plot_name] = fh.read() + + allele_modification_line_plot['htmls'] = {} + for line_plot_name, line_plot_path in allele_modification_line_plot['paths'].items(): + with open(line_plot_path) as fh: + allele_modification_line_plot['htmls'][line_plot_name] = fh.read() + + make_multi_report( + run_names, + sub_html_files, + crispresso_report_file, + crispresso_report_folder, + _ROOT, + report_name, + window_nuc_pct_quilts=window_nuc_pct_quilts, + nuc_pct_quilts=nuc_pct_quilts, + summary_plots=summary_plots, + compact_plots_to_show=compact_plots_to_show, + allele_modification_heatmap_plot=allele_modification_heatmap_plot, + allele_modification_line_plot=allele_modification_line_plot, + ) diff --git a/templates/CRISPResso_justcup.png b/templates/CRISPResso_justcup.png new file mode 100644 index 0000000000000000000000000000000000000000..3116c48c394f23cf37669c6dbb92928ef0d88b9d GIT binary patch literal 42782 zcmb5VbyQVf)CGEoAA%xWBn6~IRJsKu1VlQeQ$SLb5T!c>X$k3&?vw^e5fA~9?vn11 ze2ee<-Wc!ScZUr14(>hs?7h}pbI!HS2PFl`o7c&&BM5R+TI#6^f}rukk32RyytB_9 zW($Ae*hp!;MUWeWS3hV-d?FcwTvxOZ7gtg;x3;%_Yi?~rBP}jYV`FD+YGGx9AdX{6 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zs%h}-?+MOFw+owmecsy@dCWZbuGb5@(>av?=j;rMMTMfi$Kz)c7#knQqo+?`G?`%A zbYkx98F-lC8jXMI_VcApG3|C6>2zAuA-}}uB7YyLWxUk& zdL5Ze2Dw~LK*?khg+c+OoBUm*vs5Z2Y{?-l?@je8m5Ml`8pI$zXSiP&jEy + + + CRISPResso2 Report + + + + + + + + + + + + + + + + + + + {% block head %}{% endblock %} + + + + +
+ +
+
+
+
+
+

CRISPResso2

+

Analysis of genome editing outcomes from deep sequencing data

+
+
+ +
+
+ +
+ {% block content %}{% endblock %} + +
+ +
+ + +
+ +
+ + + + + + + + + {% block foot %}{% endblock %} + + + diff --git a/templates/multiReport.html b/templates/multiReport.html new file mode 100644 index 00000000..4f346efe --- /dev/null +++ b/templates/multiReport.html @@ -0,0 +1,285 @@ +{% extends "layout.html" %} +{% block head %} + + +{% endblock %} + +{% block content %} +
+
+ +
+
+ + {% if run_names|length > 0 %} +
+
+
{{report_name}}
+
+
+
+ {% for run_name in run_names %} + {{run_name}} + {% endfor %} +
+
+
+ {% endif %} + + {% if window_nuc_pct_quilts|length > 0 %} +
+
+
Nucleotide percentages around guides
+
+
+ {% for plot_name in window_nuc_pct_quilts %} +
{{summary_plot_titles[plot_name]}}
+ + + {% for (data_label,data_path) in summary_plot_datas[plot_name] %} +

Data: {{data_label}}

+ {% endfor %} + {% endfor %} +
+
+ {% endif %} + + {% if nuc_pct_quilts|length > 0 %} +
+
+
Nucleotide percentages in the entire amplicon
+
+
+ {% for plot_name in nuc_pct_quilts %} +
{{summary_plot_titles[plot_name]}}
+ + + {% for (data_label,data_path) in summary_plot_datas[plot_name] %} +

Data: {{data_label}}

+ {% endfor %} + {% endfor %} +
+
+ {% endif %} + + {% if window_nuc_conv_plots|length > 0 %} +
+
+
Conversion of target bases around guides
+
+
+ {% for plot_name in window_nuc_conv_plots %} +
{{summary_plot_titles[plot_name]}}
+ + + {% for (data_label,data_path) in summary_plot_datas[plot_name] %} +

Data: {{data_label}}

+ {% endfor %} + {% endfor %} +
+
+ {% endif %} + + {% if nuc_conv_plots|length > 0 %} +
+
+
Conversion of target bases in the entire amplicon
+
+
+ {% for plot_name in nuc_conv_plots %} +
{{summary_plot_titles[plot_name]}}
+ + + {% for (data_label,data_path) in summary_plot_datas[plot_name] %} +

Data: {{data_label}}

+ {% endfor %} + {% endfor %} +
+
+ {% endif %} + + {% if summary_plot_names|length > 0 %} + {% for plot_name in summary_plot_names %} +
+
+
{{summary_plot_titles[plot_name]}}
+
+
+ + + {% for (data_label,data_path) in summary_plot_datas[plot_name] %} +

Data: {{data_label}}

+ {% endfor %} +
+
+ {% endfor %} + {% endif %} + + {% if allele_modification_heatmap_plot_names|length > 0 %} + {% for heatmap_plot_name in allele_modification_heatmap_plot_names %} + {% set line_plot_name = allele_modification_line_plot_names[loop.index - 1] %} + {% set modification_type = heatmap_plot_name.split('_')[3] %} +
+
+
{{allele_modification_heatmap_plot_titles[heatmap_plot_name]}}
+ +
+
+
+
+ {{allele_modification_heatmap_plot_htmls[heatmap_plot_name]}} + + {% for (data_label, data_path) in allele_modification_heatmap_plot_datas[heatmap_plot_name] %} +

Data: {{data_label}}

+ {% endfor %} +
+
+ {{allele_modification_line_plot_htmls[line_plot_name]}} + + {% for (data_label, data_path) in allele_modification_line_plot_datas[line_plot_name] %} +

Data: {{data_label}}

+ {% endfor %} +
+
+
+
+ + {% endfor %} + + + + {% endif %} + + {% if compact_plots_to_show|length > 0 %} +
+
+
Summary Plots
+
+
+
+ {% for compact_plot in compact_plots_to_show %} + + {% endfor %} +
+
+
+ {% endif %} + + +
+ +
+ +
{# jumbotron_content #} +
{# jumbrotron #} + +
{# column #} + +
+{% endblock %} + +{% block foot %} +{% endblock %} diff --git a/templates/report.html b/templates/report.html new file mode 100644 index 00000000..ff274edd --- /dev/null +++ b/templates/report.html @@ -0,0 +1,854 @@ +{% extends "layout.html" %} +{% block head %} + + +{% endblock %} + +{% block content %} +
+
+ +
+
+ +
+
+ {% if report_data['report_display_name'] != '' %} +
{{report_data['report_display_name']}}
+ {% endif %} +
CRISPResso2 run information
+
    +
  • + +
    • +
  • + +
    • +
+
+
+
+
+ {{report_data['figures']['htmls']['plot_1a']}} + + {% for (data_label,data_path) in report_data['figures']['datas']['plot_1a'] %} +

Data: {{data_label}}

+ {% endfor %} +
+
+

CRISPResso version: {{report_data['run_data']['running_info']['version']}}

+

Run completed: {{report_data['run_data']['running_info']['end_time_string']}}

+

Amplicon sequence: 

{{report_data['run_data']['running_info']['args']['amplicon_seq']}}

+ {% if report_data['run_data']['running_info']['args']['guide_seq'] != '' %} +

Guide sequence: 

{{report_data['run_data']['running_info']['args']['guide_seq']}}

+ {% endif %} +

Command used: 

{{report_data['run_data']['running_info']['command_used']}}

+

Parameters: 

{{report_data['run_data']['running_info']['args_string']}}

+

Running log

+
+
+
+
+ +
+
+
Allele assignments
+
    +
  • + +
    • +
  • + +
    • + {% if report_data['figures']['locs']['plot_1d'] %} +
  • + +
    • + {% endif %} +
+
+
+
+
+ + + {% for (data_label,data_path) in report_data['figures']['datas']['plot_1b'] %} +

Data: {{data_label}}

+ {% endfor %} +
+
+ + + {% for (data_label,data_path) in report_data['figures']['datas']['plot_1c'] %} +

Data: {{data_label}}

+ {% endfor %} +
+ {% if report_data['figures']['locs']['plot_1d'] %} +
+ + + {% for (data_label,data_path) in report_data['figures']['datas']['plot_1d'] %} +

Data: {{data_label}}

+ {% endfor %} +
+ {% endif %} +
+ +
+
{# end card #} + + {# start global coding sequence report #} + {% if report_data['figures']['locs']['plot_5a'] %} +
+
+
Global frameshift analysis
+
+
+ + + {% for (data_label,data_path) in report_data['figures']['datas']['plot_5a'] %} +

Data: {{data_label}}

+ {% endfor %} +
+
+ {% endif %} + + {% if report_data['figures']['locs']['plot_6a'] %} +
+
+
Global frameshift mutagenesis profiles
+
+
+ + + {% for (data_label,data_path) in report_data['figures']['datas']['plot_6a'] %} +

Data: {{data_label}}

+ {% endfor %} +
+
+ {% endif %} + + {% if report_data['figures']['locs']['plot_8a'] %} +
+
+
Global splicing analysis
+
+
+ + + {% for (data_label,data_path) in report_data['figures']['datas']['plot_8a'] %} +

Data: {{data_label}}

+ {% endfor %} +
+
+ {% endif %} + {# end of global coding sequence analysis #} + + {# start hdr summary #} + {% if report_data['figures']['locs'][report_data.amplicons[0]]['plot_4g'] %} +
+
+ {% if report_data.amplicons|length == 1 %} {# if only one amplicon #} +
HDR summary plot
+ {% else %} +
HDR summary report (all reads aligned to {{report_data.amplicons[0]}})
+ {% endif %} +
+
+ + + {% for (data_label,data_path) in report_data['figures']['datas'][report_data.amplicons[0]]['plot_4g'] %} +

Data: {{data_label}}

+ {% endfor %} +
+
+ {% endif %} + {# end HDR summary #} + + {# start prime editing report #} + {% if report_data['figures']['locs'][report_data.amplicons[0]]['plot_11a'] %} +
+
+ {% if report_data.amplicons|length == 1 %} {# if only one amplicon #} +
Prime editing report
+ {% else %} +
Prime editing report (all reads aligned to {{report_data.amplicons[0]}})
+ {% endif %} +
+
+ + + {% for (data_label,data_path) in report_data['figures']['datas'][report_data.amplicons[0]]['plot_11a'] %} +

Data: {{data_label}}

+ {% endfor %} +
+
+ {% endif %} + + {% if report_data['figures']['sgRNA_based_names'][report_data.amplicons[0]] and report_data['figures']['sgRNA_based_names'][report_data.amplicons[0]]['11b']%} +
+
+ {% if report_data.amplicons|length == 1 %} {# if only one amplicon #} +
Prime editing summary plots at analysis positions
+ {% else %} +
Prime editing summary plots at analysis positions (aligned to {{report_data.amplicons[0]}})
+ {% endif %} +
+
+ {% for fig_name in report_data['figures']['sgRNA_based_names'][report_data.amplicons[0]]['11b'] %} +
+ + + {% for (data_label,data_path) in report_data['figures']['datas'][report_data.amplicons[0]][fig_name] %} +

Data: {{data_label}}

+ {% endfor %} +
+ {% endfor %} +
+
+ {% endif %} {# end plot 11b for prime editing #} + + {% if report_data['figures']['locs']['plot_11c'] %} +
+
+
Scaffold insertions
+
+
+ + + {% for (data_label,data_path) in report_data['figures']['datas']['plot_11c'] %} +

Data: {{data_label}}

+ {% endfor %} +
+
+ {% endif %} + + {# end prime editing section #} + + + {% if report_data.amplicons|length == 1 %} +
{# if only one amplicon, just a normal div #} + {% else %} + {# If there is more than one amplicon, print a navigation to show each amplicon #} +

Reads are aligned to each amplicon sequence separately. Quantification and visualization of these reads are shown for each amplicon below:

+
+
+
Amplicons
+ +
+ {% endif %} {# end if report contains more than one amplicon #} + + + {% if report_data.amplicons|length == 1 %} {# if only one amplicon, just a normal div #} +
+ {% else %} +
+ {% endif %} + + {% for amplicon_name in report_data.amplicons %} + {% if report_data.amplicons|length == 1 %} {# if only one amplicon, just a normal div #} +
+ {% elif loop.index0 == 0 %} {# if more than one amplicon, and the first, this is the active one #} +
+

Reads aligning to {{amplicon_name}}

{# this bit appears in print mode #} + {% else %} {# otherwise inactive tab #} +
+

Reads aligning to {{amplicon_name}}

{# this bit appears in print mode #} + {% endif %} + +
+
+ {% if report_data.amplicons|length == 1 %} {# if only one amplicon #} +
Nucleotide composition
+ {% else %} +
Nucleotide composition for {{amplicon_name}}
+ {% endif %} +
+
+ {% if report_data['figures']['locs'][amplicon_name]['plot_2a'] %} +
+
+
+ +
+
+ + + + {% for (data_label,data_path) in report_data['figures']['datas'][amplicon_name]['plot_2a'] %} +

Data: {{data_label}}

+ {% endfor %} + {% endif %} + + {% if report_data['figures']['sgRNA_based_names'][amplicon_name] and report_data['figures']['sgRNA_based_names'][amplicon_name]['2b']%} +
+ {% for fig_name in report_data['figures']['sgRNA_based_names'][amplicon_name]['2b'] %} + + + {% for (data_label,data_path) in report_data['figures']['datas'][amplicon_name][fig_name] %} +

Data: {{data_label}}

+ {% endfor %} + {% endfor %} +
+ {% endif %} +
+
{# end card #} + +
+
+ {% if report_data.amplicons|length == 1 %} {# if only one amplicon #} +
Modification lengths
+ {% else %} +
Modification lengths for {{amplicon_name}}
+ {% endif %} +
    + {% if report_data['figures']['locs'][amplicon_name]['plot_3a'] %} +
  • + +
    • + {% endif %} + {% if report_data['figures']['locs'][amplicon_name]['plot_3b'] %} +
  • + +
    • + {% endif %} +
+
+
+
+ {% if report_data['figures']['locs'][amplicon_name]['plot_3a'] %} +
+ + + {% for (data_label,data_path) in report_data['figures']['datas'][amplicon_name]['plot_3a'] %} +

Data: {{data_label}}

+ {% endfor %} +
+ {% endif %} + + {% if report_data['figures']['locs'][amplicon_name]['plot_3b'] %} +
+ + + {% for (data_label,data_path) in report_data['figures']['datas'][amplicon_name]['plot_3b'] %} +

Data: {{data_label}}

+ {% endfor %} +
+ {% endif %} +
+
{# end card_body #} +
{# end card #} + +
+
+ {% if report_data.amplicons|length == 1 %} {# if only one amplicon #} +
Indel characterization
+ {% else %} +
Indel characterization for {{amplicon_name}}
+ {% endif %} +
    + {% if report_data['figures']['locs'][amplicon_name]['plot_4a'] %} +
  • + +
    • + {% endif %} + {% if report_data['figures']['locs'][amplicon_name]['plot_4b'] %} +
  • + +
    • + {% endif %} + {% if report_data['figures']['locs'][amplicon_name]['plot_4c'] %} +
  • + +
    • + {% endif %} + {% if report_data['figures']['locs'][amplicon_name]['plot_4d'] %} +
  • + +
    • + {% endif %} + {% if report_data['figures']['locs'][amplicon_name]['plot_4e'] %} +
  • + +
    • + {% endif %} + {% if report_data['figures']['locs'][amplicon_name]['plot_4f'] %} +
  • + +
    • + {% endif %} +
+
{# end card head #} +
+
+ {% if report_data['figures']['locs'][amplicon_name]['plot_4a'] %} +
+ + + {% for (data_label,data_path) in report_data['figures']['datas'][amplicon_name]['plot_4a'] %} +

Data: {{data_label}}

+ {% endfor %} +
+ {% endif %} + {% if report_data['figures']['locs'][amplicon_name]['plot_4b'] %} +
+ + + {% for (data_label,data_path) in report_data['figures']['datas'][amplicon_name]['plot_4b'] %} +

Data: {{data_label}}

+ {% endfor %} +
+ {% endif %} + {% if report_data['figures']['locs'][amplicon_name]['plot_4c'] %} +
+ + + + {% for (data_label,data_path) in report_data['figures']['datas'][amplicon_name]['plot_4c'] %} +

Data: {{data_label}}

+ {% endfor %} +
+ {% endif %} + + {% if report_data['figures']['locs'][amplicon_name]['plot_4d'] %} +
+ + + {% for (data_label,data_path) in report_data['figures']['datas'][amplicon_name]['plot_4d'] %} +

Data: {{data_label}}

+ {% endfor %} +
+ {% endif %} + + {% if report_data['figures']['locs'][amplicon_name]['plot_4e'] %} +
+ + + {% for (data_label,data_path) in report_data['figures']['datas'][amplicon_name]['plot_4e'] %} +

Data: {{data_label}}

+ {% endfor %} +
+ {% endif %} + + {% if report_data['figures']['locs'][amplicon_name]['plot_4f'] %} +
+ + + {% for (data_label,data_path) in report_data['figures']['datas'][amplicon_name]['plot_4f'] %} +

Data: {{data_label}}

+ {% endfor %} +
+ {% endif %} +
+
{# end card body #} +
{# end card #} + + + {% if report_data['figures']['locs'][amplicon_name]['plot_5'] %} +
+
+ {% if report_data.amplicons|length == 1 %} {# if only one amplicon #} +
Frameshift analysis
+ {% else %} +
Frameshift analysis for {{amplicon_name}}
+ {% endif %} +
+
+ + + {% for (data_label,data_path) in report_data['figures']['datas'][amplicon_name]['plot_5'] %} +

Data: {{data_label}}

+ {% endfor %} +
+
+ {% endif %} + + {% if report_data['figures']['locs'][amplicon_name]['plot_6'] %} +
+
+ {% if report_data.amplicons|length == 1 %} {# if only one amplicon #} +
Frameshift mutagenesis profiles
+ {% else %} +
Frameshift mutagenesis profiles for {{amplicon_name}}
+ {% endif %} +
+
+ + + {% for (data_label,data_path) in report_data['figures']['datas'][amplicon_name]['plot_6'] %} +

Data: {{data_label}}

+ {% endfor %} +
+
+ {% endif %} + + {% if report_data['figures']['locs'][amplicon_name]['plot_7'] %} +
+
+ {% if report_data.amplicons|length == 1 %} {# if only one amplicon #} +
Non-coding mutations
+ {% else %} +
Coding mutations for {{amplicon_name}}
+ {% endif %} +
+
+ + + {% for (data_label,data_path) in report_data['figures']['datas'][amplicon_name]['plot_7'] %} +

Data: {{data_label}}

+ {% endfor %} +
+
+ {% endif %} + + {% if report_data['figures']['locs'][amplicon_name]['plot_8'] %} +
+
+ {% if report_data.amplicons|length == 1 %} {# if only one amplicon #} +
Splicing
+ {% else %} +
Splicing for {{amplicon_name}}
+ {% endif %} +
+
+ + + {% for (data_label,data_path) in report_data['figures']['datas'][amplicon_name]['plot_8'] %} +

Data: {{data_label}}

+ {% endfor %} +
+
+ {% endif %} + + + {% if report_data['figures']['sgRNA_based_names'][amplicon_name] and report_data['figures']['sgRNA_based_names'][amplicon_name]['9']%} +
+
+ {% if report_data.amplicons|length == 1 %} {# if only one amplicon #} +
Allele plots
+ {% else %} +
Allele plots for {{amplicon_name}}
+ {% endif %} +
+
+ {% for fig_name in report_data['figures']['sgRNA_based_names'][amplicon_name]['9'] %} +
+ + + {% for (data_label,data_path) in report_data['figures']['datas'][amplicon_name][fig_name] %} +

Data: {{data_label}}

+ {% endfor %} +
+ {% endfor %} +
+
+ {% endif %} + + {% if report_data['figures']['locs'][amplicon_name]['plot_10a'] %} +
+
+ {% if report_data.amplicons|length == 1 %} {# if only one amplicon #} +
Base editing
+ {% else %} +
Base editing for {{amplicon_name}}
+ {% endif %} +
    + {% if report_data['figures']['locs'][amplicon_name]['plot_10a'] %} +
  • + +
    • + {% endif %} + {% if report_data['figures']['sgRNA_based_names'][amplicon_name] and report_data['figures']['sgRNA_based_names'][amplicon_name]['10d']%} +
  • + +
    • + {% endif %} + {% if report_data['figures']['sgRNA_based_names'][amplicon_name] and report_data['figures']['sgRNA_based_names'][amplicon_name]['10e']%} +
  • + +
    • + {% endif %} + {% if report_data['figures']['sgRNA_based_names'][amplicon_name] and report_data['figures']['sgRNA_based_names'][amplicon_name]['10f']%} +
  • + +
    • + {% endif %} +
+
+
+
+ {% if report_data['figures']['locs'][amplicon_name]['plot_10c'] %} +
+
+ + + {% for (data_label,data_path) in report_data['figures']['datas'][amplicon_name]['plot_10a'] %} +

Data: {{data_label}}

+ {% endfor %} +
+
+ + + + {% for (data_label,data_path) in report_data['figures']['datas'][amplicon_name]['plot_10b'] %} +

Data: {{data_label}}

+ {% endfor %} + {% for (data_label,data_path) in report_data['figures']['datas'][amplicon_name]['plot_10c'] %} +

Data: {{data_label}}

+ {% endfor %} +
+
+ {% else %} +
+
+ + + {% for (data_label,data_path) in report_data['figures']['datas'][amplicon_name]['plot_10a'] %} +

Data: {{data_label}}

+ {% endfor %} +
+
+ + + {% for (data_label,data_path) in report_data['figures']['datas'][amplicon_name]['plot_10b'] %} +

Data: {{data_label}}

+ {% endfor %} +
+
+ {% endif %} + {% if report_data['figures']['sgRNA_based_names'][amplicon_name] and report_data['figures']['sgRNA_based_names'][amplicon_name]['10d']%} +
+ {% for fig_name in report_data['figures']['sgRNA_based_names'][amplicon_name]['10d'] %} +
+ + + {% for (data_label,data_path) in report_data['figures']['datas'][amplicon_name][fig_name] %} +

Data: {{data_label}}

+ {% endfor %} +
+ {% endfor %} +
+ {% endif %} + {% if report_data['figures']['sgRNA_based_names'][amplicon_name] and report_data['figures']['sgRNA_based_names'][amplicon_name]['10e']%} +
+ {% for fig_name in report_data['figures']['sgRNA_based_names'][amplicon_name]['10e'] %} +
+ + + {% for (data_label,data_path) in report_data['figures']['datas'][amplicon_name][fig_name] %} +

Data: {{data_label}}

+ {% endfor %} +
+ {% endfor %} +
+ {% endif %} + + {% if report_data['figures']['sgRNA_based_names'][amplicon_name] and report_data['figures']['sgRNA_based_names'][amplicon_name]['10f']%} +
+ {% for fig_name in report_data['figures']['sgRNA_based_names'][amplicon_name]['10f'] %} +
+ + + {% for (data_label,data_path) in report_data['figures']['datas'][amplicon_name][fig_name] %} +

Data: {{data_label}}

+ {% endfor %} +
+ {% endfor %} + + {% for fig_name in report_data['figures']['sgRNA_based_names'][amplicon_name]['10g'] %} +
+ + + {% for (data_label,data_path) in report_data['figures']['datas'][amplicon_name][fig_name] %} +

Data: {{data_label}}

+ {% endfor %} +
+ {% endfor %} +
+
+ {% endif %} + +
+
{# end card #} + {% endif %} {# end base editing card #} + +
{# end this amplicon tab #} + + {% endfor %} +
{# tab content #} + +
+ +
{# jumbotron_content #} +
{# jumbrotron #} + +
{# column #} + +
+{% endblock %} + +{% block foot %} + +{% endblock %} From 08fcd4eda347886e66c4d2a170eb03b00a02781a Mon Sep 17 00:00:00 2001 From: Samuel Nichols Date: Tue, 17 May 2022 10:08:08 -0600 Subject: [PATCH 02/33] Web updates refactoring done --- CRISPRessoReport.py | 113 ++++++++++++---------- templates/batchReport.html | 183 ++++++++++++++++++++++++++++++++++++ templates/layout.html | 176 +++++++++++++++++++++++++++++----- templates/pooledReport.html | 105 +++++++++++++++++++++ templates/report.html | 2 +- templates/wgsReport.html | 103 ++++++++++++++++++++ 6 files changed, 609 insertions(+), 73 deletions(-) create mode 100644 templates/batchReport.html create mode 100644 templates/pooledReport.html create mode 100644 templates/wgsReport.html diff --git a/CRISPRessoReport.py b/CRISPRessoReport.py index a49f2584..aa3d87c9 100644 --- a/CRISPRessoReport.py +++ b/CRISPRessoReport.py @@ -25,39 +25,37 @@ def make_report_from_folder(crispresso_report_file, crispresso_folder, _ROOT): make_report(run_data, crispresso_report_file, crispresso_folder, _ROOT) -def make_report(run_data, crispresso_report_file, crispresso_folder, _ROOT): - # dicts for each amplicon fig_names[amp_name] = [list of fig names] - # fig_locs[amp_name][fig_name] = figure location - # print('crispresso_report file: ' + crispresso_report_file + ' crispresso_folder : ' + crispresso_folder + ' root: ' + _ROOT) - figures = {'names': {}, 'locs': {}, 'titles': {}, 'captions': {}, 'datas': {}, 'htmls': {}, 'sgRNA_based_names': {}} - - def add_fig_if_exists(fig_name, fig_root, fig_title, fig_caption, fig_data, - amplicon_fig_names, amplicon_figures): +def add_fig_if_exists(fig_name, fig_root, fig_title, fig_caption, fig_data, + amplicon_fig_names, amplicon_figures, crispresso_folder): + """ + Helper function to add figure if the file exists + if fig at filename exists, + amplicon_figs[figname] is set to that file """ - Helper function to add figure if the file exists - if fig at filename exists, - amplicon_figs[figname] is set to that file - """ - # fullpath=os.path.join(crispresso_folder,fig_root+'.png') - pngfullpath = os.path.join(crispresso_folder, fig_root + '.png') - htmlfullpath = os.path.join(crispresso_folder, fig_root + '.html') - # print('adding file ' + fig_root + ' at ' + fullpath) - if os.path.exists(pngfullpath) or os.path.exists(htmlfullpath): - amplicon_fig_names.append(fig_name) - # amplicon_fig_locs[fig_name]=os.path.basename(fig_root+'.png') - amplicon_figures['locs'][fig_name] = os.path.basename(fig_root) - amplicon_figures['titles'][fig_name] = fig_title - amplicon_figures['captions'][fig_name] = fig_caption - amplicon_figures['datas'][fig_name] = [] - for (data_caption, data_file) in fig_data: - if os.path.exists(os.path.join(crispresso_folder, data_file)): - amplicon_figures['datas'][fig_name].append((data_caption, data_file)) - if os.path.exists(htmlfullpath): - with open(htmlfullpath) as html: - html_string = "
" - html_string += html.read() - html_string += "
" - amplicon_figures['htmls'][fig_name] = html_string + # fullpath=os.path.join(crispresso_folder,fig_root+'.png') + pngfullpath = os.path.join(crispresso_folder, fig_root + '.png') + htmlfullpath = os.path.join(crispresso_folder, fig_root + '.html') + # print('adding file ' + fig_root + ' at ' + fullpath) + if os.path.exists(pngfullpath) or os.path.exists(htmlfullpath): + amplicon_fig_names.append(fig_name) + # amplicon_fig_locs[fig_name]=os.path.basename(fig_root+'.png') + amplicon_figures['locs'][fig_name] = os.path.basename(fig_root) + amplicon_figures['titles'][fig_name] = fig_title + amplicon_figures['captions'][fig_name] = fig_caption + amplicon_figures['datas'][fig_name] = [] + for (data_caption, data_file) in fig_data: + if os.path.exists(os.path.join(crispresso_folder, data_file)): + amplicon_figures['datas'][fig_name].append((data_caption, data_file)) + if os.path.exists(htmlfullpath): + with open(htmlfullpath) as html: + html_string = "
" + html_string += html.read() + html_string += "
" + amplicon_figures['htmls'][fig_name] = html_string + + +def assemble_figs(run_data, crispresso_folder): + figures = {'names': {}, 'locs': {}, 'titles': {}, 'captions': {}, 'datas': {}, 'htmls': {}, 'sgRNA_based_names': {}} global_fig_names = [] for fig in ['1a', '1b', '1c', '1d', '5a', '6a', '8a', '11c']: @@ -66,7 +64,7 @@ def add_fig_if_exists(fig_name, fig_root, fig_title, fig_caption, fig_data, add_fig_if_exists(fig_name, run_data['results']['general_plots'][fig_name + '_root'], 'Figure ' + fig, run_data['results']['general_plots'][fig_name + '_caption'], run_data['results']['general_plots'][fig_name + '_data'], - global_fig_names, figures) + global_fig_names, figures, crispresso_folder) amplicons = [] for amplicon_name in run_data['results']['ref_names']: @@ -81,7 +79,7 @@ def add_fig_if_exists(fig_name, fig_root, fig_title, fig_caption, fig_data, 'Figure ' + fig_name, run_data['results']['refs'][amplicon_name][fig_name + '_caption'], run_data['results']['refs'][amplicon_name][fig_name + '_data'], - global_fig_names, amplicon_figures) + global_fig_names, amplicon_figures, crispresso_folder) this_sgRNA_based_fig_names = {} for fig in ['2b', '9', '10d', '10e', '10f', '10g', '11b']: @@ -93,7 +91,7 @@ def add_fig_if_exists(fig_name, fig_root, fig_title, fig_caption, fig_data, add_fig_if_exists(fig_name, plot_root, 'Figure ' + fig_name + ' sgRNA ' + str(idx + 1), run_data['results']['refs'][amplicon_name]['plot_' + fig + '_captions'][idx], run_data['results']['refs'][amplicon_name]['plot_' + fig + '_datas'][idx], - this_fig_names, amplicon_figures) + this_fig_names, amplicon_figures, crispresso_folder) this_sgRNA_based_fig_names[fig] = this_fig_names figures['names'][amplicon_name] = amplicon_figures['names'] @@ -103,6 +101,15 @@ def add_fig_if_exists(fig_name, fig_root, fig_title, fig_caption, fig_data, figures['titles'][amplicon_name] = amplicon_figures['titles'] figures['captions'][amplicon_name] = amplicon_figures['captions'] figures['datas'][amplicon_name] = amplicon_figures['datas'] + data = {'amplicons': amplicons, 'figures': figures} + return data + + +def make_report(run_data, crispresso_report_file, crispresso_folder, _ROOT, web_version=False): + # dicts for each amplicon fig_names[amp_name] = [list of fig names] + # fig_locs[amp_name][fig_name] = figure location + # print('crispresso_report file: ' + crispresso_report_file + ' crispresso_folder : ' + crispresso_folder + ' root: ' + _ROOT) + data = assemble_figs(run_data, crispresso_folder) report_display_name = "" if run_data['running_info']['args'].name != "": @@ -116,8 +123,8 @@ def add_fig_if_exists(fig_name, fig_root, fig_title, fig_caption, fig_data, crispresso_data_path += "/" report_data = { - 'amplicons': amplicons, - 'figures': figures, + 'amplicons': data['amplicons'], + 'figures': data['figures'], 'run_data': run_data, 'report_display_name': report_display_name, 'crispresso_data_path': crispresso_data_path, @@ -247,6 +254,7 @@ def make_batch_report_from_folder(crispressoBatch_report_file, crispresso2_info, batch_folder, _ROOT, output_title, + 'batch', summary_plots={ 'names': summary_plot_names, 'titles': summary_plot_titles, @@ -267,7 +275,7 @@ def make_pooled_report_from_folder(crispresso_report_file, crispresso2_info, fol output_title = 'CRISPResso Pooled Output' if crispresso2_info['running_info']['args'].name != '': output_title += '
{0}'.format(crispresso2_info['running_info']['args'].name) - make_multi_report_from_folder(crispresso2_info, names_arr, output_title, crispresso_report_file, folder, _ROOT) + make_multi_report_from_folder(crispresso2_info, names_arr, output_title, crispresso_report_file, folder, _ROOT, 'pooled') def make_compare_report_from_folder(crispresso_report_file, crispresso2_info, folder, _ROOT): @@ -275,7 +283,7 @@ def make_compare_report_from_folder(crispresso_report_file, crispresso2_info, fo output_title = 'CRISPResso Compare Output' if crispresso2_info['running_info']['args'].name != '': output_title += '
{0}'.format(crispresso2_info['running_info']['args'].name) - make_multi_report_from_folder(crispresso2_info, names_arr, output_title, crispresso_report_file, folder, _ROOT) + make_multi_report_from_folder(crispresso2_info, names_arr, output_title, crispresso_report_file, folder, _ROOT, 'compare') def make_meta_report_from_folder(crispresso_report_file, crispresso2_info, folder, _ROOT): @@ -284,7 +292,7 @@ def make_meta_report_from_folder(crispresso_report_file, crispresso2_info, folde output_title = 'CRISPresso Meta Output' if crispresso2_info['running_info']['args'].name != '': output_title += '
{0}'.format(crispresso2_info['running_info']['args'].name) - make_multi_report_from_folder(crispresso2_info, names_arr, output_title, crispresso_report_file, folder, _ROOT, + make_multi_report_from_folder(crispresso2_info, names_arr, output_title, crispresso_report_file, folder, _ROOT, 'meta', display_names=input_names) @@ -293,10 +301,10 @@ def make_wgs_report_from_folder(crispresso_report_file, crispresso2_info, folder output_title = 'CRISPResso WGS Output' if crispresso2_info['running_info']['args'].name != '': output_title += '
{0}'.format(crispresso2_info['running_info']['args'].name) - make_multi_report_from_folder(crispresso2_info, names_arr, output_title, crispresso_report_file, folder, _ROOT) + make_multi_report_from_folder(crispresso2_info, names_arr, output_title, crispresso_report_file, folder, _ROOT, 'wgs') -def make_multi_report_from_folder(crispresso2_info, names_arr, report_name, crispresso_report_file, folder, _ROOT, +def make_multi_report_from_folder(crispresso2_info, names_arr, report_name, crispresso_report_file, folder, _ROOT, crispresso_tool, display_names=None): """ Prepares information to make a report of multiple CRISPResso runs - like CRISPRessoWGS or CRISPRessoPooled @@ -369,6 +377,7 @@ def make_multi_report_from_folder(crispresso2_info, names_arr, report_name, cris folder, _ROOT, report_name, + crispresso_tool, summary_plots={ 'names': summary_plot_names, 'titles': summary_plot_titles, @@ -385,6 +394,7 @@ def make_multi_report( crispresso_folder, _ROOT, report_name, + crispresso_tool, window_nuc_pct_quilts=[], nuc_pct_quilts=[], window_nuc_conv_plots=[], @@ -409,12 +419,7 @@ def make_multi_report( report_name (string): description of report type to be shown at top of report crispresso_folder (string): absolute path to the crispresso output _ROOT (string): absolute path to the crispresso executable - -<<<<<<< HEAD - summary_plot (dict): a dict with the following keys: -======= summary_plots (dict): a dict with the following keys: ->>>>>>> origin/master names (list): list of plot names - keys for following dicts titles (dict): dict of plot_name->plot_title labels (dict): dict of plot_name->plot_label @@ -439,7 +444,14 @@ def fill_default(dictionary, key, default_type=list): loader=FileSystemLoader(os.path.join(_ROOT, 'templates')), ) j2_env.filters['dirname'] = dirname - template = j2_env.get_template('multiReport.html') + if crispresso_tool == 'batch': + template = j2_env.get_template('batchReport.html') + elif crispresso_tool == 'pooled': + template = j2_env.get_template('pooledReport.html') + elif crispresso_tool == 'wgs': + template = j2_env.get_template('wgsReport.html') + else: + template = j2_env.get_template('multiReport.html') crispresso_data_path = os.path.relpath( crispresso_folder, os.path.dirname(crispresso_multi_report_file), @@ -466,7 +478,10 @@ def fill_default(dictionary, key, default_type=list): key, default_type, ) - + web = False + if not web: + for html in sub_html_files: + sub_html_files[html] = crispresso_data_path + sub_html_files[html] with open(crispresso_multi_report_file, 'w') as outfile: outfile.write(template.render( window_nuc_pct_quilts=window_nuc_pct_quilts, diff --git a/templates/batchReport.html b/templates/batchReport.html new file mode 100644 index 00000000..10b4e4e2 --- /dev/null +++ b/templates/batchReport.html @@ -0,0 +1,183 @@ +{% extends "layout.html" %} +{% block head %} + + +{% endblock %} + +{% block content %} +
+
+
+ +
+
+ + {% if run_names|length > 0 %} +
+
+
{{report_name}}
+
+
+
+ {% for run_name in run_names %} + {{run_name}} + {% endfor %} +
+
+
+ {% endif %} + + {% if window_nuc_pct_quilts|length > 0 %} +
+
+
Nucleotide percentages around guides
+
+
+ {% for plot_name in window_nuc_pct_quilts %} +
{{summary_plot_titles[plot_name]}}
+ + + {% for (data_label,data_path) in summary_plot_datas[plot_name] %} +

Data: {{data_label}}

+ {% endfor %} + {% endfor %} +
+
+ {% endif %} + + {% if nuc_pct_quilts|length > 0 %} +
+
+
Nucleotide percentages in the entire amplicon
+
+
+ {% for plot_name in nuc_pct_quilts %} +
{{summary_plot_titles[plot_name]}}
+ + + {% for (data_label,data_path) in summary_plot_datas[plot_name] %} +

Data: {{data_label}}

+ {% endfor %} + {% endfor %} +
+
+ {% endif %} + + {% if window_nuc_conv_plots|length > 0 %} +
+
+
Conversion of target bases around guides
+
+
+ {% for plot_name in window_nuc_conv_plots %} +
{{summary_plot_titles[plot_name]}}
+ + + {% for (data_label,data_path) in summary_plot_datas[plot_name] %} +

Data: {{data_label}}

+ {% endfor %} + {% endfor %} +
+
+ {% endif %} + + {% if nuc_conv_plots|length > 0 %} +
+
+
Conversion of target bases in the entire amplicon
+
+
+ {% for plot_name in nuc_conv_plots %} +
{{summary_plot_titles[plot_name]}}
+ + + {% for (data_label,data_path) in summary_plot_datas[plot_name] %} +

Data: {{data_label}}

+ {% endfor %} + {% endfor %} +
+
+ {% endif %} + + {% if summary_plot_names|length > 0 %} + {% for plot_name in summary_plot_names %} +
+
+
{{summary_plot_titles[plot_name]}}
+
+
+ + + {% for (data_label,data_path) in summary_plot_datas[plot_name] %} +

Data: {{data_label}}

+ {% endfor %} +
+
+ {% endfor %} + {% endif %} + + +
+ +
+ +
+ Download report + Link to report + +
+ + {# data bit for web version: #} + {# +

Data: {{data_label}}

+ #} +
{# jumbotron_content #} +
{# jumbrotron #} + +
{# column #} + +
+
+{% endblock %} + +{% block foot %} +{% endblock %} diff --git a/templates/layout.html b/templates/layout.html index 5eba4687..05a1e959 100644 --- a/templates/layout.html +++ b/templates/layout.html @@ -1,20 +1,36 @@ - CRISPResso2 Report + CRISPResso2 - - + + + + + + + + + @@ -39,65 +71,163 @@ Remove this if you use the .htaccess --> - - - + + + + + {% block head %}{% endblock %} -
- +
+ {{ self.help_block() }} +
+ {% if get_flashed_messages != null %} + {% with messages = get_flashed_messages(with_categories=true) %} + {% if messages %} + {% for category, message in messages %} + {% if category == "error" %} + + {% else %} + + {% endif %} + {% endfor %} + {% endif %} + {% endwith %} + {% endif %} + + {# if default user (normal crispresso mode) #} + {% if current_user != null and not current_user.is_anonymous and current_user.username == "DEFAULTUSER" %} + +
-
+
-

CRISPResso2

-

Analysis of genome editing outcomes from deep sequencing data

+

CRISPResso2

+

Analysis of genome editing outcomes from deep sequencing data

-
-
- {% block content %}{% endblock %} + {% else %} + {# if doing user sessions #} + +
+ {% endif %} + +
+
+
+
+ {% block help_block %} {% endblock %} +
+
+
-
+ {% block content %}{% endblock %} + {% if current_user != null and not current_user.is_anonymous and current_user.username == "DEFAULTUSER" %} +
+
+ {% else %} +
+
+ +
+
+ {% endif %} + - - - + {% block foot %}{% endblock %} diff --git a/templates/pooledReport.html b/templates/pooledReport.html new file mode 100644 index 00000000..9ae88cc6 --- /dev/null +++ b/templates/pooledReport.html @@ -0,0 +1,105 @@ +{% extends "layout.html" %} +{% block head %} + + +{% endblock %} + +{% block content %} +
+
+
+ +
+
+ + {% if run_names|length > 0 %} +
+
+
{{report_name}}
+
+
+
+ {% for region_name in run_names %} + {{region_name}} + {% endfor %} +
+
+
+ {% endif %} + + {% if summary_plot_names|length > 0 %} + {% for plot_name in summary_plot_names %} +
+
+
{{summary_plot_titles[plot_name]}}
+
+
+ + + {% for (data_label,data_path) in summary_plot_datas[plot_name] %} +

Data: {{data_label}}

+ {% endfor %} +
+
+ {% endfor %} + {% endif %} + +
+ Download report + Link to report + +
+ {# data bit for web version: #} + {# +

Data: {{data_label}}

+ #} +
{# jumbotron_content #} +
{# jumbrotron #} + +
{# column #} + +
+
+{% endblock %} + +{% block foot %} +{% endblock %} diff --git a/templates/report.html b/templates/report.html index ff274edd..50e0868b 100644 --- a/templates/report.html +++ b/templates/report.html @@ -75,7 +75,7 @@
CRISPResso2 run information
- {{report_data['figures']['htmls']['plot_1a']}} + {{report_data['figures']['htmls']['plot_1a']|safe}} {% for (data_label,data_path) in report_data['figures']['datas']['plot_1a'] %}

Data: {{data_label}}

diff --git a/templates/wgsReport.html b/templates/wgsReport.html new file mode 100644 index 00000000..3cf2c781 --- /dev/null +++ b/templates/wgsReport.html @@ -0,0 +1,103 @@ +{% extends "layout.html" %} +{% block head %} + + +{% endblock %} + +{% block content %} +
+
+
+ +
+
+ +
+
+
{{report_name}}
+
+
+
+ {% for region_name in run_names %} + {{region_name}} + {% endfor %} +
+
+
+ + {% if summary_plot_names|length > 0 %} + {% for plot_name in summary_plot_names %} +
+
+
{{summary_plot_titles[plot_name]}}
+
+
+ + + {% for (data_label,data_path) in summary_plot_datas[plot_name] %} +

Data: {{data_label}}

+ {% endfor %} +
+
+ {% endfor %} + {% endif %} + +
+ Download report + Link to report + +
+ {# data bit for web version: #} + {# +

Data: {{data_label}}

+ #} +
{# jumbotron_content #} +
{# jumbrotron #} + +
{# column #} + +
+
+{% endblock %} + +{% block foot %} +{% endblock %} From ee721b37a97155da72d5cddba01bfded58461748 Mon Sep 17 00:00:00 2001 From: Cole Lyman Date: Wed, 29 Jun 2022 23:19:05 -0600 Subject: [PATCH 03/33] Add function to render template partials without using Flask --- CRISPRessoReport.py | 33 +++++++++++++++++++++++++++++++++ 1 file changed, 33 insertions(+) diff --git a/CRISPRessoReport.py b/CRISPRessoReport.py index aa3d87c9..c115ae69 100644 --- a/CRISPRessoReport.py +++ b/CRISPRessoReport.py @@ -6,9 +6,41 @@ import os from jinja2 import Environment, FileSystemLoader +from jinja_partials import generate_render_partial, render_partial from CRISPResso2 import CRISPRessoShared +def render_template(template_name, jinja2_env, **data): + """Render a template with partials. + + Parameters + ---------- + template_name: str + The name of the template to render. For example, if you have a template + file called `templates/my_template.html` you would pass in + `my_template.html`. + jinja2_env: jinja2.Environment + The Jinja2 environment being used. + **data: keyword arguments of any type + Additional keyword arguments that are passed to the template. + + Returns + ------- + The rendered template. + """ + def custom_partial_render(partial_template_name, **partial_data): + template = jinja2_env.get_template(partial_template_name) + partial_data.update( + render_partial=generate_render_partial( + custom_partial_render, + ), + ) + return template.render(**partial_data) + return render_partial( + template_name, custom_partial_render, **data, + ) + + def make_report_from_folder(crispresso_report_file, crispresso_folder, _ROOT): """ Makes an html report for a crispresso run @@ -131,6 +163,7 @@ def make_report(run_data, crispresso_report_file, crispresso_folder, _ROOT, web_ } j2_env = Environment(loader=FileSystemLoader(os.path.join(_ROOT, 'templates'))) + breakpoint() template = j2_env.get_template('report.html') # dest_dir = os.path.dirname(crispresso_report_file) From 84e0969968218bf74478a62754370937f1bc7312 Mon Sep 17 00:00:00 2001 From: Cole Lyman Date: Wed, 29 Jun 2022 23:42:26 -0600 Subject: [PATCH 04/33] Use the `render_template` function for each report --- CRISPRessoReport.py | 21 +++++++++++---------- 1 file changed, 11 insertions(+), 10 deletions(-) diff --git a/CRISPRessoReport.py b/CRISPRessoReport.py index c115ae69..1cc809b2 100644 --- a/CRISPRessoReport.py +++ b/CRISPRessoReport.py @@ -163,16 +163,15 @@ def make_report(run_data, crispresso_report_file, crispresso_folder, _ROOT, web_ } j2_env = Environment(loader=FileSystemLoader(os.path.join(_ROOT, 'templates'))) - breakpoint() - template = j2_env.get_template('report.html') # dest_dir = os.path.dirname(crispresso_report_file) # shutil.copy2(os.path.join(_ROOT,'templates','CRISPResso_justcup.png'),dest_dir) # shutil.copy2(os.path.join(_ROOT,'templates','favicon.ico'),dest_dir) - outfile = open(crispresso_report_file, 'w') - outfile.write(template.render(report_data=report_data)) - outfile.close() + with open(crispresso_report_file, 'w') as outfile: + outfile.write(render_template( + 'report.html', j2_env, report_data=report_data, + )) def make_batch_report_from_folder(crispressoBatch_report_file, crispresso2_info, batch_folder, _ROOT): @@ -478,13 +477,13 @@ def fill_default(dictionary, key, default_type=list): ) j2_env.filters['dirname'] = dirname if crispresso_tool == 'batch': - template = j2_env.get_template('batchReport.html') + template = 'batchReport.html' elif crispresso_tool == 'pooled': - template = j2_env.get_template('pooledReport.html') + template = 'pooledReport.html' elif crispresso_tool == 'wgs': - template = j2_env.get_template('wgsReport.html') + template = 'wgsReport.html' else: - template = j2_env.get_template('multiReport.html') + template = 'multiReport.html' crispresso_data_path = os.path.relpath( crispresso_folder, os.path.dirname(crispresso_multi_report_file), @@ -516,7 +515,9 @@ def fill_default(dictionary, key, default_type=list): for html in sub_html_files: sub_html_files[html] = crispresso_data_path + sub_html_files[html] with open(crispresso_multi_report_file, 'w') as outfile: - outfile.write(template.render( + outfile.write(render_template( + template, + j2_env, window_nuc_pct_quilts=window_nuc_pct_quilts, nuc_pct_quilts=nuc_pct_quilts, window_nuc_conv_plots=window_nuc_conv_plots, From c3781e9c71e20f8b11bfa51d709df1f50bb95e6b Mon Sep 17 00:00:00 2001 From: Cole Lyman Date: Thu, 30 Jun 2022 00:05:40 -0600 Subject: [PATCH 05/33] Update path to template directory to include `CRISPRessoReports` --- CRISPRessoReport.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/CRISPRessoReport.py b/CRISPRessoReport.py index 1cc809b2..83d94ed6 100644 --- a/CRISPRessoReport.py +++ b/CRISPRessoReport.py @@ -162,7 +162,7 @@ def make_report(run_data, crispresso_report_file, crispresso_folder, _ROOT, web_ 'crispresso_data_path': crispresso_data_path, } - j2_env = Environment(loader=FileSystemLoader(os.path.join(_ROOT, 'templates'))) + j2_env = Environment(loader=FileSystemLoader(os.path.join(_ROOT, 'CRISPRessoReports', 'templates'))) # dest_dir = os.path.dirname(crispresso_report_file) # shutil.copy2(os.path.join(_ROOT,'templates','CRISPResso_justcup.png'),dest_dir) @@ -473,7 +473,7 @@ def fill_default(dictionary, key, default_type=list): dictionary[key] = default_type() j2_env = Environment( - loader=FileSystemLoader(os.path.join(_ROOT, 'templates')), + loader=FileSystemLoader(os.path.join(_ROOT, 'CRISPRessoReports', 'templates')), ) j2_env.filters['dirname'] = dirname if crispresso_tool == 'batch': From 1061ebb3de0f0c0a4773213f5f0b5aa97f28fc79 Mon Sep 17 00:00:00 2001 From: Cole Lyman Date: Thu, 30 Jun 2022 00:25:14 -0600 Subject: [PATCH 06/33] Update indentation in report.html and extract log params into partial --- templates/report.html | 72 ++++++++++------------- templates/shared/partials/log_params.html | 11 ++++ 2 files changed, 42 insertions(+), 41 deletions(-) create mode 100644 templates/shared/partials/log_params.html diff --git a/templates/report.html b/templates/report.html index 50e0868b..b3ef054f 100644 --- a/templates/report.html +++ b/templates/report.html @@ -54,47 +54,37 @@
-
-
- -
-
- {% if report_data['report_display_name'] != '' %} -
{{report_data['report_display_name']}}
- {% endif %} -
CRISPResso2 run information
-
    -
  • - -
    • -
  • - -
    • -
-
-
-
-
- {{report_data['figures']['htmls']['plot_1a']|safe}} - - {% for (data_label,data_path) in report_data['figures']['datas']['plot_1a'] %} -

Data: {{data_label}}

- {% endfor %} -
-
-

CRISPResso version: {{report_data['run_data']['running_info']['version']}}

-

Run completed: {{report_data['run_data']['running_info']['end_time_string']}}

-

Amplicon sequence: 

{{report_data['run_data']['running_info']['args']['amplicon_seq']}}

- {% if report_data['run_data']['running_info']['args']['guide_seq'] != '' %} -

Guide sequence: 

{{report_data['run_data']['running_info']['args']['guide_seq']}}

- {% endif %} -

Command used: 

{{report_data['run_data']['running_info']['command_used']}}

-

Parameters: 

{{report_data['run_data']['running_info']['args_string']}}

-

Running log

-
-
-
-
+
+
+ +
+
+ {% if report_data['report_display_name'] != '' %} +
{{report_data['report_display_name']}}
+ {% endif %} +
CRISPResso2 run information
+
    +
  • + +
    • +
  • + +
    • +
+
+
+
+
+ {{report_data['figures']['htmls']['plot_1a']|safe}} + + {% for (data_label,data_path) in report_data['figures']['datas']['plot_1a'] %} +

Data: {{data_label}}

+ {% endfor %} +
+ {{ render_partial('shared/partials/log_params.html', report_data=report_data) }} +
+
+
diff --git a/templates/shared/partials/log_params.html b/templates/shared/partials/log_params.html new file mode 100644 index 00000000..ad035ae3 --- /dev/null +++ b/templates/shared/partials/log_params.html @@ -0,0 +1,11 @@ +
+

CRISPResso version: {{report_data['run_data']['running_info']['version']}}

+

Run completed: {{report_data['run_data']['running_info']['end_time_string']}}

+

Amplicon sequence: 

{{report_data['run_data']['running_info']['args']['amplicon_seq']}}

+ {% if report_data['run_data']['running_info']['args']['guide_seq'] != '' %} +

Guide sequence: 

{{report_data['run_data']['running_info']['args']['guide_seq']}}

+ {% endif %} +

Command used: 

{{report_data['run_data']['running_info']['command_used']}}

+

Parameters: 

{{report_data['run_data']['running_info']['args_string']}}

+

Running log

+
From 073f1fe5c55941cc5a759c63782783bbbfb2a5a8 Mon Sep 17 00:00:00 2001 From: Cole Lyman Date: Wed, 6 Jul 2022 15:02:30 -0600 Subject: [PATCH 07/33] Added a few changes from the selenium-tests branch on C2Web --- templates/batchReport.html | 4 ++-- templates/pooledReport.html | 2 +- templates/report.html | 2 +- 3 files changed, 4 insertions(+), 4 deletions(-) diff --git a/templates/batchReport.html b/templates/batchReport.html index 10b4e4e2..030d0450 100644 --- a/templates/batchReport.html +++ b/templates/batchReport.html @@ -54,12 +54,12 @@ {% if run_names|length > 0 %}
-
{{report_name}}
+
{{report_name}}
{% for run_name in run_names %} - {{run_name}} + {{run_name}} {% endfor %}
diff --git a/templates/pooledReport.html b/templates/pooledReport.html index 9ae88cc6..aa31ba15 100644 --- a/templates/pooledReport.html +++ b/templates/pooledReport.html @@ -70,7 +70,7 @@
{{report_name}}
{% for plot_name in summary_plot_names %}
-
{{summary_plot_titles[plot_name]}}
+
{{summary_plot_titles[plot_name]}}
diff --git a/templates/report.html b/templates/report.html index b3ef054f..b85fe2ea 100644 --- a/templates/report.html +++ b/templates/report.html @@ -402,7 +402,7 @@
Indel characterization
{% else %}
Indel characterization for {{amplicon_name}}
{% endif %} -
    +
      {% if report_data['figures']['locs'][amplicon_name]['plot_4a'] %}
    • From 858a7517d24caee7e3333594477d9aa0dad56ac4 Mon Sep 17 00:00:00 2001 From: Samuel Nichols Date: Wed, 6 Jul 2022 11:27:46 -0400 Subject: [PATCH 08/33] fig_reports and replacement --- CRISPRessoReport.py | 3 +- templates/pooledReport.html | 6 +- templates/report.html | 428 +++++++------------ templates/shared/partials/fig_reports.html | 23 + templates/shared/partials/fig_summaries.html | 11 + 5 files changed, 183 insertions(+), 288 deletions(-) create mode 100644 templates/shared/partials/fig_reports.html create mode 100644 templates/shared/partials/fig_summaries.html diff --git a/CRISPRessoReport.py b/CRISPRessoReport.py index 83d94ed6..2880d7f4 100644 --- a/CRISPRessoReport.py +++ b/CRISPRessoReport.py @@ -101,7 +101,7 @@ def assemble_figs(run_data, crispresso_folder): amplicons = [] for amplicon_name in run_data['results']['ref_names']: amplicons.append(amplicon_name) - amplicon_figures = {'names': [], 'locs': {}, 'titles': {}, 'captions': {}, 'datas': {}} + amplicon_figures = {'names': [], 'locs': {}, 'titles': {}, 'captions': {}, 'datas': {}, 'htmls': {}} for fig in ['2a', '3a', '3b', '4a', '4b', '4c', '4d', '4e', '4f', '4g', '5', '6', '7', '8', '10a', '10b', '10c', '11a']: @@ -133,6 +133,7 @@ def assemble_figs(run_data, crispresso_folder): figures['titles'][amplicon_name] = amplicon_figures['titles'] figures['captions'][amplicon_name] = amplicon_figures['captions'] figures['datas'][amplicon_name] = amplicon_figures['datas'] + figures['htmls'][amplicon_name] = amplicon_figures['htmls'] data = {'amplicons': amplicons, 'figures': figures} return data diff --git a/templates/pooledReport.html b/templates/pooledReport.html index aa31ba15..bf29ed9b 100644 --- a/templates/pooledReport.html +++ b/templates/pooledReport.html @@ -73,11 +73,7 @@
      {{report_name}}
      {{summary_plot_titles[plot_name]}}
- - - {% for (data_label,data_path) in summary_plot_datas[plot_name] %} -

Data: {{data_label}}

- {% endfor %} + {{ render_partials('shared/partials/fig_summaries.html', plot_name=plot_name, summary_plot_htmls=summary_plot_htmls, crispresso_data_path=crispresso_data_path, summary_plot_labels=summary_plot_labels, summary_plot_datas=summary_plot_datas) }}
{% endfor %} diff --git a/templates/report.html b/templates/report.html index b85fe2ea..84c849e9 100644 --- a/templates/report.html +++ b/templates/report.html @@ -75,11 +75,7 @@
CRISPResso2 run information
- {{report_data['figures']['htmls']['plot_1a']|safe}} - - {% for (data_label,data_path) in report_data['figures']['datas']['plot_1a'] %} -

Data: {{data_label}}

- {% endfor %} + {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_1a')}}
{{ render_partial('shared/partials/log_params.html', report_data=report_data) }}
@@ -105,156 +101,116 @@
Allele assignments
-
- - - {% for (data_label,data_path) in report_data['figures']['datas']['plot_1b'] %} -

Data: {{data_label}}

- {% endfor %} +
+ {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_1b')}}
-
- - - {% for (data_label,data_path) in report_data['figures']['datas']['plot_1c'] %} -

Data: {{data_label}}

- {% endfor %} +
+ {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_1c')}}
{% if report_data['figures']['locs']['plot_1d'] %}
- - - {% for (data_label,data_path) in report_data['figures']['datas']['plot_1d'] %} -

Data: {{data_label}}

- {% endfor %} -
- {% endif %} + {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_1d')}} +
+ {% endif %}
{# end card #} {# start global coding sequence report #} - {% if report_data['figures']['locs']['plot_5a'] %} -
-
-
Global frameshift analysis
-
-
- - - {% for (data_label,data_path) in report_data['figures']['datas']['plot_5a'] %} -

Data: {{data_label}}

- {% endfor %} -
-
- {% endif %} + {% if report_data['figures']['locs']['plot_5a'] %} +
+
+
Global frameshift analysis
+
+
+ {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_5a')}} +
+
+ {% endif %} - {% if report_data['figures']['locs']['plot_6a'] %} -
-
-
Global frameshift mutagenesis profiles
-
-
- - - {% for (data_label,data_path) in report_data['figures']['datas']['plot_6a'] %} -

Data: {{data_label}}

- {% endfor %} -
-
- {% endif %} + {% if report_data['figures']['locs']['plot_6a'] %} +
+
+
Global frameshift mutagenesis profiles
+
+
+ {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_6a')}} +
+
+ {% endif %} - {% if report_data['figures']['locs']['plot_8a'] %} -
-
-
Global splicing analysis
-
-
- - - {% for (data_label,data_path) in report_data['figures']['datas']['plot_8a'] %} -

Data: {{data_label}}

- {% endfor %} -
-
- {% endif %} - {# end of global coding sequence analysis #} + {% if report_data['figures']['locs']['plot_8a'] %} +
+
+
Global splicing analysis
+
+
+ {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_8a')}} +
+
+ {% endif %} + {# end of global coding sequence analysis #} {# start hdr summary #} - {% if report_data['figures']['locs'][report_data.amplicons[0]]['plot_4g'] %} -
-
- {% if report_data.amplicons|length == 1 %} {# if only one amplicon #} -
HDR summary plot
- {% else %} -
HDR summary report (all reads aligned to {{report_data.amplicons[0]}})
- {% endif %} -
-
- - - {% for (data_label,data_path) in report_data['figures']['datas'][report_data.amplicons[0]]['plot_4g'] %} -

Data: {{data_label}}

- {% endfor %} -
-
+ {% if report_data['figures']['locs'][report_data.amplicons[0]]['plot_4g'] %} +
+
+ {% if report_data.amplicons|length == 1 %} {# if only one amplicon #} +
HDR summary plot
+ {% else %} +
HDR summary report (all reads aligned to {{report_data.amplicons[0]}})
{% endif %} +
+
+ {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_4g', amplicon_name=report_data.amplicons[0])}} +
+
+ {% endif %} {# end HDR summary #} {# start prime editing report #} - {% if report_data['figures']['locs'][report_data.amplicons[0]]['plot_11a'] %} -
-
+ {% if report_data['figures']['locs'][report_data.amplicons[0]]['plot_11a'] %} +
+
{% if report_data.amplicons|length == 1 %} {# if only one amplicon #} -
Prime editing report
+
Prime editing report
{% else %} -
Prime editing report (all reads aligned to {{report_data.amplicons[0]}})
+
Prime editing report (all reads aligned to {{report_data.amplicons[0]}})
{% endif %} -
-
- - - {% for (data_label,data_path) in report_data['figures']['datas'][report_data.amplicons[0]]['plot_11a'] %} -

Data: {{data_label}}

- {% endfor %} -
- {% endif %} +
+ {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_11a', amplicon_name=report_data.amplicons[0])}} +
+
+ {% endif %} {% if report_data['figures']['sgRNA_based_names'][report_data.amplicons[0]] and report_data['figures']['sgRNA_based_names'][report_data.amplicons[0]]['11b']%} -
-
+
+
{% if report_data.amplicons|length == 1 %} {# if only one amplicon #} -
Prime editing summary plots at analysis positions
+
Prime editing summary plots at analysis positions
{% else %} -
Prime editing summary plots at analysis positions (aligned to {{report_data.amplicons[0]}})
+
Prime editing summary plots at analysis positions (aligned to {{report_data.amplicons[0]}})
{% endif %} -
-
- {% for fig_name in report_data['figures']['sgRNA_based_names'][report_data.amplicons[0]]['11b'] %} -
- - - {% for (data_label,data_path) in report_data['figures']['datas'][report_data.amplicons[0]][fig_name] %} -

Data: {{data_label}}

- {% endfor %} -
+
+
+ {% for fig_name in report_data['figures']['sgRNA_based_names'][report_data.amplicons[0]]['11b'] %} +
+ {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name=fig_name, amplicon_name=report_data.amplicons[0])}} +
{% endfor %}
{% endif %} {# end plot 11b for prime editing #} - {% if report_data['figures']['locs']['plot_11c'] %} -
-
-
Scaffold insertions
-
-
- - - {% for (data_label,data_path) in report_data['figures']['datas']['plot_11c'] %} -

Data: {{data_label}}

- {% endfor %} + {% if report_data['figures']['locs']['plot_11c'] %} +
+
+
Scaffold insertions
+
+
+ {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_11c')}}
{% endif %} @@ -339,11 +295,7 @@
Nucleotide composition for {{amplicon_name}}
{% if report_data['figures']['sgRNA_based_names'][amplicon_name] and report_data['figures']['sgRNA_based_names'][amplicon_name]['2b']%}
{% for fig_name in report_data['figures']['sgRNA_based_names'][amplicon_name]['2b'] %} - - - {% for (data_label,data_path) in report_data['figures']['datas'][amplicon_name][fig_name] %} -

Data: {{data_label}}

- {% endfor %} + {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name=fig_name, amplicon_name=amplicon_name)}} {% endfor %}
{% endif %} @@ -374,22 +326,14 @@
Modification lengths for {{amplicon_name}}
{% if report_data['figures']['locs'][amplicon_name]['plot_3a'] %}
- - - {% for (data_label,data_path) in report_data['figures']['datas'][amplicon_name]['plot_3a'] %} -

Data: {{data_label}}

- {% endfor %} -
+ {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_3a', amplicon_name=amplicon_name)}} +
{% endif %} {% if report_data['figures']['locs'][amplicon_name]['plot_3b'] %}
- - - {% for (data_label,data_path) in report_data['figures']['datas'][amplicon_name]['plot_3b'] %} -

Data: {{data_label}}

- {% endfor %} -
+ {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_3b', amplicon_name=amplicon_name)}} +
{% endif %}
{# end card_body #} @@ -438,61 +382,36 @@
Indel characterization for {{amplicon_name}}
{% if report_data['figures']['locs'][amplicon_name]['plot_4a'] %} -
- - - {% for (data_label,data_path) in report_data['figures']['datas'][amplicon_name]['plot_4a'] %} -

Data: {{data_label}}

- {% endfor %} +
+ {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_4a', amplicon_name=amplicon_name)}}
{% endif %} {% if report_data['figures']['locs'][amplicon_name]['plot_4b'] %} -
- - - {% for (data_label,data_path) in report_data['figures']['datas'][amplicon_name]['plot_4b'] %} -

Data: {{data_label}}

- {% endfor %} +
+ {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_4b', amplicon_name=amplicon_name)}}
{% endif %} {% if report_data['figures']['locs'][amplicon_name]['plot_4c'] %} -
- - - - {% for (data_label,data_path) in report_data['figures']['datas'][amplicon_name]['plot_4c'] %} -

Data: {{data_label}}

- {% endfor %} +
+ {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_4c', amplicon_name=amplicon_name)}}
{% endif %} {% if report_data['figures']['locs'][amplicon_name]['plot_4d'] %} -
- - - {% for (data_label,data_path) in report_data['figures']['datas'][amplicon_name]['plot_4d'] %} -

Data: {{data_label}}

- {% endfor %} +
+ {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_4d', amplicon_name=amplicon_name)}}
{% endif %} {% if report_data['figures']['locs'][amplicon_name]['plot_4e'] %} -
- - - {% for (data_label,data_path) in report_data['figures']['datas'][amplicon_name]['plot_4e'] %} -

Data: {{data_label}}

- {% endfor %} +
+ {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_4e', amplicon_name=amplicon_name)}}
{% endif %} {% if report_data['figures']['locs'][amplicon_name]['plot_4f'] %} -
- - - {% for (data_label,data_path) in report_data['figures']['datas'][amplicon_name]['plot_4f'] %} -

Data: {{data_label}}

- {% endfor %} +
+ {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_4f', amplicon_name=amplicon_name)}}
{% endif %}
@@ -510,11 +429,7 @@
Frameshift analysis for {{amplicon_name}}
{% endif %}
- - - {% for (data_label,data_path) in report_data['figures']['datas'][amplicon_name]['plot_5'] %} -

Data: {{data_label}}

- {% endfor %} + {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_5', amplicon_name=amplicon_name)}}
{% endif %} @@ -529,11 +444,7 @@
Frameshift mutagenesis profiles for {{amplicon_name}}
{% endif %}
- - - {% for (data_label,data_path) in report_data['figures']['datas'][amplicon_name]['plot_6'] %} -

Data: {{data_label}}

- {% endfor %} + {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_6', amplicon_name=amplicon_name)}}
{% endif %} @@ -548,11 +459,7 @@
Coding mutations for {{amplicon_name}}
{% endif %}
- - - {% for (data_label,data_path) in report_data['figures']['datas'][amplicon_name]['plot_7'] %} -

Data: {{data_label}}

- {% endfor %} + {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_7', amplicon_name=amplicon_name)}}
{% endif %} @@ -567,11 +474,7 @@
Splicing for {{amplicon_name}}
{% endif %}
- - - {% for (data_label,data_path) in report_data['figures']['datas'][amplicon_name]['plot_8'] %} -

Data: {{data_label}}

- {% endfor %} + {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_8', amplicon_name=amplicon_name)}}
{% endif %} @@ -588,13 +491,9 @@
Allele plots for {{amplicon_name}}
{% for fig_name in report_data['figures']['sgRNA_based_names'][amplicon_name]['9'] %} -
- - - {% for (data_label,data_path) in report_data['figures']['datas'][amplicon_name][fig_name] %} -

Data: {{data_label}}

- {% endfor %} -
+
+ {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name=fig_name, amplicon_name=amplicon_name)}} +
{% endfor %}
@@ -630,96 +529,61 @@
Base editing for {{amplicon_name}}
{% endif %} -
-
-
+
+
+
{% if report_data['figures']['locs'][amplicon_name]['plot_10c'] %} -
-
- - - {% for (data_label,data_path) in report_data['figures']['datas'][amplicon_name]['plot_10a'] %} -

Data: {{data_label}}

- {% endfor %} -
-
- - +
+
+ {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_10a', amplicon_name=amplicon_name)}} +
+
- {% for (data_label,data_path) in report_data['figures']['datas'][amplicon_name]['plot_10b'] %} -

Data: {{data_label}}

- {% endfor %} - {% for (data_label,data_path) in report_data['figures']['datas'][amplicon_name]['plot_10c'] %} -

Data: {{data_label}}

- {% endfor %} -
+ {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_10b', amplicon_name=amplicon_name)}} + {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_10c', amplicon_name=amplicon_name)}}
+
{% else %} -
-
- - - {% for (data_label,data_path) in report_data['figures']['datas'][amplicon_name]['plot_10a'] %} -

Data: {{data_label}}

- {% endfor %} -
-
- - - {% for (data_label,data_path) in report_data['figures']['datas'][amplicon_name]['plot_10b'] %} -

Data: {{data_label}}

- {% endfor %} -
+
+
+ {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_10a', amplicon_name=amplicon_name)}} +
+
+ {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_10b', amplicon_name=amplicon_name)}} +
{% endif %} {% if report_data['figures']['sgRNA_based_names'][amplicon_name] and report_data['figures']['sgRNA_based_names'][amplicon_name]['10d']%} -
- {% for fig_name in report_data['figures']['sgRNA_based_names'][amplicon_name]['10d'] %} -
- - - {% for (data_label,data_path) in report_data['figures']['datas'][amplicon_name][fig_name] %} -

Data: {{data_label}}

- {% endfor %} -
- {% endfor %} -
+
+ {% for fig_name in report_data['figures']['sgRNA_based_names'][amplicon_name]['10d'] %} +
+ {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name=fig_name, amplicon_name=amplicon_name)}} +
+ {% endfor %} +
{% endif %} {% if report_data['figures']['sgRNA_based_names'][amplicon_name] and report_data['figures']['sgRNA_based_names'][amplicon_name]['10e']%} -
- {% for fig_name in report_data['figures']['sgRNA_based_names'][amplicon_name]['10e'] %} -
- - - {% for (data_label,data_path) in report_data['figures']['datas'][amplicon_name][fig_name] %} -

Data: {{data_label}}

- {% endfor %} -
- {% endfor %} -
+
+ {% for fig_name in report_data['figures']['sgRNA_based_names'][amplicon_name]['10e'] %} +
+ {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name=fig_name, amplicon_name=amplicon_name)}} +
+ {% endfor %} +
{% endif %} {% if report_data['figures']['sgRNA_based_names'][amplicon_name] and report_data['figures']['sgRNA_based_names'][amplicon_name]['10f']%} -
- {% for fig_name in report_data['figures']['sgRNA_based_names'][amplicon_name]['10f'] %} -
- - - {% for (data_label,data_path) in report_data['figures']['datas'][amplicon_name][fig_name] %} -

Data: {{data_label}}

- {% endfor %} -
- {% endfor %} - - {% for fig_name in report_data['figures']['sgRNA_based_names'][amplicon_name]['10g'] %} -
- - - {% for (data_label,data_path) in report_data['figures']['datas'][amplicon_name][fig_name] %} -

Data: {{data_label}}

- {% endfor %} -
- {% endfor %} +
+ {% for fig_name in report_data['figures']['sgRNA_based_names'][amplicon_name]['10f'] %} +
+ {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_10f', amplicon_name=amplicon_name)}} +
+ {% endfor %} + {% for fig_name in report_data['figures']['sgRNA_based_names'][amplicon_name]['10g'] %} +
+ {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_10g', amplicon_name=amplicon_name)}} +
+ {% endfor %}
{% endif %} diff --git a/templates/shared/partials/fig_reports.html b/templates/shared/partials/fig_reports.html new file mode 100644 index 00000000..4ee65aa2 --- /dev/null +++ b/templates/shared/partials/fig_reports.html @@ -0,0 +1,23 @@ +
+ {% if amplicon_name %} + {% if report_data['figures']['htmls'][amplicon_name][fig_name] %} + {{report_data['figures']['htmls'][amplicon_name][fig_name]|safe}} + {% else %} + + {% endif %} + + {% for (data_label,data_path) in report_data['figures']['datas'][amplicon_name][fig_name] %} +

Data: {{data_label}}

+ {% endfor %} + {% else %} + {% if report_data['figures']['htmls'][fig_name] %} + {{report_data['figures']['htmls'][fig_name]|safe}} + {% else %} + + {% endif %} + + {% for (data_label,data_path) in report_data['figures']['datas'][fig_name] %} +

Data: {{data_label}}

+ {% endfor %} + {% endif %} +
\ No newline at end of file diff --git a/templates/shared/partials/fig_summaries.html b/templates/shared/partials/fig_summaries.html new file mode 100644 index 00000000..404e8a26 --- /dev/null +++ b/templates/shared/partials/fig_summaries.html @@ -0,0 +1,11 @@ +
+ {% if summary_plot_htmls[plot_name] %} + {{summary_plot_htmls[plot_name]|safe}} + {% else %} + + {% endif %} + + {% for (data_label,data_path) in summary_plot_datas[plot_name] %} +

Data: {{data_label}}

+ {% endfor %} +
\ No newline at end of file From 546397a73d59288205b1a5772cf83a8f513b7e5b Mon Sep 17 00:00:00 2001 From: Samuel Nichols Date: Thu, 7 Jul 2022 10:11:15 -0400 Subject: [PATCH 09/33] summaries partials and html updates --- CRISPRessoReport.py | 11 +++-- templates/batchReport.html | 46 +++++------------ templates/multiReport.html | 52 ++++++-------------- templates/pooledReport.html | 10 ++-- templates/shared/partials/fig_summaries.html | 12 ++--- templates/wgsReport.html | 14 ++---- 6 files changed, 52 insertions(+), 93 deletions(-) diff --git a/CRISPRessoReport.py b/CRISPRessoReport.py index 2880d7f4..305e0fe6 100644 --- a/CRISPRessoReport.py +++ b/CRISPRessoReport.py @@ -524,10 +524,13 @@ def fill_default(dictionary, key, default_type=list): window_nuc_conv_plots=window_nuc_conv_plots, nuc_conv_plots=nuc_conv_plots, crispresso_data_path=crispresso_data_path, - summary_plot_names=summary_plots['names'], - summary_plot_titles=summary_plots['titles'], - summary_plot_labels=summary_plots['labels'], - summary_plot_datas=summary_plots['datas'], + report_data={ + 'names': summary_plots['names'], + 'titles': summary_plots['titles'], + 'labels': summary_plots['labels'], + 'datas': summary_plots['datas'], + 'crispresso_data_path': crispresso_data_path, + }, run_names=run_names, sub_html_files=sub_html_files, report_name=report_name, diff --git a/templates/batchReport.html b/templates/batchReport.html index 030d0450..93a6996b 100644 --- a/templates/batchReport.html +++ b/templates/batchReport.html @@ -73,12 +73,8 @@
Nucleotide percentages around guides
{% for plot_name in window_nuc_pct_quilts %} -
{{summary_plot_titles[plot_name]}}
- - - {% for (data_label,data_path) in summary_plot_datas[plot_name] %} -

Data: {{data_label}}

- {% endfor %} +
{{report_data['titles'][plot_name]}}
+ {{ render_partials('shared/partials/fig_summaries.html', report_data=report_data, plot_name=plot_name) }} {% endfor %}
@@ -91,12 +87,8 @@
Nucleotide percentages in the entire amplicon
{% for plot_name in nuc_pct_quilts %} -
{{summary_plot_titles[plot_name]}}
- - - {% for (data_label,data_path) in summary_plot_datas[plot_name] %} -

Data: {{data_label}}

- {% endfor %} +
{{report_data['titles'][plot_name]}}
+ {{ render_partials('shared/partials/fig_summaries.html', report_data=report_data, plot_name=plot_name) }} {% endfor %}
@@ -109,12 +101,8 @@
Conversion of target bases around guides
{% for plot_name in window_nuc_conv_plots %} -
{{summary_plot_titles[plot_name]}}
- - - {% for (data_label,data_path) in summary_plot_datas[plot_name] %} -

Data: {{data_label}}

- {% endfor %} +
{{report_data['titles'][plot_name]}}
+ {{ render_partials('shared/partials/fig_summaries.html', report_data=report_data, plot_name=plot_name) }} {% endfor %}
@@ -127,29 +115,21 @@
Conversion of target bases in the entire amplicon
{% for plot_name in nuc_conv_plots %} -
{{summary_plot_titles[plot_name]}}
- - - {% for (data_label,data_path) in summary_plot_datas[plot_name] %} -

Data: {{data_label}}

- {% endfor %} +
{{report_data['titles'][plot_name]}}
+ {{ render_partials('shared/partials/fig_summaries.html', report_data=report_data, plot_name=plot_name) }} {% endfor %}
{% endif %} - {% if summary_plot_names|length > 0 %} - {% for plot_name in summary_plot_names %} + {% if report_data['names']|length > 0 %} + {% for plot_name in report_data['names'] %}
-
{{summary_plot_titles[plot_name]}}
+
{{report_data['titles'][plot_name]}}
- - - {% for (data_label,data_path) in summary_plot_datas[plot_name] %} -

Data: {{data_label}}

- {% endfor %} + {{ render_partials('shared/partials/fig_summaries.html', report_data=report_data, plot_name=plot_name) }}
{% endfor %} @@ -168,7 +148,7 @@
{{summary_plot_titles[plot_name]}}
{# data bit for web version: #} {# -

Data: {{data_label}}

+

Data: {{data_label}}

#}
{# jumbotron_content #}
{# jumbrotron #} diff --git a/templates/multiReport.html b/templates/multiReport.html index 4f346efe..7cd6dd5b 100644 --- a/templates/multiReport.html +++ b/templates/multiReport.html @@ -58,7 +58,7 @@
{{report_name}}
{% for run_name in run_names %} - {{run_name}} + {{run_name}} {% endfor %}
@@ -72,12 +72,8 @@
Nucleotide percentages around guides
{% for plot_name in window_nuc_pct_quilts %} -
{{summary_plot_titles[plot_name]}}
- - - {% for (data_label,data_path) in summary_plot_datas[plot_name] %} -

Data: {{data_label}}

- {% endfor %} +
{{report_data['titles'][plot_name]}}
+ {{ render_partials('shared/partials/fig_summaries.html', report_data=report_data, plot_name=plot_name) }} {% endfor %}
@@ -90,12 +86,8 @@
Nucleotide percentages in the entire amplicon
{% for plot_name in nuc_pct_quilts %} -
{{summary_plot_titles[plot_name]}}
- - - {% for (data_label,data_path) in summary_plot_datas[plot_name] %} -

Data: {{data_label}}

- {% endfor %} +
{{report_data['titles'][plot_name]}}
+ {{ render_partials('shared/partials/fig_summaries.html', report_data=report_data, plot_name=plot_name) }} {% endfor %}
@@ -108,12 +100,8 @@
Conversion of target bases around guides
{% for plot_name in window_nuc_conv_plots %} -
{{summary_plot_titles[plot_name]}}
- - - {% for (data_label,data_path) in summary_plot_datas[plot_name] %} -

Data: {{data_label}}

- {% endfor %} +
{{report_data['titles'][plot_name]}}
+ {{ render_partials('shared/partials/fig_summaries.html', report_data=report_data, plot_name=plot_name) }} {% endfor %}
@@ -126,29 +114,21 @@
Conversion of target bases in the entire amplicon
{% for plot_name in nuc_conv_plots %} -
{{summary_plot_titles[plot_name]}}
- - - {% for (data_label,data_path) in summary_plot_datas[plot_name] %} -

Data: {{data_label}}

- {% endfor %} +
{{report_data['titles'][plot_name]}}
+ {{ render_partials('shared/partials/fig_summaries.html', report_data=report_data, plot_name=plot_name) }} {% endfor %}
{% endif %} - {% if summary_plot_names|length > 0 %} - {% for plot_name in summary_plot_names %} + {% if report_data['names']|length > 0 %} + {% for plot_name in report_data['names'] %}
-
{{summary_plot_titles[plot_name]}}
+
{{report_data['titles'][plot_name]}}
- - - {% for (data_label,data_path) in summary_plot_datas[plot_name] %} -

Data: {{data_label}}

- {% endfor %} + {{ render_partials('shared/partials/fig_summaries.html', report_data=report_data, plot_name=plot_name) }}
{% endfor %} @@ -176,14 +156,14 @@
{{allele_modification_heatmap_plot_titles[heatmap_plot_name]}}
{{allele_modification_heatmap_plot_htmls[heatmap_plot_name]}} {% for (data_label, data_path) in allele_modification_heatmap_plot_datas[heatmap_plot_name] %} -

Data: {{data_label}}

+

Data: {{data_label}}

{% endfor %}
{{allele_modification_line_plot_htmls[line_plot_name]}} {% for (data_label, data_path) in allele_modification_line_plot_datas[line_plot_name] %} -

Data: {{data_label}}

+

Data: {{data_label}}

{% endfor %}
@@ -261,7 +241,7 @@
Summary Plots
{% for compact_plot in compact_plots_to_show %} - + {% endfor %}
diff --git a/templates/pooledReport.html b/templates/pooledReport.html index bf29ed9b..93b2ed0b 100644 --- a/templates/pooledReport.html +++ b/templates/pooledReport.html @@ -66,14 +66,14 @@
{{report_name}}
{% endif %} - {% if summary_plot_names|length > 0 %} - {% for plot_name in summary_plot_names %} + {% if report_data['names']|length > 0 %} + {% for plot_name in report_data['names'] %}
-
{{summary_plot_titles[plot_name]}}
+
{{report_data['titles'][plot_name]}}
- {{ render_partials('shared/partials/fig_summaries.html', plot_name=plot_name, summary_plot_htmls=summary_plot_htmls, crispresso_data_path=crispresso_data_path, summary_plot_labels=summary_plot_labels, summary_plot_datas=summary_plot_datas) }} + {{ render_partials('shared/partials/fig_summaries.html', report_data=report_data, plot_name=plot_name) }}
{% endfor %} @@ -86,7 +86,7 @@
{{summary_plot_titles[plot_name]}}
{# data bit for web version: #} {# -

Data: {{data_label}}

+

Data: {{data_label}}

#} {# jumbotron_content #} {# jumbrotron #} diff --git a/templates/shared/partials/fig_summaries.html b/templates/shared/partials/fig_summaries.html index 404e8a26..384b7d8a 100644 --- a/templates/shared/partials/fig_summaries.html +++ b/templates/shared/partials/fig_summaries.html @@ -1,11 +1,11 @@
- {% if summary_plot_htmls[plot_name] %} - {{summary_plot_htmls[plot_name]|safe}} + {% if report_data['htmls'][plot_name] %} + {{report_data['htmls'][plot_name]|safe}} {% else %} - + {% endif %} - - {% for (data_label,data_path) in summary_plot_datas[plot_name] %} -

Data: {{data_label}}

+ + {% for (data_label,data_path) in report_data['datas'][plot_name] %} +

Data: {{data_label}}

{% endfor %}
\ No newline at end of file diff --git a/templates/wgsReport.html b/templates/wgsReport.html index 3cf2c781..74b0447c 100644 --- a/templates/wgsReport.html +++ b/templates/wgsReport.html @@ -64,18 +64,14 @@
{{report_name}}
- {% if summary_plot_names|length > 0 %} - {% for plot_name in summary_plot_names %} + {% if report_data['names']|length > 0 %} + {% for plot_name in report_data['names'] %}
-
{{summary_plot_titles[plot_name]}}
+
{{report_data['titles'][plot_name]}}
- - - {% for (data_label,data_path) in summary_plot_datas[plot_name] %} -

Data: {{data_label}}

- {% endfor %} + {{ render_partials('shared/partials/fig_summaries.html', report_data=report_data, plot_name=plot_name) }}
{% endfor %} @@ -88,7 +84,7 @@
{{summary_plot_titles[plot_name]}}
{# data bit for web version: #} {# -

Data: {{data_label}}

+

Data: {{data_label}}

#} {# jumbotron_content #} {# jumbrotron #} From 290d829f3b20f4186694a3895bb31200ef4a6d8f Mon Sep 17 00:00:00 2001 From: Cole Lyman Date: Thu, 7 Jul 2022 09:11:02 -0600 Subject: [PATCH 10/33] Fix error when rendering multi reports --- templates/batchReport.html | 10 +++++----- templates/multiReport.html | 10 +++++----- templates/pooledReport.html | 2 +- templates/wgsReport.html | 2 +- 4 files changed, 12 insertions(+), 12 deletions(-) diff --git a/templates/batchReport.html b/templates/batchReport.html index 93a6996b..d02c6269 100644 --- a/templates/batchReport.html +++ b/templates/batchReport.html @@ -74,7 +74,7 @@
Nucleotide percentages around guides
{% for plot_name in window_nuc_pct_quilts %}
{{report_data['titles'][plot_name]}}
- {{ render_partials('shared/partials/fig_summaries.html', report_data=report_data, plot_name=plot_name) }} + {{ render_partial('shared/partials/fig_summaries.html', report_data=report_data, plot_name=plot_name) }} {% endfor %}
@@ -88,7 +88,7 @@
Nucleotide percentages in the entire amplicon
{% for plot_name in nuc_pct_quilts %}
{{report_data['titles'][plot_name]}}
- {{ render_partials('shared/partials/fig_summaries.html', report_data=report_data, plot_name=plot_name) }} + {{ render_partial('shared/partials/fig_summaries.html', report_data=report_data, plot_name=plot_name) }} {% endfor %}
@@ -102,7 +102,7 @@
Conversion of target bases around guides
{% for plot_name in window_nuc_conv_plots %}
{{report_data['titles'][plot_name]}}
- {{ render_partials('shared/partials/fig_summaries.html', report_data=report_data, plot_name=plot_name) }} + {{ render_partial('shared/partials/fig_summaries.html', report_data=report_data, plot_name=plot_name) }} {% endfor %}
@@ -116,7 +116,7 @@
Conversion of target bases in the entire amplicon
{% for plot_name in nuc_conv_plots %}
{{report_data['titles'][plot_name]}}
- {{ render_partials('shared/partials/fig_summaries.html', report_data=report_data, plot_name=plot_name) }} + {{ render_partial('shared/partials/fig_summaries.html', report_data=report_data, plot_name=plot_name) }} {% endfor %}
@@ -129,7 +129,7 @@
{{report_data['titles'][plot_name]}}
{{report_data['titles'][plot_name]}}
- {{ render_partials('shared/partials/fig_summaries.html', report_data=report_data, plot_name=plot_name) }} + {{ render_partial('shared/partials/fig_summaries.html', report_data=report_data, plot_name=plot_name) }}
{% endfor %} diff --git a/templates/multiReport.html b/templates/multiReport.html index 7cd6dd5b..8e8d83ca 100644 --- a/templates/multiReport.html +++ b/templates/multiReport.html @@ -73,7 +73,7 @@
Nucleotide percentages around guides
{% for plot_name in window_nuc_pct_quilts %}
{{report_data['titles'][plot_name]}}
- {{ render_partials('shared/partials/fig_summaries.html', report_data=report_data, plot_name=plot_name) }} + {{ render_partial('shared/partials/fig_summaries.html', report_data=report_data, plot_name=plot_name) }} {% endfor %}
@@ -87,7 +87,7 @@
Nucleotide percentages in the entire amplicon
{% for plot_name in nuc_pct_quilts %}
{{report_data['titles'][plot_name]}}
- {{ render_partials('shared/partials/fig_summaries.html', report_data=report_data, plot_name=plot_name) }} + {{ render_partial('shared/partials/fig_summaries.html', report_data=report_data, plot_name=plot_name) }} {% endfor %}
@@ -101,7 +101,7 @@
Conversion of target bases around guides
{% for plot_name in window_nuc_conv_plots %}
{{report_data['titles'][plot_name]}}
- {{ render_partials('shared/partials/fig_summaries.html', report_data=report_data, plot_name=plot_name) }} + {{ render_partial('shared/partials/fig_summaries.html', report_data=report_data, plot_name=plot_name) }} {% endfor %}
@@ -115,7 +115,7 @@
Conversion of target bases in the entire amplicon
{% for plot_name in nuc_conv_plots %}
{{report_data['titles'][plot_name]}}
- {{ render_partials('shared/partials/fig_summaries.html', report_data=report_data, plot_name=plot_name) }} + {{ render_partial('shared/partials/fig_summaries.html', report_data=report_data, plot_name=plot_name) }} {% endfor %}
@@ -128,7 +128,7 @@
{{report_data['titles'][plot_name]}}
{{report_data['titles'][plot_name]}}
- {{ render_partials('shared/partials/fig_summaries.html', report_data=report_data, plot_name=plot_name) }} + {{ render_partial('shared/partials/fig_summaries.html', report_data=report_data, plot_name=plot_name) }}
{% endfor %} diff --git a/templates/pooledReport.html b/templates/pooledReport.html index 93b2ed0b..5128785a 100644 --- a/templates/pooledReport.html +++ b/templates/pooledReport.html @@ -73,7 +73,7 @@
{{report_name}}
{{report_data['titles'][plot_name]}}
- {{ render_partials('shared/partials/fig_summaries.html', report_data=report_data, plot_name=plot_name) }} + {{ render_partial('shared/partials/fig_summaries.html', report_data=report_data, plot_name=plot_name) }}
{% endfor %} diff --git a/templates/wgsReport.html b/templates/wgsReport.html index 74b0447c..0a5a1277 100644 --- a/templates/wgsReport.html +++ b/templates/wgsReport.html @@ -71,7 +71,7 @@
{{report_name}}
{{report_data['titles'][plot_name]}}
- {{ render_partials('shared/partials/fig_summaries.html', report_data=report_data, plot_name=plot_name) }} + {{ render_partial('shared/partials/fig_summaries.html', report_data=report_data, plot_name=plot_name) }}
{% endfor %} From 8f5d8a1136cbe16c5daf78da24655374e01b4f5d Mon Sep 17 00:00:00 2001 From: Samuel Nichols Date: Mon, 22 Aug 2022 10:21:10 -0600 Subject: [PATCH 11/33] Layout.html for C2WEB and CLI --- templates/layout.html | 93 +++++++++++++++++++++++-------------------- 1 file changed, 50 insertions(+), 43 deletions(-) diff --git a/templates/layout.html b/templates/layout.html index 05a1e959..0efa21f7 100644 --- a/templates/layout.html +++ b/templates/layout.html @@ -7,7 +7,8 @@ - + + @@ -22,12 +23,14 @@ - + - -{% endblock %} - -{% block content %} -
-
-
- -
-
- - {% if run_names|length > 0 %} -
-
-
{{report_name}}
-
-
-
- {% for run_name in run_names %} - {{run_name}} - {% endfor %} -
-
-
- {% endif %} - - {% if window_nuc_pct_quilts|length > 0 %} -
-
-
Nucleotide percentages around guides
-
-
- {% for plot_name in window_nuc_pct_quilts %} -
{{report_data['titles'][plot_name]}}
- {{ render_partial('CRISPRessoReports/templates/shared/partials/fig_summaries.html', report_data=report_data, plot_name=plot_name) }} - {% endfor %} -
-
- {% endif %} - - {% if nuc_pct_quilts|length > 0 %} -
-
-
Nucleotide percentages in the entire amplicon
-
-
- {% for plot_name in nuc_pct_quilts %} -
{{report_data['titles'][plot_name]}}
- {{ render_partial('CRISPRessoReports/templates/shared/partials/fig_summaries.html', report_data=report_data, plot_name=plot_name) }} - {% endfor %} -
-
- {% endif %} - - {% if window_nuc_conv_plots|length > 0 %} -
-
-
Conversion of target bases around guides
-
-
- {% for plot_name in window_nuc_conv_plots %} -
{{report_data['titles'][plot_name]}}
- {{ render_partial('CRISPRessoReports/templates/shared/partials/fig_summaries.html', report_data=report_data, plot_name=plot_name) }} - {% endfor %} -
-
- {% endif %} - - {% if nuc_conv_plots|length > 0 %} -
-
-
Conversion of target bases in the entire amplicon
-
-
- {% for plot_name in nuc_conv_plots %} -
{{report_data['titles'][plot_name]}}
- {{ render_partial('CRISPRessoReports/templates/shared/partials/fig_summaries.html', report_data=report_data, plot_name=plot_name) }} - {% endfor %} -
-
- {% endif %} - - {% if report_data['names']|length > 0 %} - {% for plot_name in report_data['names'] %} -
-
-
{{report_data['titles'][plot_name]}}
-
-
- {{ render_partial('CRISPRessoReports/templates/shared/partials/fig_summaries.html', report_data=report_data, plot_name=plot_name) }} -
-
- {% endfor %} - {% endif %} - - -
- -
- -
- Download report - Link to report - -
- - {# data bit for web version: #} - {# -

Data: {{data_label}}

- #} -
{# jumbotron_content #} -
{# jumbrotron #} - - {# column #} - -
- -{% endblock %} - -{% block foot %} -{% endblock %} diff --git a/templates/favicon.ico b/templates/favicon.ico deleted file mode 100644 index 8aed2d0743b52f12c1f0f8b2b4c439ba77091af3..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 1150 zcmbVMTWeE65MIGIUy2Vt`{*xIQTtGpYE@zjwT6~P+tO3xNz+rB6BBFO#3;0l0Sg5a zZAl=|kQxgi_XiV_ko)E9&Xx@^1Pab!cV@nwZ)Rt5au~b9pOF#9_nYkQRmN^G#%}S& zA&y+&TrtMau3x)Y!si1jMS7+{#1gs$u8 zbUGr3j2X-&@p8G0S4Jb0RSQPWS&7j;UxRtyjV~aI9)ri>NaQ} z>~Oeuu(+b&=h3fA`*^3SaBOd3!|A}9U5943;giRWWz~!c!wYD(4dnBAQA^%g>LQ<) zs%h}-?+MOFw+owmecsy@dCWZbuGb5@(>av?=j;rMMTMfi$Kz)c7#knQqo+?`G?`%A zbYkx98F-lC8jXMI_VcApG3|C6>2zAuA-}}uB7YyLWxUk& zdL5Ze2Dw~LK*?khg+c+OoBUm*vs5Z2Y{?-l?@je8m5Ml`8pI$zXSiP&jEy - - - CRISPResso2 - - - - - - - - - - - - - - - - - - - - - - - {% if current_user is defined %} - - {% else %} - - {% endif %} - - - - - {% block head %}{% endblock %} - - - - - {% if current_user is defined %} -
- {{ self.help_block() }} -
- - {% with messages = get_flashed_messages(with_categories=true) %} - {% if messages %} - {% for category, message in messages %} - {% if category == "error" %} - - {% else %} - - {% endif %} - {% endfor %} - {% endif %} - {% endwith %} - {% endif %} - - {# if default user (normal crispresso mode) #} - {% if current_user == null or not current_user.is_anonymous and current_user.username == "DEFAULTUSER" %} - -
-
-
- {% if current_user is defined %} -
- {% else %} -
- {% endif %} -
-
-

CRISPResso2

-

Analysis of genome editing outcomes from deep sequencing data

-
-
-
-
- - - {% else %} - {# if doing user sessions #} - -
- {% endif %} - -
-
-
-
- {% block help_block %} {% endblock %} -
-
-
-
- - {% block content %}{% endblock %} - - {% if current_user is defined and (not current_user.is_anonymous and current_user.username == "DEFAULTUSER") %} -
-
- -
-
- {% else %} -
-
- -
-
- {% endif %} - - - - - - - {% block foot %}{% endblock %} - - - diff --git a/templates/multiReport.html b/templates/multiReport.html deleted file mode 100644 index b6784e4a..00000000 --- a/templates/multiReport.html +++ /dev/null @@ -1,265 +0,0 @@ -{% extends "layout.html" %} -{% block head %} - - -{% endblock %} - -{% block content %} -
-
- -
-
- - {% if run_names|length > 0 %} -
-
-
{{report_name}}
-
-
-
- {% for run_name in run_names %} - {{run_name}} - {% endfor %} -
-
-
- {% endif %} - - {% if window_nuc_pct_quilts|length > 0 %} -
-
-
Nucleotide percentages around guides
-
-
- {% for plot_name in window_nuc_pct_quilts %} -
{{report_data['titles'][plot_name]}}
- {{ render_partial('CRISPRessoReports/templates/shared/partials/fig_summaries.html', report_data=report_data, plot_name=plot_name) }} - {% endfor %} -
-
- {% endif %} - - {% if nuc_pct_quilts|length > 0 %} -
-
-
Nucleotide percentages in the entire amplicon
-
-
- {% for plot_name in nuc_pct_quilts %} -
{{report_data['titles'][plot_name]}}
- {{ render_partial('CRISPRessoReports/templates/shared/partials/fig_summaries.html', report_data=report_data, plot_name=plot_name) }} - {% endfor %} -
-
- {% endif %} - - {% if window_nuc_conv_plots|length > 0 %} -
-
-
Conversion of target bases around guides
-
-
- {% for plot_name in window_nuc_conv_plots %} -
{{report_data['titles'][plot_name]}}
- {{ render_partial('CRISPRessoReports/templates/shared/partials/fig_summaries.html', report_data=report_data, plot_name=plot_name) }} - {% endfor %} -
-
- {% endif %} - - {% if nuc_conv_plots|length > 0 %} -
-
-
Conversion of target bases in the entire amplicon
-
-
- {% for plot_name in nuc_conv_plots %} -
{{report_data['titles'][plot_name]}}
- {{ render_partial('CRISPRessoReports/templates/shared/partials/fig_summaries.html', report_data=report_data, plot_name=plot_name) }} - {% endfor %} -
-
- {% endif %} - - {% if report_data['names']|length > 0 %} - {% for plot_name in report_data['names'] %} -
-
-
{{report_data['titles'][plot_name]}}
-
-
- {{ render_partial('CRISPRessoReports/templates/shared/partials/fig_summaries.html', report_data=report_data, plot_name=plot_name) }} -
-
- {% endfor %} - {% endif %} - - {% if allele_modification_heatmap_plot_names|length > 0 %} - {% for heatmap_plot_name in allele_modification_heatmap_plot_names %} - {% set line_plot_name = allele_modification_line_plot_names[loop.index - 1] %} - {% set modification_type = heatmap_plot_name.split('_')[3] %} -
-
-
{{allele_modification_heatmap_plot_titles[heatmap_plot_name]}}
- -
-
-
-
- {{allele_modification_heatmap_plot_htmls[heatmap_plot_name]}} - - {% for (data_label, data_path) in allele_modification_heatmap_plot_datas[heatmap_plot_name] %} -

Data: {{data_label}}

- {% endfor %} -
-
- {{allele_modification_line_plot_htmls[line_plot_name]}} - - {% for (data_label, data_path) in allele_modification_line_plot_datas[line_plot_name] %} -

Data: {{data_label}}

- {% endfor %} -
-
-
-
- - {% endfor %} - - - - {% endif %} - - {% if compact_plots_to_show|length > 0 %} -
-
-
Summary Plots
-
-
-
- {% for compact_plot in compact_plots_to_show %} - - {% endfor %} -
-
-
- {% endif %} - - -
- -
- -
{# jumbotron_content #} -
{# jumbrotron #} - -
{# column #} - -
-{% endblock %} - -{% block foot %} -{% endblock %} diff --git a/templates/pooledReport.html b/templates/pooledReport.html deleted file mode 100644 index ceb40426..00000000 --- a/templates/pooledReport.html +++ /dev/null @@ -1,101 +0,0 @@ -{% extends "CRISPRessoReports/templates/layout.html" %} -{% block head %} - - -{% endblock %} - -{% block content %} -
-
-
- -
-
- - {% if run_names|length > 0 %} -
-
-
{{report_name}}
-
-
-
- {% for region_name in run_names %} - {{region_name}} - {% endfor %} -
-
-
- {% endif %} - - {% if report_data['names']|length > 0 %} - {% for plot_name in report_data['names'] %} -
-
-
{{report_data['titles'][plot_name]}}
-
-
- {{ render_partial('CRISPRessoReports/templates/shared/partials/fig_summaries.html', report_data=report_data, plot_name=plot_name) }} -
-
- {% endfor %} - {% endif %} - -
- Download report - Link to report - -
- {# data bit for web version: #} - {# -

Data: {{data_label}}

- #} -
{# jumbotron_content #} -
{# jumbrotron #} - -
{# column #} - -
-
-{% endblock %} - -{% block foot %} -{% endblock %} diff --git a/templates/report.html b/templates/report.html deleted file mode 100644 index 882d6731..00000000 --- a/templates/report.html +++ /dev/null @@ -1,698 +0,0 @@ -{% extends "layout.html" %} -{% block head %} - - -{% endblock %} - -{% block content %} -
-
-
-
-
-
- {% if report_data['report_display_name'] != '' %} -
{{report_data['report_display_name']}}
- {% endif %} -
CRISPResso2 run information
-
    -
  • - -
    • -
  • - -
    • -
-
-
-
-
- {{ render_partial('CRISPRessoReports/templates/shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_1a')}} -
- {{ render_partial('CRISPRessoReports/templates/shared/partials/log_params.html', report_data=report_data) }} -
-
-
- -
-
-
Allele assignments
-
    -
  • - -
    • -
  • - -
    • - {% if report_data['figures']['locs']['plot_1d'] %} -
  • - -
    • - {% endif %} -
-
-
-
-
- {{ render_partial('CRISPRessoReports/templates/shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_1b')}} -
-
- {{ render_partial('CRISPRessoReports/templates/shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_1c')}} -
- {% if report_data['figures']['locs']['plot_1d'] %} -
- {{ render_partial('CRISPRessoReports/templates/shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_1d')}} -
- {% endif %} -
-
-
{# end card #} - - {# start global coding sequence report #} - {% if report_data['figures']['locs']['plot_5a'] %} -
-
-
Global frameshift analysis
-
-
- {{ render_partial('CRISPRessoReports/templates/shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_5a')}} -
-
- {% endif %} - - {% if report_data['figures']['locs']['plot_6a'] %} -
-
-
Global frameshift mutagenesis profiles
-
-
- {{ render_partial('CRISPRessoReports/templates/shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_6a')}} -
-
- {% endif %} - - {% if report_data['figures']['locs']['plot_8a'] %} -
-
-
Global splicing analysis
-
-
- {{ render_partial('CRISPRessoReports/templates/shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_8a')}} -
-
- {% endif %} - {# end of global coding sequence analysis #} - - {# start hdr summary #} - {% if report_data['figures']['locs'][report_data.amplicons[0]]['plot_4g'] %} -
-
- {% if report_data.amplicons|length == 1 %} {# if only one amplicon #} -
HDR summary plot
- {% else %} -
HDR summary report (all reads aligned to {{report_data.amplicons[0]}})
- {% endif %} -
-
- {{ render_partial('CRISPRessoReports/templates/shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_4g', amplicon_name=report_data.amplicons[0])}} -
-
- {% endif %} - {# end HDR summary #} - - {# start prime editing report #} - {% if report_data['figures']['locs'][report_data.amplicons[0]]['plot_11a'] %} -
-
- {% if report_data.amplicons|length == 1 %} {# if only one amplicon #} -
Prime editing report
- {% else %} -
Prime editing report (all reads aligned to {{report_data.amplicons[0]}})
- {% endif %} -
-
- {{ render_partial('CRISPRessoReports/templates/shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_11a', amplicon_name=report_data.amplicons[0])}} -
-
- {% endif %} - - {% if report_data['figures']['sgRNA_based_names'][report_data.amplicons[0]] and report_data['figures']['sgRNA_based_names'][report_data.amplicons[0]]['11b']%} -
-
- {% if report_data.amplicons|length == 1 %} {# if only one amplicon #} -
Prime editing summary plots at analysis positions
- {% else %} -
Prime editing summary plots at analysis positions (aligned to {{report_data.amplicons[0]}})
- {% endif %} -
-
- {% for fig_name in report_data['figures']['sgRNA_based_names'][report_data.amplicons[0]]['11b'] %} -
- {{ render_partial('CRISPRessoReports/templates/shared/partials/fig_reports.html', report_data=report_data, fig_name=fig_name, amplicon_name=report_data.amplicons[0])}} -
- {% endfor %} -
-
- {% endif %} - {# end plot 11b for prime editing #} - - {% if report_data['figures']['locs']['plot_11c'] %} -
-
-
Scaffold insertions
-
-
- {{ render_partial('CRISPRessoReports/templates/shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_11c')}} -
-
- {% endif %} - {# end prime editing section #} - - {% if report_data.amplicons|length == 1 %} -
{# if only one amplicon, just a normal div #} - {% else %} - {# If there is more than one amplicon, print a navigation to show each amplicon #} -

Reads are aligned to each amplicon sequence separately. Quantification and visualization of these reads are shown for each amplicon below:

-
-
-
Amplicons
- -
- {% endif %} {# end if report contains more than one amplicon #} - - - {% if report_data.amplicons|length == 1 %} {# if only one amplicon, just a normal div #} -
- {% else %} -
- {% endif %} - - {% for amplicon_name in report_data.amplicons %} - {% if report_data.amplicons|length == 1 %} {# if only one amplicon, just a normal div #} -
- {% elif loop.index0 == 0 %} {# if more than one amplicon, and the first, this is the active one #} -
-

Reads aligning to {{amplicon_name}}

{# this bit appears in print mode #} - {% else %} {# otherwise inactive tab #} -
-

Reads aligning to {{amplicon_name}}

{# this bit appears in print mode #} - {% endif %} - -
-
- {% if report_data.amplicons|length == 1 %} {# if only one amplicon #} -
Nucleotide composition
- {% else %} -
Nucleotide composition for {{amplicon_name}}
- {% endif %} -
-
- {% if report_data['figures']['locs'][amplicon_name]['plot_2a'] %} -
-
-
- -
-
-
- -
- -
- - {% for (data_label,data_path) in report_data['figures']['datas'][amplicon_name]['plot_2a'] %} -

Data: {{data_label}}

- {% endfor %} -
-
- {% endif %} - - {% if report_data['figures']['sgRNA_based_names'][amplicon_name] and report_data['figures']['sgRNA_based_names'][amplicon_name]['2b']%} -
- {% for fig_name in report_data['figures']['sgRNA_based_names'][amplicon_name]['2b'] %} - {{ render_partial('CRISPRessoReports/templates/shared/partials/fig_reports.html', report_data=report_data, fig_name=fig_name, amplicon_name=amplicon_name)}} - {% endfor %} -
- {% endif %} -
-
{# end card #} - -
-
- {% if report_data.amplicons|length == 1 %} {# if only one amplicon #} -
Modification lengths
- {% else %} -
Modification lengths for {{amplicon_name}}
- {% endif %} -
    - {% if report_data['figures']['locs'][amplicon_name]['plot_3a'] %} -
  • - -
    • - {% endif %} - {% if report_data['figures']['locs'][amplicon_name]['plot_3b'] %} -
  • - -
    • - {% endif %} -
-
-
-
- {% if report_data['figures']['locs'][amplicon_name]['plot_3a'] %} -
- {{ render_partial('CRISPRessoReports/templates/shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_3a', amplicon_name=amplicon_name)}} -
- {% endif %} - - {% if report_data['figures']['locs'][amplicon_name]['plot_3b'] %} -
- {{ render_partial('CRISPRessoReports/templates/shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_3b', amplicon_name=amplicon_name)}} -
- {% endif %} -
-
{# end card_body #} -
{# end card #} - -
-
- {% if report_data.amplicons|length == 1 %} {# if only one amplicon #} -
Indel characterization
- {% else %} -
Indel characterization for {{amplicon_name}}
- {% endif %} -
    - {% if report_data['figures']['locs'][amplicon_name]['plot_4a'] %} -
  • - -
    • - {% endif %} - {% if report_data['figures']['locs'][amplicon_name]['plot_4b'] %} -
  • - -
    • - {% endif %} - {% if report_data['figures']['locs'][amplicon_name]['plot_4c'] %} -
  • - -
    • - {% endif %} - {% if report_data['figures']['locs'][amplicon_name]['plot_4d'] %} -
  • - -
    • - {% endif %} - {% if report_data['figures']['locs'][amplicon_name]['plot_4e'] %} -
  • - -
    • - {% endif %} - {% if report_data['figures']['locs'][amplicon_name]['plot_4f'] %} -
  • - -
    • - {% endif %} -
-
{# end card head #} -
-
- {% if report_data['figures']['locs'][amplicon_name]['plot_4a'] %} -
- {{ render_partial('CRISPRessoReports/templates/shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_4a', amplicon_name=amplicon_name)}} -
- {% endif %} - {% if report_data['figures']['locs'][amplicon_name]['plot_4b'] %} -
- {{ render_partial('CRISPRessoReports/templates/shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_4b', amplicon_name=amplicon_name)}} -
- {% endif %} - {% if report_data['figures']['locs'][amplicon_name]['plot_4c'] %} -
- {{ render_partial('CRISPRessoReports/templates/shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_4c', amplicon_name=amplicon_name)}} -
- {% endif %} - - {% if report_data['figures']['locs'][amplicon_name]['plot_4d'] %} -
- {{ render_partial('CRISPRessoReports/templates/shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_4d', amplicon_name=amplicon_name)}} -
- {% endif %} - - {% if report_data['figures']['locs'][amplicon_name]['plot_4e'] %} -
- {{ render_partial('CRISPRessoReports/templates/shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_4e', amplicon_name=amplicon_name)}} -
- {% endif %} - - {% if report_data['figures']['locs'][amplicon_name]['plot_4f'] %} -
- {{ render_partial('CRISPRessoReports/templates/shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_4f', amplicon_name=amplicon_name)}} -
- {% endif %} -
-
{# end card body #} -
{# end card #} - - - {% if report_data['figures']['locs'][amplicon_name]['plot_5'] %} -
-
- {% if report_data.amplicons|length == 1 %} {# if only one amplicon #} -
Frameshift analysis
- {% else %} -
Frameshift analysis for {{amplicon_name}}
- {% endif %} -
-
- {{ render_partial('CRISPRessoReports/templates/shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_5', amplicon_name=amplicon_name)}} -
-
- {% endif %} - - {% if report_data['figures']['locs'][amplicon_name]['plot_6'] %} -
-
- {% if report_data.amplicons|length == 1 %} {# if only one amplicon #} -
Frameshift mutagenesis profiles
- {% else %} -
Frameshift mutagenesis profiles for {{amplicon_name}}
- {% endif %} -
-
- {{ render_partial('CRISPRessoReports/templates/shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_6', amplicon_name=amplicon_name)}} -
-
- {% endif %} - - {% if report_data['figures']['locs'][amplicon_name]['plot_7'] %} -
-
- {% if report_data.amplicons|length == 1 %} {# if only one amplicon #} -
Non-coding mutations
- {% else %} -
Coding mutations for {{amplicon_name}}
- {% endif %} -
-
- {{ render_partial('CRISPRessoReports/templates/shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_7', amplicon_name=amplicon_name)}} -
-
- {% endif %} - - {% if report_data['figures']['locs'][amplicon_name]['plot_8'] %} -
-
- {% if report_data.amplicons|length == 1 %} {# if only one amplicon #} -
Splicing
- {% else %} -
Splicing for {{amplicon_name}}
- {% endif %} -
-
- {{ render_partial('CRISPRessoReports/templates/shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_8', amplicon_name=amplicon_name)}} -
-
- {% endif %} - - {% if report_data['figures']['sgRNA_based_names'][amplicon_name] and report_data['figures']['sgRNA_based_names'][amplicon_name]['9']%} -
-
- {% if report_data.amplicons|length == 1 %} {# if only one amplicon #} -
Allele plots
- {% else %} -
Allele plots for {{amplicon_name}}
- {% endif %} -
-
- {% for fig_name in report_data['figures']['sgRNA_based_names'][amplicon_name]['9'] %} -
- {{ render_partial('CRISPRessoReports/templates/shared/partials/fig_reports.html', report_data=report_data, fig_name=fig_name, amplicon_name=amplicon_name)}} -
- {% endfor %} -
-
- {% endif %} - - {% if report_data['figures']['locs'][amplicon_name]['plot_10a'] %} -
-
- {% if report_data.amplicons|length == 1 %} {# if only one amplicon #} -
Base editing
- {% else %} -
Base editing for {{amplicon_name}}
- {% endif %} -
    - {% if report_data['figures']['locs'][amplicon_name]['plot_10a'] %} -
  • - -
    • - {% endif %} - {% if report_data['figures']['sgRNA_based_names'][amplicon_name] and report_data['figures']['sgRNA_based_names'][amplicon_name]['10d']%} -
  • - -
    • - {% endif %} - {% if report_data['figures']['sgRNA_based_names'][amplicon_name] and report_data['figures']['sgRNA_based_names'][amplicon_name]['10e']%} -
  • - -
    • - {% endif %} - {% if report_data['figures']['sgRNA_based_names'][amplicon_name] and report_data['figures']['sgRNA_based_names'][amplicon_name]['10f']%} -
  • - -
    • - {% endif %} -
-
-
-
- {% if report_data['figures']['locs'][amplicon_name]['plot_10c'] %} -
-
- {{ render_partial('CRISPRessoReports/templates/shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_10a', amplicon_name=amplicon_name)}} -
-
- - {{ render_partial('CRISPRessoReports/templates/shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_10b', amplicon_name=amplicon_name)}} - {{ render_partial('CRISPRessoReports/templates/shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_10c', amplicon_name=amplicon_name)}} -
-
- {% else %} -
-
- {{ render_partial('CRISPRessoReports/templates/shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_10a', amplicon_name=amplicon_name)}} -
-
- {{ render_partial('CRISPRessoReports/templates/shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_10b', amplicon_name=amplicon_name)}} -
-
- {% endif %} - {% if report_data['figures']['sgRNA_based_names'][amplicon_name] and report_data['figures']['sgRNA_based_names'][amplicon_name]['10d']%} -
- {% for fig_name in report_data['figures']['sgRNA_based_names'][amplicon_name]['10d'] %} -
- {{ render_partial('CRISPRessoReports/templates/shared/partials/fig_reports.html', report_data=report_data, fig_name=fig_name, amplicon_name=amplicon_name)}} -
- {% endfor %} -
- {% endif %} - {% if report_data['figures']['sgRNA_based_names'][amplicon_name] and report_data['figures']['sgRNA_based_names'][amplicon_name]['10e']%} -
- {% for fig_name in report_data['figures']['sgRNA_based_names'][amplicon_name]['10e'] %} -
- {{ render_partial('CRISPRessoReports/templates/shared/partials/fig_reports.html', report_data=report_data, fig_name=fig_name, amplicon_name=amplicon_name)}} -
- {% endfor %} -
- {% endif %} - {% if report_data['figures']['sgRNA_based_names'][amplicon_name] and report_data['figures']['sgRNA_based_names'][amplicon_name]['10f']%} -
- {% for fig_name in report_data['figures']['sgRNA_based_names'][amplicon_name]['10f'] %} -
- {{ render_partial('CRISPRessoReports/templates/shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_10f', amplicon_name=amplicon_name)}} -
- {% endfor %} - {% for fig_name in report_data['figures']['sgRNA_based_names'][amplicon_name]['10g'] %} -
- {{ render_partial('CRISPRessoReports/templates/shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_10g', amplicon_name=amplicon_name)}} -
- {% endfor %} -
-
- {% endif %} -
-
{# end card #} - {% endif %} {# end base editing card #} -
{# end this amplicon tab #} - - {% endfor %} -
{# tab content #} -
-
{# jumbotron_content #} -
{# jumbrotron #} -
{# column #} -
- -
-{% endblock %} - -{% block foot %} - -{% endblock %} diff --git a/templates/shared/partials/fig_reports.html b/templates/shared/partials/fig_reports.html deleted file mode 100644 index 6f7e448e..00000000 --- a/templates/shared/partials/fig_reports.html +++ /dev/null @@ -1,31 +0,0 @@ -
- {% if amplicon_name is defined %} - {% if 'htmls' in report_data['figures'] and fig_name in report_data['figures']['htmls'][amplicon_name] %} - {{report_data['figures']['htmls'][amplicon_name][fig_name]|safe}} - {% else %} - {% if fig_name in ['plot_1a', 'plot_1b', 'plot_1c', 'plot_3a', 'plot_4a', 'plot_4b', 'plot_4c'] %} - - {% else %} - - {% endif %} - {% endif %} - - {% for (data_label,data_path) in report_data['figures']['datas'][amplicon_name][fig_name] %} -

Data: {{data_label}}

- {% endfor %} - {% else %} - {% if 'htmls' in report_data['figures'] and fig_name in report_data['figures']['htmls'] %} - {{report_data['figures']['htmls'][fig_name]|safe}} - {% else %} - {% if fig_name in ['plot_1a', 'plot_1b', 'plot_1c', 'plot_3a', 'plot_4a', 'plot_4b', 'plot_4c'] %} - - {% else %} - - {% endif %} - {% endif %} - - {% for (data_label,data_path) in report_data['figures']['datas'][fig_name] %} -

Data: {{data_label}}

- {% endfor %} - {% endif %} -
\ No newline at end of file diff --git a/templates/shared/partials/fig_summaries.html b/templates/shared/partials/fig_summaries.html deleted file mode 100644 index 384b7d8a..00000000 --- a/templates/shared/partials/fig_summaries.html +++ /dev/null @@ -1,11 +0,0 @@ -
- {% if report_data['htmls'][plot_name] %} - {{report_data['htmls'][plot_name]|safe}} - {% else %} - - {% endif %} - - {% for (data_label,data_path) in report_data['datas'][plot_name] %} -

Data: {{data_label}}

- {% endfor %} -
\ No newline at end of file diff --git a/templates/shared/partials/log_params.html b/templates/shared/partials/log_params.html deleted file mode 100644 index ad035ae3..00000000 --- a/templates/shared/partials/log_params.html +++ /dev/null @@ -1,11 +0,0 @@ -
-

CRISPResso version: {{report_data['run_data']['running_info']['version']}}

-

Run completed: {{report_data['run_data']['running_info']['end_time_string']}}

-

Amplicon sequence: 

{{report_data['run_data']['running_info']['args']['amplicon_seq']}}

- {% if report_data['run_data']['running_info']['args']['guide_seq'] != '' %} -

Guide sequence: 

{{report_data['run_data']['running_info']['args']['guide_seq']}}

- {% endif %} -

Command used: 

{{report_data['run_data']['running_info']['command_used']}}

-

Parameters: 

{{report_data['run_data']['running_info']['args_string']}}

-

Running log

-
diff --git a/templates/wgsReport.html b/templates/wgsReport.html deleted file mode 100644 index aba5afc6..00000000 --- a/templates/wgsReport.html +++ /dev/null @@ -1,99 +0,0 @@ -{% extends "CRISPRessoReports/templates/layout.html" %} -{% block head %} - - -{% endblock %} - -{% block content %} -
-
-
- -
-
- -
-
-
{{report_name}}
-
-
-
- {% for region_name in run_names %} - {{region_name}} - {% endfor %} -
-
-
- - {% if report_data['names']|length > 0 %} - {% for plot_name in report_data['names'] %} -
-
-
{{report_data['titles'][plot_name]}}
-
-
- {{ render_partial('CRISPRessoReports/templates/shared/partials/fig_summaries.html', report_data=report_data, plot_name=plot_name) }} -
-
- {% endfor %} - {% endif %} - -
- Download report - Link to report - -
- {# data bit for web version: #} - {# -

Data: {{data_label}}

- #} -
{# jumbotron_content #} -
{# jumbrotron #} - -
{# column #} - -
-
-{% endblock %} - -{% block foot %} -{% endblock %} From 84174e6393ac68874698e910e1ba3d5daf098e3e Mon Sep 17 00:00:00 2001 From: Samuel Nichols Date: Sat, 10 Sep 2022 13:02:11 -0600 Subject: [PATCH 16/33] Squashed 'CRISPRessoWEB/CRISPRessoReports/' content from commit 7d9b4e5 git-subtree-dir: CRISPRessoWEB/CRISPRessoReports git-subtree-split: 7d9b4e54795c7459c917da50797c0fc5e30f8de7 --- CRISPRessoReport.py | 18 +- templates/CRISPResso_justcup.png | Bin 0 -> 42782 bytes templates/batchReport.html | 163 +++++ templates/favicon.ico | Bin 0 -> 1150 bytes templates/layout.html | 237 +++++++ templates/multiReport.html | 265 +++++++ templates/pooledReport.html | 101 +++ templates/report.html | 693 +++++++++++++++++++ templates/shared/partials/fig_reports.html | 31 + templates/shared/partials/fig_summaries.html | 11 + templates/shared/partials/log_params.html | 11 + templates/wgsReport.html | 99 +++ 12 files changed, 1617 insertions(+), 12 deletions(-) create mode 100644 templates/CRISPResso_justcup.png create mode 100644 templates/batchReport.html create mode 100644 templates/favicon.ico create mode 100644 templates/layout.html create mode 100644 templates/multiReport.html create mode 100644 templates/pooledReport.html create mode 100644 templates/report.html create mode 100644 templates/shared/partials/fig_reports.html create mode 100644 templates/shared/partials/fig_summaries.html create mode 100644 templates/shared/partials/log_params.html create mode 100644 templates/wgsReport.html diff --git a/CRISPRessoReport.py b/CRISPRessoReport.py index 79a4cd1e..58cf42ac 100644 --- a/CRISPRessoReport.py +++ b/CRISPRessoReport.py @@ -5,7 +5,7 @@ ''' import os -from jinja2 import Environment, FileSystemLoader, ChoiceLoader +from jinja2 import Environment, FileSystemLoader from jinja_partials import generate_render_partial, render_partial from CRISPResso2 import CRISPRessoShared @@ -163,11 +163,7 @@ def make_report(run_data, crispresso_report_file, crispresso_folder, _ROOT, web_ 'crispresso_data_path': crispresso_data_path, } - loader1 = FileSystemLoader(os.path.join(_ROOT, 'CRISPRessoReports', 'templates')) - loader2 = FileSystemLoader(os.path.join(_ROOT, 'templates')) - loader = ChoiceLoader([loader1, loader2]) - - j2_env = Environment(loader=loader) + j2_env = Environment(loader=FileSystemLoader(os.path.join(_ROOT, 'CRISPRessoReports', 'templates'))) # dest_dir = os.path.dirname(crispresso_report_file) # shutil.copy2(os.path.join(_ROOT,'templates','CRISPResso_justcup.png'),dest_dir) @@ -477,12 +473,9 @@ def fill_default(dictionary, key, default_type=list): if key not in dictionary: dictionary[key] = default_type() - loader1 = FileSystemLoader(os.path.join(_ROOT, 'CRISPRessoReports', 'templates')) - loader2 = FileSystemLoader(os.path.join(_ROOT, 'templates')) - loader = ChoiceLoader([loader1, loader2]) - - j2_env = Environment(loader=loader) - + j2_env = Environment( + loader=FileSystemLoader(os.path.join(_ROOT, 'CRISPRessoReports', 'templates')), + ) j2_env.filters['dirname'] = dirname if crispresso_tool == 'batch': template = 'batchReport.html' @@ -536,6 +529,7 @@ def fill_default(dictionary, key, default_type=list): 'titles': summary_plots['titles'], 'labels': summary_plots['labels'], 'datas': summary_plots['datas'], + 'htmls': [], 'crispresso_data_path': crispresso_data_path, }, run_names=run_names, diff --git a/templates/CRISPResso_justcup.png b/templates/CRISPResso_justcup.png new file mode 100644 index 0000000000000000000000000000000000000000..3116c48c394f23cf37669c6dbb92928ef0d88b9d GIT binary patch literal 42782 zcmb5VbyQVf)CGEoAA%xWBn6~IRJsKu1VlQeQ$SLb5T!c>X$k3&?vw^e5fA~9?vn11 ze2ee<-Wc!ScZUr14(>hs?7h}pbI!HS2PFl`o7c&&BM5R+TI#6^f}rukk32RyytB_9 zW($Ae*hp!;MUWeWS3hV-d?FcwTvxOZ7gtg;x3;%_Yi?~rBP}jYV`FD+YGGx9AdX{6 z&&^byuaF2GP3?=x26}#ywN@dXP3@x;v) zqav8`>1^wmU0{9Ub)DV@L1CA_qP&qhQlA{3n%2>dKhLp3T+XNTh|= zjE*iYER4vsiRl>r&~UpjYcXinIJf%eE_ilyFw;0k@5QO-C5d@F)6%mqmr2zdfk;!od{%j!kGtI~Is$6r_1K6r1$3 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zof`w6qZzR-3by*(-d0#FO+!O6ljh4yOBk>7#?Up!ILl8D!FmwYcLHpTB7yN0X_d{J zap`cE!EB9+j>aOv!H)(#&UlKNT4LKc+J}`j`dJoU((tdE7#|lA7G6p8Q!o7f`=3au zN;kGn6hCuGc;+G*KY@JK?SVwa(~(Ce{aJU3k&|5PyQn+i2@pxkgHCLNgoKJZ4*~d# z;FrK&yXK~OWbz^mhXHxSErb5u2NF^C@|PecJwl)kEd$W$NPEo91z%_LHzG>F;&9&C zjjtw0#{+`z4}fEOI_S#~<4Z|OzQaCq>5`j+=X)Zz_UyAcbZ9-9Op?(-W_}K6??f4(CJQ!ap`Vg1|YsFwE{X*>-=X& z*!Lq1g!~ktIDR@h_CF2^koK_gz7S>SX|VP9%R68#XJkm%9%jI;SwzJ5*OL8UR{M*` zRjA2IUwAT7niuJ6|E~$N^rZ$ln+I`&wlG@j((4?fC17BO&#FV^J|C%^h8yne=HS9KqZyZ{l$*~;b z{}M(5gc4v8j6D&yMB9m!{e3&8$0G>SWZ_>3-vahy1JSDvKruFNkqT`9eD_jW`;4db z&=Yu>3z6#mrAYOW$>8ny^_`nVlAfENzn~a{Ot!Em&n?0}PmKx`CAzmjh9Eg?1S$5eCoHeTPuGiaEnxm45-TZ~#h5{r&xDec(bP0*dCf23ayY>Sd(? z|46hvYI@*760k|+8X|_m#7E_0fK@d7?@hER@aCE_)&Jf^fRY{c-^YkI|L@2C|L>B_ cU%E)@U7zi*&~S_mcSq7bLvw>-np4RC0_{x7ApigX literal 0 HcmV?d00001 diff --git a/templates/batchReport.html b/templates/batchReport.html new file mode 100644 index 00000000..d02c6269 --- /dev/null +++ b/templates/batchReport.html @@ -0,0 +1,163 @@ +{% extends "layout.html" %} +{% block head %} + + +{% endblock %} + +{% block content %} +
+
+
+ +
+
+ + {% if run_names|length > 0 %} +
+
+
{{report_name}}
+
+
+
+ {% for run_name in run_names %} + {{run_name}} + {% endfor %} +
+
+
+ {% endif %} + + {% if window_nuc_pct_quilts|length > 0 %} +
+
+
Nucleotide percentages around guides
+
+
+ {% for plot_name in window_nuc_pct_quilts %} +
{{report_data['titles'][plot_name]}}
+ {{ render_partial('shared/partials/fig_summaries.html', report_data=report_data, plot_name=plot_name) }} + {% endfor %} +
+
+ {% endif %} + + {% if nuc_pct_quilts|length > 0 %} +
+
+
Nucleotide percentages in the entire amplicon
+
+
+ {% for plot_name in nuc_pct_quilts %} +
{{report_data['titles'][plot_name]}}
+ {{ render_partial('shared/partials/fig_summaries.html', report_data=report_data, plot_name=plot_name) }} + {% endfor %} +
+
+ {% endif %} + + {% if window_nuc_conv_plots|length > 0 %} +
+
+
Conversion of target bases around guides
+
+
+ {% for plot_name in window_nuc_conv_plots %} +
{{report_data['titles'][plot_name]}}
+ {{ render_partial('shared/partials/fig_summaries.html', report_data=report_data, plot_name=plot_name) }} + {% endfor %} +
+
+ {% endif %} + + {% if nuc_conv_plots|length > 0 %} +
+
+
Conversion of target bases in the entire amplicon
+
+
+ {% for plot_name in nuc_conv_plots %} +
{{report_data['titles'][plot_name]}}
+ {{ render_partial('shared/partials/fig_summaries.html', report_data=report_data, plot_name=plot_name) }} + {% endfor %} +
+
+ {% endif %} + + {% if report_data['names']|length > 0 %} + {% for plot_name in report_data['names'] %} +
+
+
{{report_data['titles'][plot_name]}}
+
+
+ {{ render_partial('shared/partials/fig_summaries.html', report_data=report_data, plot_name=plot_name) }} +
+
+ {% endfor %} + {% endif %} + + +
+ +
+ +
+ Download report + Link to report + +
+ + {# data bit for web version: #} + {# +

Data: {{data_label}}

+ #} +
{# jumbotron_content #} +
{# jumbrotron #} + +
{# column #} + +
+ +{% endblock %} + +{% block foot %} +{% endblock %} diff --git a/templates/favicon.ico b/templates/favicon.ico new file mode 100644 index 0000000000000000000000000000000000000000..8aed2d0743b52f12c1f0f8b2b4c439ba77091af3 GIT binary patch literal 1150 zcmbVMTWeE65MIGIUy2Vt`{*xIQTtGpYE@zjwT6~P+tO3xNz+rB6BBFO#3;0l0Sg5a zZAl=|kQxgi_XiV_ko)E9&Xx@^1Pab!cV@nwZ)Rt5au~b9pOF#9_nYkQRmN^G#%}S& zA&y+&TrtMau3x)Y!si1jMS7+{#1gs$u8 zbUGr3j2X-&@p8G0S4Jb0RSQPWS&7j;UxRtyjV~aI9)ri>NaQ} z>~Oeuu(+b&=h3fA`*^3SaBOd3!|A}9U5943;giRWWz~!c!wYD(4dnBAQA^%g>LQ<) zs%h}-?+MOFw+owmecsy@dCWZbuGb5@(>av?=j;rMMTMfi$Kz)c7#knQqo+?`G?`%A zbYkx98F-lC8jXMI_VcApG3|C6>2zAuA-}}uB7YyLWxUk& zdL5Ze2Dw~LK*?khg+c+OoBUm*vs5Z2Y{?-l?@je8m5Ml`8pI$zXSiP&jEy + + + CRISPResso2 + + + + + + + + + + + + + + + + + + + + + + + {% if current_user is defined %} + + {% else %} + + {% endif %} + + + + + {% block head %}{% endblock %} + + + + + {% if current_user is defined %} +
+ {{ self.help_block() }} +
+ + {% with messages = get_flashed_messages(with_categories=true) %} + {% if messages %} + {% for category, message in messages %} + {% if category == "error" %} + + {% else %} + + {% endif %} + {% endfor %} + {% endif %} + {% endwith %} + {% endif %} + + {# if default user (normal crispresso mode) #} + {% if current_user == null or not current_user.is_anonymous and current_user.username == "DEFAULTUSER" %} + +
+
+
+ {% if current_user is defined %} +
+ {% else %} +
+ {% endif %} +
+
+

CRISPResso2

+

Analysis of genome editing outcomes from deep sequencing data

+
+
+
+
+ + + {% else %} + {# if doing user sessions #} + +
+ {% endif %} + +
+
+
+
+ {% block help_block %} {% endblock %} +
+
+
+
+ + {% block content %}{% endblock %} + + {% if current_user is defined and (not current_user.is_anonymous and current_user.username == "DEFAULTUSER") %} +
+
+ +
+
+ {% else %} +
+
+ +
+
+ {% endif %} +
+ + + + + + + {% block foot %}{% endblock %} + + + diff --git a/templates/multiReport.html b/templates/multiReport.html new file mode 100644 index 00000000..8e8d83ca --- /dev/null +++ b/templates/multiReport.html @@ -0,0 +1,265 @@ +{% extends "layout.html" %} +{% block head %} + + +{% endblock %} + +{% block content %} +
+
+ +
+
+ + {% if run_names|length > 0 %} +
+
+
{{report_name}}
+
+
+
+ {% for run_name in run_names %} + {{run_name}} + {% endfor %} +
+
+
+ {% endif %} + + {% if window_nuc_pct_quilts|length > 0 %} +
+
+
Nucleotide percentages around guides
+
+
+ {% for plot_name in window_nuc_pct_quilts %} +
{{report_data['titles'][plot_name]}}
+ {{ render_partial('shared/partials/fig_summaries.html', report_data=report_data, plot_name=plot_name) }} + {% endfor %} +
+
+ {% endif %} + + {% if nuc_pct_quilts|length > 0 %} +
+
+
Nucleotide percentages in the entire amplicon
+
+
+ {% for plot_name in nuc_pct_quilts %} +
{{report_data['titles'][plot_name]}}
+ {{ render_partial('shared/partials/fig_summaries.html', report_data=report_data, plot_name=plot_name) }} + {% endfor %} +
+
+ {% endif %} + + {% if window_nuc_conv_plots|length > 0 %} +
+
+
Conversion of target bases around guides
+
+
+ {% for plot_name in window_nuc_conv_plots %} +
{{report_data['titles'][plot_name]}}
+ {{ render_partial('shared/partials/fig_summaries.html', report_data=report_data, plot_name=plot_name) }} + {% endfor %} +
+
+ {% endif %} + + {% if nuc_conv_plots|length > 0 %} +
+
+
Conversion of target bases in the entire amplicon
+
+
+ {% for plot_name in nuc_conv_plots %} +
{{report_data['titles'][plot_name]}}
+ {{ render_partial('shared/partials/fig_summaries.html', report_data=report_data, plot_name=plot_name) }} + {% endfor %} +
+
+ {% endif %} + + {% if report_data['names']|length > 0 %} + {% for plot_name in report_data['names'] %} +
+
+
{{report_data['titles'][plot_name]}}
+
+
+ {{ render_partial('shared/partials/fig_summaries.html', report_data=report_data, plot_name=plot_name) }} +
+
+ {% endfor %} + {% endif %} + + {% if allele_modification_heatmap_plot_names|length > 0 %} + {% for heatmap_plot_name in allele_modification_heatmap_plot_names %} + {% set line_plot_name = allele_modification_line_plot_names[loop.index - 1] %} + {% set modification_type = heatmap_plot_name.split('_')[3] %} +
+
+
{{allele_modification_heatmap_plot_titles[heatmap_plot_name]}}
+ +
+
+
+
+ {{allele_modification_heatmap_plot_htmls[heatmap_plot_name]}} + + {% for (data_label, data_path) in allele_modification_heatmap_plot_datas[heatmap_plot_name] %} +

Data: {{data_label}}

+ {% endfor %} +
+
+ {{allele_modification_line_plot_htmls[line_plot_name]}} + + {% for (data_label, data_path) in allele_modification_line_plot_datas[line_plot_name] %} +

Data: {{data_label}}

+ {% endfor %} +
+
+
+
+ + {% endfor %} + + + + {% endif %} + + {% if compact_plots_to_show|length > 0 %} +
+
+
Summary Plots
+
+
+
+ {% for compact_plot in compact_plots_to_show %} + + {% endfor %} +
+
+
+ {% endif %} + + +
+ +
+ +
{# jumbotron_content #} +
{# jumbrotron #} + +
{# column #} + +
+{% endblock %} + +{% block foot %} +{% endblock %} diff --git a/templates/pooledReport.html b/templates/pooledReport.html new file mode 100644 index 00000000..f4550e82 --- /dev/null +++ b/templates/pooledReport.html @@ -0,0 +1,101 @@ +{% extends "layout.html" %} +{% block head %} + + +{% endblock %} + +{% block content %} +
+
+
+ +
+
+ + {% if run_names|length > 0 %} +
+
+
{{report_name}}
+
+
+
+ {% for region_name in run_names %} + {{region_name}} + {% endfor %} +
+
+
+ {% endif %} + + {% if report_data['names']|length > 0 %} + {% for plot_name in report_data['names'] %} +
+
+
{{report_data['titles'][plot_name]}}
+
+
+ {{ render_partial('shared/partials/fig_summaries.html', report_data=report_data, plot_name=plot_name) }} +
+
+ {% endfor %} + {% endif %} + +
+ Download report + Link to report + +
+ {# data bit for web version: #} + {# +

Data: {{data_label}}

+ #} +
{# jumbotron_content #} +
{# jumbrotron #} + +
{# column #} + +
+
+{% endblock %} + +{% block foot %} +{% endblock %} diff --git a/templates/report.html b/templates/report.html new file mode 100644 index 00000000..fb755d18 --- /dev/null +++ b/templates/report.html @@ -0,0 +1,693 @@ +{% extends "layout.html" %} +{% block head %} + + +{% endblock %} + +{% block content %} +
+
+
+
+
+
+ {% if report_data['report_display_name'] != '' %} +
{{report_data['report_display_name']}}
+ {% endif %} +
CRISPResso2 run information
+
    +
  • + +
    • +
  • + +
    • +
+
+
+
+
+ {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_1a')}} +
+ {{ render_partial('shared/partials/log_params.html', report_data=report_data) }} +
+
+
+ +
+
+
Allele assignments
+
    +
  • + +
    • +
  • + +
    • + {% if report_data['figures']['locs']['plot_1d'] %} +
  • + +
    • + {% endif %} +
+
+
+
+
+ {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_1b')}} +
+
+ {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_1c')}} +
+ {% if report_data['figures']['locs']['plot_1d'] %} +
+ {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_1d')}} +
+ {% endif %} +
+
+
{# end card #} + + {# start global coding sequence report #} + {% if report_data['figures']['locs']['plot_5a'] %} +
+
+
Global frameshift analysis
+
+
+ {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_5a')}} +
+
+ {% endif %} + + {% if report_data['figures']['locs']['plot_6a'] %} +
+
+
Global frameshift mutagenesis profiles
+
+
+ {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_6a')}} +
+
+ {% endif %} + + {% if report_data['figures']['locs']['plot_8a'] %} +
+
+
Global splicing analysis
+
+
+ {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_8a')}} +
+
+ {% endif %} + {# end of global coding sequence analysis #} + + {# start hdr summary #} + {% if report_data['figures']['locs'][report_data.amplicons[0]]['plot_4g'] %} +
+
+ {% if report_data.amplicons|length == 1 %} {# if only one amplicon #} +
HDR summary plot
+ {% else %} +
HDR summary report (all reads aligned to {{report_data.amplicons[0]}})
+ {% endif %} +
+
+ {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_4g', amplicon_name=report_data.amplicons[0])}} +
+
+ {% endif %} + {# end HDR summary #} + + {# start prime editing report #} + {% if report_data['figures']['locs'][report_data.amplicons[0]]['plot_11a'] %} +
+
+ {% if report_data.amplicons|length == 1 %} {# if only one amplicon #} +
Prime editing report
+ {% else %} +
Prime editing report (all reads aligned to {{report_data.amplicons[0]}})
+ {% endif %} +
+
+ {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_11a', amplicon_name=report_data.amplicons[0])}} +
+
+ {% endif %} + + {% if report_data['figures']['sgRNA_based_names'][report_data.amplicons[0]] and report_data['figures']['sgRNA_based_names'][report_data.amplicons[0]]['11b']%} +
+
+ {% if report_data.amplicons|length == 1 %} {# if only one amplicon #} +
Prime editing summary plots at analysis positions
+ {% else %} +
Prime editing summary plots at analysis positions (aligned to {{report_data.amplicons[0]}})
+ {% endif %} +
+
+ {% for fig_name in report_data['figures']['sgRNA_based_names'][report_data.amplicons[0]]['11b'] %} +
+ {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name=fig_name, amplicon_name=report_data.amplicons[0])}} +
+ {% endfor %} +
+
+ {% endif %} + {# end plot 11b for prime editing #} + + {% if report_data['figures']['locs']['plot_11c'] %} +
+
+
Scaffold insertions
+
+
+ {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_11c')}} +
+
+ {% endif %} + {# end prime editing section #} + + {% if report_data.amplicons|length == 1 %} +
{# if only one amplicon, just a normal div #} + {% else %} + {# If there is more than one amplicon, print a navigation to show each amplicon #} +

Reads are aligned to each amplicon sequence separately. Quantification and visualization of these reads are shown for each amplicon below:

+
+
+
Amplicons
+ +
+ {% endif %} {# end if report contains more than one amplicon #} + + + {% if report_data.amplicons|length == 1 %} {# if only one amplicon, just a normal div #} +
+ {% else %} +
+ {% endif %} + + {% for amplicon_name in report_data.amplicons %} + {% if report_data.amplicons|length == 1 %} {# if only one amplicon, just a normal div #} +
+ {% elif loop.index0 == 0 %} {# if more than one amplicon, and the first, this is the active one #} +
+

Reads aligning to {{amplicon_name}}

{# this bit appears in print mode #} + {% else %} {# otherwise inactive tab #} +
+

Reads aligning to {{amplicon_name}}

{# this bit appears in print mode #} + {% endif %} + +
+
+ {% if report_data.amplicons|length == 1 %} {# if only one amplicon #} +
Nucleotide composition
+ {% else %} +
Nucleotide composition for {{amplicon_name}}
+ {% endif %} +
+
+ {% if report_data['figures']['locs'][amplicon_name]['plot_2a'] %} +
+
+
+ +
+
+
+ +
+ +
+ + {% for (data_label,data_path) in report_data['figures']['datas'][amplicon_name]['plot_2a'] %} +

Data: {{data_label}}

+ {% endfor %} + {% endif %} + + {% if report_data['figures']['sgRNA_based_names'][amplicon_name] and report_data['figures']['sgRNA_based_names'][amplicon_name]['2b']%} + {% for fig_name in report_data['figures']['sgRNA_based_names'][amplicon_name]['2b'] %} + {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name=fig_name, amplicon_name=amplicon_name)}} + {% endfor %} + {% endif %} +
+
{# end card #} + +
+
+ {% if report_data.amplicons|length == 1 %} {# if only one amplicon #} +
Modification lengths
+ {% else %} +
Modification lengths for {{amplicon_name}}
+ {% endif %} +
    + {% if report_data['figures']['locs'][amplicon_name]['plot_3a'] %} +
  • + +
    • + {% endif %} + {% if report_data['figures']['locs'][amplicon_name]['plot_3b'] %} +
  • + +
    • + {% endif %} +
+
+
+
+ {% if report_data['figures']['locs'][amplicon_name]['plot_3a'] %} +
+ {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_3a', amplicon_name=amplicon_name)}} +
+ {% endif %} + + {% if report_data['figures']['locs'][amplicon_name]['plot_3b'] %} +
+ {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_3b', amplicon_name=amplicon_name)}} +
+ {% endif %} +
+
{# end card_body #} +
{# end card #} + +
+
+ {% if report_data.amplicons|length == 1 %} {# if only one amplicon #} +
Indel characterization
+ {% else %} +
Indel characterization for {{amplicon_name}}
+ {% endif %} +
    + {% if report_data['figures']['locs'][amplicon_name]['plot_4a'] %} +
  • + +
    • + {% endif %} + {% if report_data['figures']['locs'][amplicon_name]['plot_4b'] %} +
  • + +
    • + {% endif %} + {% if report_data['figures']['locs'][amplicon_name]['plot_4c'] %} +
  • + +
    • + {% endif %} + {% if report_data['figures']['locs'][amplicon_name]['plot_4d'] %} +
  • + +
    • + {% endif %} + {% if report_data['figures']['locs'][amplicon_name]['plot_4e'] %} +
  • + +
    • + {% endif %} + {% if report_data['figures']['locs'][amplicon_name]['plot_4f'] %} +
  • + +
    • + {% endif %} +
+
{# end card head #} +
+
+ {% if report_data['figures']['locs'][amplicon_name]['plot_4a'] %} +
+ {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_4a', amplicon_name=amplicon_name)}} +
+ {% endif %} + {% if report_data['figures']['locs'][amplicon_name]['plot_4b'] %} +
+ {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_4b', amplicon_name=amplicon_name)}} +
+ {% endif %} + {% if report_data['figures']['locs'][amplicon_name]['plot_4c'] %} +
+ {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_4c', amplicon_name=amplicon_name)}} +
+ {% endif %} + + {% if report_data['figures']['locs'][amplicon_name]['plot_4d'] %} +
+ {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_4d', amplicon_name=amplicon_name)}} +
+ {% endif %} + + {% if report_data['figures']['locs'][amplicon_name]['plot_4e'] %} +
+ {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_4e', amplicon_name=amplicon_name)}} +
+ {% endif %} + + {% if report_data['figures']['locs'][amplicon_name]['plot_4f'] %} +
+ {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_4f', amplicon_name=amplicon_name)}} +
+ {% endif %} +
+
{# end card body #} +
{# end card #} + + + {% if report_data['figures']['locs'][amplicon_name]['plot_5'] %} +
+
+ {% if report_data.amplicons|length == 1 %} {# if only one amplicon #} +
Frameshift analysis
+ {% else %} +
Frameshift analysis for {{amplicon_name}}
+ {% endif %} +
+
+ {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_5', amplicon_name=amplicon_name)}} +
+
+ {% endif %} + + {% if report_data['figures']['locs'][amplicon_name]['plot_6'] %} +
+
+ {% if report_data.amplicons|length == 1 %} {# if only one amplicon #} +
Frameshift mutagenesis profiles
+ {% else %} +
Frameshift mutagenesis profiles for {{amplicon_name}}
+ {% endif %} +
+
+ {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_6', amplicon_name=amplicon_name)}} +
+
+ {% endif %} + + {% if report_data['figures']['locs'][amplicon_name]['plot_7'] %} +
+
+ {% if report_data.amplicons|length == 1 %} {# if only one amplicon #} +
Non-coding mutations
+ {% else %} +
Coding mutations for {{amplicon_name}}
+ {% endif %} +
+
+ {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_7', amplicon_name=amplicon_name)}} +
+
+ {% endif %} + + {% if report_data['figures']['locs'][amplicon_name]['plot_8'] %} +
+
+ {% if report_data.amplicons|length == 1 %} {# if only one amplicon #} +
Splicing
+ {% else %} +
Splicing for {{amplicon_name}}
+ {% endif %} +
+
+ {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_8', amplicon_name=amplicon_name)}} +
+
+ {% endif %} + + {% if report_data['figures']['sgRNA_based_names'][amplicon_name] and report_data['figures']['sgRNA_based_names'][amplicon_name]['9']%} +
+
+ {% if report_data.amplicons|length == 1 %} {# if only one amplicon #} +
Allele plots
+ {% else %} +
Allele plots for {{amplicon_name}}
+ {% endif %} +
+
+ {% for fig_name in report_data['figures']['sgRNA_based_names'][amplicon_name]['9'] %} +
+ {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name=fig_name, amplicon_name=amplicon_name)}} +
+ {% endfor %} +
+
+ {% endif %} + + {% if report_data['figures']['locs'][amplicon_name]['plot_10a'] %} +
+
+ {% if report_data.amplicons|length == 1 %} {# if only one amplicon #} +
Base editing
+ {% else %} +
Base editing for {{amplicon_name}}
+ {% endif %} +
    + {% if report_data['figures']['locs'][amplicon_name]['plot_10a'] %} +
  • + +
    • + {% endif %} + {% if report_data['figures']['sgRNA_based_names'][amplicon_name] and report_data['figures']['sgRNA_based_names'][amplicon_name]['10d']%} +
  • + +
    • + {% endif %} + {% if report_data['figures']['sgRNA_based_names'][amplicon_name] and report_data['figures']['sgRNA_based_names'][amplicon_name]['10e']%} +
  • + +
    • + {% endif %} + {% if report_data['figures']['sgRNA_based_names'][amplicon_name] and report_data['figures']['sgRNA_based_names'][amplicon_name]['10f']%} +
  • + +
    • + {% endif %} +
+
+
+
+ {% if report_data['figures']['locs'][amplicon_name]['plot_10c'] %} +
+
+ {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_10a', amplicon_name=amplicon_name)}} +
+
+ + {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_10b', amplicon_name=amplicon_name)}} + {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_10c', amplicon_name=amplicon_name)}} +
+
+ {% else %} +
+
+ {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_10a', amplicon_name=amplicon_name)}} +
+
+ {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_10b', amplicon_name=amplicon_name)}} +
+
+ {% endif %} + {% if report_data['figures']['sgRNA_based_names'][amplicon_name] and report_data['figures']['sgRNA_based_names'][amplicon_name]['10d']%} +
+ {% for fig_name in report_data['figures']['sgRNA_based_names'][amplicon_name]['10d'] %} +
+ {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name=fig_name, amplicon_name=amplicon_name)}} +
+ {% endfor %} +
+ {% endif %} + {% if report_data['figures']['sgRNA_based_names'][amplicon_name] and report_data['figures']['sgRNA_based_names'][amplicon_name]['10e']%} +
+ {% for fig_name in report_data['figures']['sgRNA_based_names'][amplicon_name]['10e'] %} +
+ {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name=fig_name, amplicon_name=amplicon_name)}} +
+ {% endfor %} +
+ {% endif %} + {% if report_data['figures']['sgRNA_based_names'][amplicon_name] and report_data['figures']['sgRNA_based_names'][amplicon_name]['10f']%} +
+ {% for fig_name in report_data['figures']['sgRNA_based_names'][amplicon_name]['10f'] %} +
+ {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_10f', amplicon_name=amplicon_name)}} +
+ {% endfor %} + {% for fig_name in report_data['figures']['sgRNA_based_names'][amplicon_name]['10g'] %} +
+ {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_10g', amplicon_name=amplicon_name)}} +
+ {% endfor %} +
+
+ {% endif %} +
+
{# end card #} + {% endif %} {# end base editing card #} +
{# end this amplicon tab #} + {% endfor %} +
{# tab content #} +
+
{# jumbotron_content #} +
{# jumbrotron #} +
{# column #} +
+ +
+{% endblock %} + +{% block foot %} + +{% endblock %} diff --git a/templates/shared/partials/fig_reports.html b/templates/shared/partials/fig_reports.html new file mode 100644 index 00000000..6f7e448e --- /dev/null +++ b/templates/shared/partials/fig_reports.html @@ -0,0 +1,31 @@ +
+ {% if amplicon_name is defined %} + {% if 'htmls' in report_data['figures'] and fig_name in report_data['figures']['htmls'][amplicon_name] %} + {{report_data['figures']['htmls'][amplicon_name][fig_name]|safe}} + {% else %} + {% if fig_name in ['plot_1a', 'plot_1b', 'plot_1c', 'plot_3a', 'plot_4a', 'plot_4b', 'plot_4c'] %} + + {% else %} + + {% endif %} + {% endif %} + + {% for (data_label,data_path) in report_data['figures']['datas'][amplicon_name][fig_name] %} +

Data: {{data_label}}

+ {% endfor %} + {% else %} + {% if 'htmls' in report_data['figures'] and fig_name in report_data['figures']['htmls'] %} + {{report_data['figures']['htmls'][fig_name]|safe}} + {% else %} + {% if fig_name in ['plot_1a', 'plot_1b', 'plot_1c', 'plot_3a', 'plot_4a', 'plot_4b', 'plot_4c'] %} + + {% else %} + + {% endif %} + {% endif %} + + {% for (data_label,data_path) in report_data['figures']['datas'][fig_name] %} +

Data: {{data_label}}

+ {% endfor %} + {% endif %} +
\ No newline at end of file diff --git a/templates/shared/partials/fig_summaries.html b/templates/shared/partials/fig_summaries.html new file mode 100644 index 00000000..e4e3297a --- /dev/null +++ b/templates/shared/partials/fig_summaries.html @@ -0,0 +1,11 @@ +
+ {% if report_data['htmls'][plot_name] %} + {{report_data['htmls'][plot_name]|safe}} + {% else %} + + {% endif %} + + {% for (data_label,data_path) in report_data['datas'][plot_name] %} +

Data: {{data_label}}

+ {% endfor %} +
diff --git a/templates/shared/partials/log_params.html b/templates/shared/partials/log_params.html new file mode 100644 index 00000000..ad035ae3 --- /dev/null +++ b/templates/shared/partials/log_params.html @@ -0,0 +1,11 @@ +
+

CRISPResso version: {{report_data['run_data']['running_info']['version']}}

+

Run completed: {{report_data['run_data']['running_info']['end_time_string']}}

+

Amplicon sequence: 

{{report_data['run_data']['running_info']['args']['amplicon_seq']}}

+ {% if report_data['run_data']['running_info']['args']['guide_seq'] != '' %} +

Guide sequence: 

{{report_data['run_data']['running_info']['args']['guide_seq']}}

+ {% endif %} +

Command used: 

{{report_data['run_data']['running_info']['command_used']}}

+

Parameters: 

{{report_data['run_data']['running_info']['args_string']}}

+

Running log

+
diff --git a/templates/wgsReport.html b/templates/wgsReport.html new file mode 100644 index 00000000..0a5a1277 --- /dev/null +++ b/templates/wgsReport.html @@ -0,0 +1,99 @@ +{% extends "layout.html" %} +{% block head %} + + +{% endblock %} + +{% block content %} +
+
+
+ +
+
+ +
+
+
{{report_name}}
+
+
+
+ {% for region_name in run_names %} + {{region_name}} + {% endfor %} +
+
+
+ + {% if report_data['names']|length > 0 %} + {% for plot_name in report_data['names'] %} +
+
+
{{report_data['titles'][plot_name]}}
+
+
+ {{ render_partial('shared/partials/fig_summaries.html', report_data=report_data, plot_name=plot_name) }} +
+
+ {% endfor %} + {% endif %} + +
+ Download report + Link to report + +
+ {# data bit for web version: #} + {# +

Data: {{data_label}}

+ #} +
{# jumbotron_content #} +
{# jumbrotron #} + +
{# column #} + +
+
+{% endblock %} + +{% block foot %} +{% endblock %} From 321815d0c3599408afb6b1506f793275ff673f42 Mon Sep 17 00:00:00 2001 From: Samuel Nichols Date: Tue, 13 Sep 2022 11:01:52 -0600 Subject: [PATCH 17/33] Removing CRISPRessoReport files --- CRISPRessoReport.py | 690 ------------------ templates/CRISPResso_justcup.png | Bin 42782 -> 0 bytes templates/batchReport.html | 163 ----- templates/favicon.ico | Bin 1150 -> 0 bytes templates/layout.html | 237 ------- templates/multiReport.html | 265 ------- templates/pooledReport.html | 101 --- templates/report.html | 693 ------------------- templates/shared/partials/fig_reports.html | 31 - templates/shared/partials/fig_summaries.html | 11 - templates/shared/partials/log_params.html | 11 - templates/wgsReport.html | 99 --- 12 files changed, 2301 deletions(-) delete mode 100644 CRISPRessoReport.py delete mode 100644 templates/CRISPResso_justcup.png delete mode 100644 templates/batchReport.html delete mode 100644 templates/favicon.ico delete mode 100644 templates/layout.html delete mode 100644 templates/multiReport.html delete mode 100644 templates/pooledReport.html delete mode 100644 templates/report.html delete mode 100644 templates/shared/partials/fig_reports.html delete mode 100644 templates/shared/partials/fig_summaries.html delete mode 100644 templates/shared/partials/log_params.html delete mode 100644 templates/wgsReport.html diff --git a/CRISPRessoReport.py b/CRISPRessoReport.py deleted file mode 100644 index 58cf42ac..00000000 --- a/CRISPRessoReport.py +++ /dev/null @@ -1,690 +0,0 @@ -''' -CRISPResso2 - Kendell Clement and Luca Pinello 2018 -Software pipeline for the analysis of genome editing outcomes from deep sequencing data -(c) 2020 The General Hospital Corporation. All Rights Reserved. -''' - -import os -from jinja2 import Environment, FileSystemLoader -from jinja_partials import generate_render_partial, render_partial -from CRISPResso2 import CRISPRessoShared - - -def render_template(template_name, jinja2_env, **data): - """Render a template with partials. - - Parameters - ---------- - template_name: str - The name of the template to render. For example, if you have a template - file called `templates/my_template.html` you would pass in - `my_template.html`. - jinja2_env: jinja2.Environment - The Jinja2 environment being used. - **data: keyword arguments of any type - Additional keyword arguments that are passed to the template. - - Returns - ------- - The rendered template. - """ - def custom_partial_render(partial_template_name, **partial_data): - template = jinja2_env.get_template(partial_template_name) - partial_data.update( - render_partial=generate_render_partial( - custom_partial_render, - ), - ) - return template.render(**partial_data) - return render_partial( - template_name, custom_partial_render, **data, - ) - - -def make_report_from_folder(crispresso_report_file, crispresso_folder, _ROOT): - """ - Makes an html report for a crispresso run - - Parameters: - crispresso_report_file (string): name of the html file to create - crispresso_folder (string): path to the crispresso output - _ROOT (string): path to crispresso executables (for templates) - - Returns: - Nothin - """ - run_data = CRISPRessoShared.load_crispresso_info(crispresso_folder) - make_report(run_data, crispresso_report_file, crispresso_folder, _ROOT) - - -def add_fig_if_exists(fig_name, fig_root, fig_title, fig_caption, fig_data, - amplicon_fig_names, amplicon_figures, crispresso_folder): - """ - Helper function to add figure if the file exists - if fig at filename exists, - amplicon_figs[figname] is set to that file - """ - # fullpath=os.path.join(crispresso_folder,fig_root+'.png') - pngfullpath = os.path.join(crispresso_folder, fig_root + '.png') - htmlfullpath = os.path.join(crispresso_folder, fig_root + '.html') - # print('adding file ' + fig_root + ' at ' + fullpath) - if os.path.exists(pngfullpath) or os.path.exists(htmlfullpath): - amplicon_fig_names.append(fig_name) - # amplicon_fig_locs[fig_name]=os.path.basename(fig_root+'.png') - amplicon_figures['locs'][fig_name] = os.path.basename(fig_root) - amplicon_figures['titles'][fig_name] = fig_title - amplicon_figures['captions'][fig_name] = fig_caption - amplicon_figures['datas'][fig_name] = [] - for (data_caption, data_file) in fig_data: - if os.path.exists(os.path.join(crispresso_folder, data_file)): - amplicon_figures['datas'][fig_name].append((data_caption, data_file)) - if os.path.exists(htmlfullpath): - with open(htmlfullpath) as html: - html_string = "
" - html_string += html.read() - html_string += "
" - amplicon_figures['htmls'][fig_name] = html_string - - -def assemble_figs(run_data, crispresso_folder): - figures = {'names': {}, 'locs': {}, 'titles': {}, 'captions': {}, 'datas': {}, 'htmls': {}, 'sgRNA_based_names': {}} - - global_fig_names = [] - for fig in ['1a', '1b', '1c', '1d', '5a', '6a', '8a', '11c']: - fig_name = 'plot_' + fig - if fig_name + '_root' in run_data['results']['general_plots']: - add_fig_if_exists(fig_name, run_data['results']['general_plots'][fig_name + '_root'], 'Figure ' + fig, - run_data['results']['general_plots'][fig_name + '_caption'], - run_data['results']['general_plots'][fig_name + '_data'], - global_fig_names, figures, crispresso_folder) - - amplicons = [] - for amplicon_name in run_data['results']['ref_names']: - amplicons.append(amplicon_name) - amplicon_figures = {'names': [], 'locs': {}, 'titles': {}, 'captions': {}, 'datas': {}, 'htmls': {}} - - for fig in ['2a', '3a', '3b', '4a', '4b', '4c', '4d', '4e', '4f', '4g', '5', '6', '7', '8', '10a', '10b', '10c', - '11a']: - fig_name = 'plot_' + fig - if fig_name + '_root' in run_data['results']['refs'][amplicon_name]: - add_fig_if_exists(fig_name, run_data['results']['refs'][amplicon_name][fig_name + '_root'], - 'Figure ' + fig_name, - run_data['results']['refs'][amplicon_name][fig_name + '_caption'], - run_data['results']['refs'][amplicon_name][fig_name + '_data'], - global_fig_names, amplicon_figures, crispresso_folder) - - this_sgRNA_based_fig_names = {} - for fig in ['2b', '9', '10d', '10e', '10f', '10g', '11b']: - # fig 2b's - this_fig_names = [] - if 'plot_' + fig + '_roots' in run_data['results']['refs'][amplicon_name]: - for idx, plot_root in enumerate(run_data['results']['refs'][amplicon_name]['plot_' + fig + '_roots']): - fig_name = "plot_" + fig + "_" + str(idx) - add_fig_if_exists(fig_name, plot_root, 'Figure ' + fig_name + ' sgRNA ' + str(idx + 1), - run_data['results']['refs'][amplicon_name]['plot_' + fig + '_captions'][idx], - run_data['results']['refs'][amplicon_name]['plot_' + fig + '_datas'][idx], - this_fig_names, amplicon_figures, crispresso_folder) - this_sgRNA_based_fig_names[fig] = this_fig_names - - figures['names'][amplicon_name] = amplicon_figures['names'] - figures['sgRNA_based_names'][amplicon_name] = this_sgRNA_based_fig_names - - figures['locs'][amplicon_name] = amplicon_figures['locs'] - figures['titles'][amplicon_name] = amplicon_figures['titles'] - figures['captions'][amplicon_name] = amplicon_figures['captions'] - figures['datas'][amplicon_name] = amplicon_figures['datas'] - figures['htmls'][amplicon_name] = amplicon_figures['htmls'] - data = {'amplicons': amplicons, 'figures': figures} - return data - - -def make_report(run_data, crispresso_report_file, crispresso_folder, _ROOT, web_version=False): - # dicts for each amplicon fig_names[amp_name] = [list of fig names] - # fig_locs[amp_name][fig_name] = figure location - # print('crispresso_report file: ' + crispresso_report_file + ' crispresso_folder : ' + crispresso_folder + ' root: ' + _ROOT) - data = assemble_figs(run_data, crispresso_folder) - - report_display_name = "" - if run_data['running_info']['args'].name != "": - report_display_name = run_data['running_info']['args'].name - - # find path between the report and the data (if the report is in another directory vs in the same directory as the data) - crispresso_data_path = os.path.relpath(crispresso_folder, os.path.dirname(crispresso_report_file)) - if crispresso_data_path == ".": - crispresso_data_path = "" - else: - crispresso_data_path += "/" - - report_data = { - 'amplicons': data['amplicons'], - 'figures': data['figures'], - 'run_data': run_data, - 'report_display_name': report_display_name, - 'crispresso_data_path': crispresso_data_path, - } - - j2_env = Environment(loader=FileSystemLoader(os.path.join(_ROOT, 'CRISPRessoReports', 'templates'))) - - # dest_dir = os.path.dirname(crispresso_report_file) - # shutil.copy2(os.path.join(_ROOT,'templates','CRISPResso_justcup.png'),dest_dir) - # shutil.copy2(os.path.join(_ROOT,'templates','favicon.ico'),dest_dir) - - with open(crispresso_report_file, 'w') as outfile: - outfile.write(render_template( - 'report.html', j2_env, report_data=report_data, - )) - - -def make_batch_report_from_folder(crispressoBatch_report_file, crispresso2_info, batch_folder, _ROOT): - batch_names = crispresso2_info['results']['completed_batch_arr'] - display_names = crispresso2_info['results']['batch_input_names'] - - window_nuc_pct_quilts = crispresso2_info['results']['general_plots']['window_nuc_pct_quilt_plot_names'] - nuc_pct_quilts = crispresso2_info['results']['general_plots']['nuc_pct_quilt_plot_names'] - - window_nuc_conv_plots = crispresso2_info['results']['general_plots']['window_nuc_conv_plot_names'] - nuc_conv_plots = crispresso2_info['results']['general_plots']['nuc_conv_plot_names'] - - summary_plot_names = [] - if 'summary_plot_names' in crispresso2_info['results']['general_plots']: - summary_plot_names = crispresso2_info['results']['general_plots']['summary_plot_names'] - summary_plot_titles = {} - if 'summary_plot_titles' in crispresso2_info['results']['general_plots']: - summary_plot_titles = crispresso2_info['results']['general_plots']['summary_plot_titles'] - summary_plot_labels = {} - if 'summary_plot_labels' in crispresso2_info['results']['general_plots']: - summary_plot_labels = crispresso2_info['results']['general_plots']['summary_plot_labels'] - summary_plot_datas = {} - if 'summary_plot_datas' in crispresso2_info['results']['general_plots']: - summary_plot_datas = crispresso2_info['results']['general_plots']['summary_plot_datas'] - - allele_modification_heatmap_plot = {} - if 'allele_modification_heatmap_plot_names' in crispresso2_info['results']['general_plots']: - allele_modification_heatmap_plot['names'] = crispresso2_info['results']['general_plots']['allele_modification_heatmap_plot_names'] - else: - allele_modification_heatmap_plot['names'] = [] - if 'allele_modification_heatmap_plot_paths' in crispresso2_info['results']['general_plots']: - allele_modification_heatmap_plot['paths'] = crispresso2_info['results']['general_plots']['allele_modification_heatmap_plot_paths'] - else: - allele_modification_heatmap_plot['paths'] = {} - if 'allele_modification_heatmap_plot_titles' in crispresso2_info['results']['general_plots']: - allele_modification_heatmap_plot['titles'] = crispresso2_info['results']['general_plots']['allele_modification_heatmap_plot_titles'] - else: - allele_modification_heatmap_plot['titles'] = [] - if 'allele_modification_heatmap_plot_labels' in crispresso2_info['results']['general_plots']: - allele_modification_heatmap_plot['labels'] = crispresso2_info['results']['general_plots']['allele_modification_heatmap_plot_labels'] - else: - allele_modification_heatmap_plot['labels'] = {} - if 'allele_modification_heatmap_plot_datas' in crispresso2_info['results']['general_plots']: - allele_modification_heatmap_plot['datas'] = crispresso2_info['results']['general_plots']['allele_modification_heatmap_plot_datas'] - else: - allele_modification_heatmap_plot['datas'] = {} - - allele_modification_line_plot = {} - if 'allele_modification_line_plot_names' in crispresso2_info['results']['general_plots']: - allele_modification_line_plot['names'] = crispresso2_info['results']['general_plots']['allele_modification_line_plot_names'] - else: - allele_modification_line_plot['names'] = [] - if 'allele_modification_line_plot_paths' in crispresso2_info['results']['general_plots']: - allele_modification_line_plot['paths'] = crispresso2_info['results']['general_plots']['allele_modification_line_plot_paths'] - else: - allele_modification_line_plot['paths'] = {} - if 'allele_modification_line_plot_titles' in crispresso2_info['results']['general_plots']: - allele_modification_line_plot['titles'] = crispresso2_info['results']['general_plots']['allele_modification_line_plot_titles'] - else: - allele_modification_line_plot['titles'] = [] - if 'allele_modification_line_plot_labels' in crispresso2_info['results']['general_plots']: - allele_modification_line_plot['labels'] = crispresso2_info['results']['general_plots']['allele_modification_line_plot_labels'] - else: - allele_modification_line_plot['labels'] = {} - if 'allele_modification_line_plot_datas' in crispresso2_info['results']['general_plots']: - allele_modification_line_plot['datas'] = crispresso2_info['results']['general_plots']['allele_modification_line_plot_datas'] - else: - allele_modification_line_plot['datas'] = {} - - allele_modification_heatmap_plot['htmls'] = {} - for heatmap_plot_name, heatmap_plot_path in allele_modification_heatmap_plot['paths'].items(): - with open(heatmap_plot_path) as fh: - allele_modification_heatmap_plot['htmls'][heatmap_plot_name] = fh.read() - - allele_modification_line_plot['htmls'] = {} - for line_plot_name, line_plot_path in allele_modification_line_plot['paths'].items(): - with open(line_plot_path) as fh: - allele_modification_line_plot['htmls'][line_plot_name] = fh.read() - - #find path between the report and the data (if the report is in another directory vs in the same directory as the data) - crispresso_data_path = os.path.relpath(batch_folder, os.path.dirname(crispressoBatch_report_file)) - if crispresso_data_path == ".": - crispresso_data_path = "" - else: - crispresso_data_path += "/"; - - sub_html_files = {} - run_names = [] - for name in batch_names: - display_name = display_names[name] - sub_folder = 'CRISPResso_on_' + name - crispresso_folder = os.path.join(batch_folder, sub_folder) - run_data = CRISPRessoShared.load_crispresso_info(crispresso_folder) - if 'running_info' not in run_data: - raise Exception('CRISPResso run %s has no report. Cannot add to batch report.' % sub_folder) - - this_sub_html_file = sub_folder + ".html" - if run_data['running_info']['args'].place_report_in_output_folder: - this_sub_html_file = os.path.join(sub_folder, run_data['running_info']['report_filename']) - sub_html_files[display_name] = this_sub_html_file - - run_names.append(display_name) - - output_title = 'CRISPResso Batch Output' - if crispresso2_info['running_info']['args'].name != '': - output_title += '
{0}'.format(crispresso2_info['running_info']['args'].name) - - make_multi_report( - run_names, - sub_html_files, - crispressoBatch_report_file, - batch_folder, - _ROOT, - output_title, - 'batch', - summary_plots={ - 'names': summary_plot_names, - 'titles': summary_plot_titles, - 'labels': summary_plot_labels, - 'datas': summary_plot_datas, - }, - window_nuc_pct_quilts=window_nuc_pct_quilts, - nuc_pct_quilts=nuc_pct_quilts, - window_nuc_conv_plots=window_nuc_conv_plots, - nuc_conv_plots=nuc_conv_plots, - allele_modification_heatmap_plot=allele_modification_heatmap_plot, - allele_modification_line_plot=allele_modification_line_plot, - ) - - -def make_pooled_report_from_folder(crispresso_report_file, crispresso2_info, folder, _ROOT): - names_arr = crispresso2_info['results']['good_region_names'] - output_title = 'CRISPResso Pooled Output' - if crispresso2_info['running_info']['args'].name != '': - output_title += '
{0}'.format(crispresso2_info['running_info']['args'].name) - make_multi_report_from_folder(crispresso2_info, names_arr, output_title, crispresso_report_file, folder, _ROOT, 'pooled') - - -def make_compare_report_from_folder(crispresso_report_file, crispresso2_info, folder, _ROOT): - names_arr = [] - output_title = 'CRISPResso Compare Output' - if crispresso2_info['running_info']['args'].name != '': - output_title += '
{0}'.format(crispresso2_info['running_info']['args'].name) - make_multi_report_from_folder(crispresso2_info, names_arr, output_title, crispresso_report_file, folder, _ROOT, 'compare') - - -def make_meta_report_from_folder(crispresso_report_file, crispresso2_info, folder, _ROOT): - names_arr = crispresso2_info['meta_names_arr'] - input_names = crispresso2_info['meta_input_names'] - output_title = 'CRISPresso Meta Output' - if crispresso2_info['running_info']['args'].name != '': - output_title += '
{0}'.format(crispresso2_info['running_info']['args'].name) - make_multi_report_from_folder(crispresso2_info, names_arr, output_title, crispresso_report_file, folder, _ROOT, 'meta', - display_names=input_names) - - -def make_wgs_report_from_folder(crispresso_report_file, crispresso2_info, folder, _ROOT): - names_arr = crispresso2_info['results']['good_region_names'] - output_title = 'CRISPResso WGS Output' - if crispresso2_info['running_info']['args'].name != '': - output_title += '
{0}'.format(crispresso2_info['running_info']['args'].name) - make_multi_report_from_folder(crispresso2_info, names_arr, output_title, crispresso_report_file, folder, _ROOT, 'wgs') - - -def make_multi_report_from_folder(crispresso2_info, names_arr, report_name, crispresso_report_file, folder, _ROOT, crispresso_tool, - display_names=None): - """ - Prepares information to make a report of multiple CRISPResso runs - like CRISPRessoWGS or CRISPRessoPooled - - Parameters: - crispresso2_info (dict): information from the crispresso multi run - names_arr (arr of strings): Names of the crispresso runs - report_name (string): text to be shown at top of report - crispresso_report_file (string): path to write report to - folder (string): folder containing crispresso runs - _ROOT (string): location of crispresso assets (images, templates, etc) - display_names (dict): report_name->display_name; Titles to be shown for crispresso runs (if different from names_arr, e.g. if display_names have spaces or bad chars, they won't be the same as names_arr) - - Returns: - Nothin - """ - - summary_plot_names = [] - if 'summary_plot_names' in crispresso2_info['results']['general_plots']: - summary_plot_names = crispresso2_info['results']['general_plots']['summary_plot_names'] - summary_plot_titles = {} - if 'summary_plot_titles' in crispresso2_info['results']['general_plots']: - summary_plot_titles = crispresso2_info['results']['general_plots']['summary_plot_titles'] - summary_plot_labels = {} - if 'summary_plot_labels' in crispresso2_info['results']['general_plots']: - summary_plot_labels = crispresso2_info['results']['general_plots']['summary_plot_labels'] - summary_plot_datas = {} - if 'summary_plot_datas' in crispresso2_info['results']['general_plots']: - summary_plot_datas = crispresso2_info['results']['general_plots']['summary_plot_datas'] - - run_names = [] - sub_html_files = {} - sub_2a_labels = {} - sub_2a_pdfs = {} - - for name in names_arr: - display_name = name - if display_names is not None: - display_name = display_names[name] - - folder_name = 'CRISPResso_on_%s' % name - sub_folder = os.path.join(folder, folder_name) - run_data = CRISPRessoShared.load_crispresso_info(sub_folder) - if 'running_info' not in run_data: - raise Exception('CRISPResso run %s has no report. Cannot add to report.' % sub_folder) - - run_names.append(display_name) - - this_sub_html_file = os.path.basename(folder_name) + ".html" - if run_data['running_info']['args'].place_report_in_output_folder: - this_sub_html_file = os.path.join(os.path.basename(sub_folder), run_data['running_info']['report_filename']) - sub_html_files[display_name] = this_sub_html_file - - this_sub_2a_labels = [] - this_sub_2a_pdfs = [] - for ref_name in run_data['results']['ref_names']: - if 'plot_2a_root' in run_data['results']['refs'][ref_name]: - pdf_file = run_data['results']['refs'][ref_name]['plot_2a_root'] + ".pdf" - if os.path.exists(pdf_file): - this_sub_2a_pdfs.append(run_data['results']['refs'][ref_name]['plot_2a_root'] + ".pdf") - this_sub_2a_labels.append("Nucleotide distribution across " + ref_name) - - sub_2a_labels[display_name] = this_sub_2a_labels - sub_2a_pdfs[display_name] = this_sub_2a_pdfs - - make_multi_report( - run_names, - sub_html_files, - crispresso_report_file, - folder, - _ROOT, - report_name, - crispresso_tool, - summary_plots={ - 'names': summary_plot_names, - 'titles': summary_plot_titles, - 'labels': summary_plot_labels, - 'datas': summary_plot_datas, - }, - ) - - -def make_multi_report( - run_names, - sub_html_files, - crispresso_multi_report_file, - crispresso_folder, - _ROOT, - report_name, - crispresso_tool, - window_nuc_pct_quilts=[], - nuc_pct_quilts=[], - window_nuc_conv_plots=[], - nuc_conv_plots=[], - summary_plots={ - 'names': [], - 'titles': [], - 'labels': [], - 'datas': [], - }, - compact_plots_to_show={}, - allele_modification_heatmap_plot={}, - allele_modification_line_plot={}, -): - """ - Makes an HTML report for a run containing multiple crispresso runs - - Parameters: - run_names (arr of strings): names of runs - sub_html_files (dict): dict of run_name->file_loc - crispresso_multi_report_file (string): path of file to write to - report_name (string): description of report type to be shown at top of report - crispresso_folder (string): absolute path to the crispresso output - _ROOT (string): absolute path to the crispresso executable - summary_plots (dict): a dict with the following keys: - names (list): list of plot names - keys for following dicts - titles (dict): dict of plot_name->plot_title - labels (dict): dict of plot_name->plot_label - datas (dict): dict of plot_name->[(datafile_description, data_filename), ...] - compact_plots_to_show (dict): name=>{'href': path to target(report) when user clicks on image, 'img': path to png image to show} - allele_modification_heatmap_plot (dict): a dict with the following keys: - names (list): list of plot names for heatmaps, keys for dicts below - htmls (dict): dict of plot_name->HTML for the plot - titles (dict): dict of plot_name->plot_title - labels (dict): dict of plot_name->plot_label - datas (dict): dict of plot_name->[(datafile_description, data_filename), ...] - """ - - def dirname(path): - return os.path.basename(os.path.dirname(path)) - - def fill_default(dictionary, key, default_type=list): - if key not in dictionary: - dictionary[key] = default_type() - - j2_env = Environment( - loader=FileSystemLoader(os.path.join(_ROOT, 'CRISPRessoReports', 'templates')), - ) - j2_env.filters['dirname'] = dirname - if crispresso_tool == 'batch': - template = 'batchReport.html' - elif crispresso_tool == 'pooled': - template = 'pooledReport.html' - elif crispresso_tool == 'wgs': - template = 'wgsReport.html' - else: - template = 'multiReport.html' - - crispresso_data_path = os.path.relpath( - crispresso_folder, os.path.dirname(crispresso_multi_report_file), - ) - if crispresso_data_path == ".": - crispresso_data_path = "" - else: - crispresso_data_path += "/" - - dictionaries = [ - allele_modification_heatmap_plot, allele_modification_line_plot, - ] - keys_and_default_types = [ - ('names', list), - ('htmls', dict), - ('titles', list), - ('labels', dict), - ('datas', dict), - ] - for dictionary in dictionaries: - for key, default_type in keys_and_default_types: - fill_default( - dictionary, - key, - default_type, - ) - web = False - if not web: - for html in sub_html_files: - sub_html_files[html] = crispresso_data_path + sub_html_files[html] - with open(crispresso_multi_report_file, 'w') as outfile: - outfile.write(render_template( - template, - j2_env, - window_nuc_pct_quilts=window_nuc_pct_quilts, - nuc_pct_quilts=nuc_pct_quilts, - window_nuc_conv_plots=window_nuc_conv_plots, - nuc_conv_plots=nuc_conv_plots, - crispresso_data_path=crispresso_data_path, - report_data={ - 'names': summary_plots['names'], - 'titles': summary_plots['titles'], - 'labels': summary_plots['labels'], - 'datas': summary_plots['datas'], - 'htmls': [], - 'crispresso_data_path': crispresso_data_path, - }, - run_names=run_names, - sub_html_files=sub_html_files, - report_name=report_name, - compact_plots_to_show=compact_plots_to_show, - allele_modification_heatmap_plot_names=allele_modification_heatmap_plot['names'], - allele_modification_heatmap_plot_htmls=allele_modification_heatmap_plot['htmls'], - allele_modification_heatmap_plot_titles=allele_modification_heatmap_plot['titles'], - allele_modification_heatmap_plot_labels=allele_modification_heatmap_plot['labels'], - allele_modification_heatmap_plot_datas=allele_modification_heatmap_plot['datas'], - allele_modification_line_plot_names=allele_modification_line_plot['names'], - allele_modification_line_plot_htmls=allele_modification_line_plot['htmls'], - allele_modification_line_plot_titles=allele_modification_line_plot['titles'], - allele_modification_line_plot_labels=allele_modification_line_plot['labels'], - allele_modification_line_plot_datas=allele_modification_line_plot['datas'], - )) - - -def make_aggregate_report( - crispresso2_info, - report_name, - crispresso_report_file, - crispresso_report_folder, - _ROOT, - folder_arr, - crispresso_html_reports, - compact_plots_to_show={}, - display_names=None, -): - """ - Prepares information to make a report of a CRISPRessoAggregate run - - Parameters: - crispresso2_info (dict): information from the crispresso aggregate run - report_name (string): text to be shown at top of report - crispresso_report_file (string): path to write report to - crispresso_report_folder (string): path containing aggregated plots, etc. - _ROOT (string): location of crispresso assets (images, templates, etc) - folder_arr (arr of strings): paths to the aggregated crispresso folders - crispresso_html_reports (dict): folder->html_path; Paths to the aggregated crispresso run html reports - compact_plots_to_show (dict): name=>{'href': path to target(report) when user clicks on image, 'img': path to png image to show} - display_names (dict): folder->display_name; Titles to be shown for crispresso runs (if different from names_arr, e.g. if display_names have spaces or bad chars, they won't be the same as names_arr) - - Returns: - Nothin - """ - summary_plots = {} - if 'summary_plot_names' in crispresso2_info['results']['general_plots']: - summary_plots['names'] = crispresso2_info['results']['general_plots']['summary_plot_names'] - else: - summary_plots['names'] = [] - if 'summary_plot_titles' in crispresso2_info['results']['general_plots']: - summary_plots['titles'] = crispresso2_info['results']['general_plots']['summary_plot_titles'] - else: - summary_plots['titles'] = {} - if 'summary_plot_labels' in crispresso2_info['results']['general_plots']: - summary_plots['labels'] = crispresso2_info['results']['general_plots']['summary_plot_labels'] - else: - summary_plots['labels'] = {} - if 'summary_plot_datas' in crispresso2_info['results']['general_plots']: - summary_plots['datas'] = crispresso2_info['results']['general_plots']['summary_plot_datas'] - else: - summary_plots['datas'] = {} - - allele_modification_heatmap_plot = {} - if 'allele_modification_heatmap_plot_names' in crispresso2_info['results']['general_plots']: - allele_modification_heatmap_plot['names'] = crispresso2_info['results']['general_plots']['allele_modification_heatmap_plot_names'] - else: - allele_modification_heatmap_plot['names'] = [] - if 'allele_modification_heatmap_plot_paths' in crispresso2_info['results']['general_plots']: - allele_modification_heatmap_plot['paths'] = crispresso2_info['results']['general_plots']['allele_modification_heatmap_plot_paths'] - else: - allele_modification_heatmap_plot['paths'] = {} - if 'allele_modification_heatmap_plot_titles' in crispresso2_info['results']['general_plots']: - allele_modification_heatmap_plot['titles'] = crispresso2_info['results']['general_plots']['allele_modification_heatmap_plot_titles'] - else: - allele_modification_heatmap_plot['titles'] = {} - if 'allele_modification_heatmap_plot_labels' in crispresso2_info['results']['general_plots']: - allele_modification_heatmap_plot['labels'] = crispresso2_info['results']['general_plots']['allele_modification_heatmap_plot_labels'] - else: - allele_modification_heatmap_plot['labels'] = {} - if 'allele_modification_heatmap_plot_datas' in crispresso2_info['results']['general_plots']: - allele_modification_heatmap_plot['datas'] = crispresso2_info['results']['general_plots']['allele_modification_heatmap_plot_datas'] - else: - allele_modification_heatmap_plot['datas'] = {} - - allele_modification_line_plot = {} - if 'allele_modification_line_plot_names' in crispresso2_info['results']['general_plots']: - allele_modification_line_plot['names'] = crispresso2_info['results']['general_plots']['allele_modification_line_plot_names'] - else: - allele_modification_line_plot['names'] = [] - if 'allele_modification_line_plot_paths' in crispresso2_info['results']['general_plots']: - allele_modification_line_plot['paths'] = crispresso2_info['results']['general_plots']['allele_modification_line_plot_paths'] - else: - allele_modification_line_plot['paths'] = {} - if 'allele_modification_line_plot_titles' in crispresso2_info['results']['general_plots']: - allele_modification_line_plot['titles'] = crispresso2_info['results']['general_plots']['allele_modification_line_plot_titles'] - else: - allele_modification_line_plot['titles'] = {} - if 'allele_modification_line_plot_labels' in crispresso2_info['results']['general_plots']: - allele_modification_line_plot['labels'] = crispresso2_info['results']['general_plots']['allele_modification_line_plot_labels'] - else: - allele_modification_line_plot['labels'] = {} - if 'allele_modification_line_plot_datas' in crispresso2_info['results']['general_plots']: - allele_modification_line_plot['datas'] = crispresso2_info['results']['general_plots']['allele_modification_line_plot_datas'] - else: - allele_modification_line_plot['datas'] = {} - - window_nuc_pct_quilts = [] - if 'window_nuc_pct_quilt_plot_names' in crispresso2_info['results']['general_plots']: - window_nuc_pct_quilts = crispresso2_info['results']['general_plots']['window_nuc_pct_quilt_plot_names'] - nuc_pct_quilts = [] - if 'nuc_pct_quilt_plot_names' in crispresso2_info['results']['general_plots']: - nuc_pct_quilts = crispresso2_info['results']['general_plots']['nuc_pct_quilt_plot_names'] - - run_names = [] - sub_html_files = {} - - for idx, folder in enumerate(folder_arr): - display_name = folder - if display_names is not None: - display_name = display_names[folder] - - run_names.append(display_name) - sub_html_file = os.path.relpath(crispresso_html_reports[folder], crispresso_report_folder) - sub_html_files[display_name] = sub_html_file - - for compact_plot in compact_plots_to_show: - old_href = compact_plots_to_show[compact_plot]['href'] - compact_plots_to_show[compact_plot]['href'] = os.path.relpath(old_href, crispresso_report_folder) - old_img = compact_plots_to_show[compact_plot]['img'] - compact_plots_to_show[compact_plot]['img'] = os.path.relpath(old_img, crispresso_report_folder) - - allele_modification_heatmap_plot['htmls'] = {} - for heatmap_plot_name, heatmap_plot_path in allele_modification_heatmap_plot['paths'].items(): - with open(heatmap_plot_path) as fh: - allele_modification_heatmap_plot['htmls'][heatmap_plot_name] = fh.read() - - allele_modification_line_plot['htmls'] = {} - for line_plot_name, line_plot_path in allele_modification_line_plot['paths'].items(): - with open(line_plot_path) as fh: - allele_modification_line_plot['htmls'][line_plot_name] = fh.read() - - make_multi_report( - run_names, - sub_html_files, - crispresso_report_file, - crispresso_report_folder, - _ROOT, - report_name, - window_nuc_pct_quilts=window_nuc_pct_quilts, - nuc_pct_quilts=nuc_pct_quilts, - summary_plots=summary_plots, - compact_plots_to_show=compact_plots_to_show, - allele_modification_heatmap_plot=allele_modification_heatmap_plot, - allele_modification_line_plot=allele_modification_line_plot, - ) diff --git a/templates/CRISPResso_justcup.png 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-
-
- -
-
- - {% if run_names|length > 0 %} -
-
-
{{report_name}}
-
-
-
- {% for run_name in run_names %} - {{run_name}} - {% endfor %} -
-
-
- {% endif %} - - {% if window_nuc_pct_quilts|length > 0 %} -
-
-
Nucleotide percentages around guides
-
-
- {% for plot_name in window_nuc_pct_quilts %} -
{{report_data['titles'][plot_name]}}
- {{ render_partial('shared/partials/fig_summaries.html', report_data=report_data, plot_name=plot_name) }} - {% endfor %} -
-
- {% endif %} - - {% if nuc_pct_quilts|length > 0 %} -
-
-
Nucleotide percentages in the entire amplicon
-
-
- {% for plot_name in nuc_pct_quilts %} -
{{report_data['titles'][plot_name]}}
- {{ render_partial('shared/partials/fig_summaries.html', report_data=report_data, plot_name=plot_name) }} - {% endfor %} -
-
- {% endif %} - - {% if window_nuc_conv_plots|length > 0 %} -
-
-
Conversion of target bases around guides
-
-
- {% for plot_name in window_nuc_conv_plots %} -
{{report_data['titles'][plot_name]}}
- {{ render_partial('shared/partials/fig_summaries.html', report_data=report_data, plot_name=plot_name) }} - {% endfor %} -
-
- {% endif %} - - {% if nuc_conv_plots|length > 0 %} -
-
-
Conversion of target bases in the entire amplicon
-
-
- {% for plot_name in nuc_conv_plots %} -
{{report_data['titles'][plot_name]}}
- {{ render_partial('shared/partials/fig_summaries.html', report_data=report_data, plot_name=plot_name) }} - {% endfor %} -
-
- {% endif %} - - {% if report_data['names']|length > 0 %} - {% for plot_name in report_data['names'] %} -
-
-
{{report_data['titles'][plot_name]}}
-
-
- {{ render_partial('shared/partials/fig_summaries.html', report_data=report_data, plot_name=plot_name) }} -
-
- {% endfor %} - {% endif %} - - -
- -
- -
- Download report - Link to report - -
- - {# data bit for web version: #} - {# -

Data: {{data_label}}

- #} -
{# jumbotron_content #} -
{# jumbrotron #} - - {# column #} - -
- -{% endblock %} - -{% block foot %} -{% endblock %} diff --git a/templates/favicon.ico b/templates/favicon.ico deleted file mode 100644 index 8aed2d0743b52f12c1f0f8b2b4c439ba77091af3..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 1150 zcmbVMTWeE65MIGIUy2Vt`{*xIQTtGpYE@zjwT6~P+tO3xNz+rB6BBFO#3;0l0Sg5a zZAl=|kQxgi_XiV_ko)E9&Xx@^1Pab!cV@nwZ)Rt5au~b9pOF#9_nYkQRmN^G#%}S& zA&y+&TrtMau3x)Y!si1jMS7+{#1gs$u8 zbUGr3j2X-&@p8G0S4Jb0RSQPWS&7j;UxRtyjV~aI9)ri>NaQ} z>~Oeuu(+b&=h3fA`*^3SaBOd3!|A}9U5943;giRWWz~!c!wYD(4dnBAQA^%g>LQ<) zs%h}-?+MOFw+owmecsy@dCWZbuGb5@(>av?=j;rMMTMfi$Kz)c7#knQqo+?`G?`%A zbYkx98F-lC8jXMI_VcApG3|C6>2zAuA-}}uB7YyLWxUk& zdL5Ze2Dw~LK*?khg+c+OoBUm*vs5Z2Y{?-l?@je8m5Ml`8pI$zXSiP&jEy - - - CRISPResso2 - - - - - - - - - - - - - - - - - - - - - - - {% if current_user is defined %} - - {% else %} - - {% endif %} - - - - - {% block head %}{% endblock %} - - - - - {% if current_user is defined %} -
- {{ self.help_block() }} -
- - {% with messages = get_flashed_messages(with_categories=true) %} - {% if messages %} - {% for category, message in messages %} - {% if category == "error" %} - - {% else %} - - {% endif %} - {% endfor %} - {% endif %} - {% endwith %} - {% endif %} - - {# if default user (normal crispresso mode) #} - {% if current_user == null or not current_user.is_anonymous and current_user.username == "DEFAULTUSER" %} - -
-
-
- {% if current_user is defined %} -
- {% else %} -
- {% endif %} -
-
-

CRISPResso2

-

Analysis of genome editing outcomes from deep sequencing data

-
-
-
-
- - - {% else %} - {# if doing user sessions #} - -
- {% endif %} - -
-
-
-
- {% block help_block %} {% endblock %} -
-
-
-
- - {% block content %}{% endblock %} - - {% if current_user is defined and (not current_user.is_anonymous and current_user.username == "DEFAULTUSER") %} -
-
- -
-
- {% else %} -
-
- -
-
- {% endif %} -
- - - - - - - {% block foot %}{% endblock %} - - - diff --git a/templates/multiReport.html b/templates/multiReport.html deleted file mode 100644 index 8e8d83ca..00000000 --- a/templates/multiReport.html +++ /dev/null @@ -1,265 +0,0 @@ -{% extends "layout.html" %} -{% block head %} - - -{% endblock %} - -{% block content %} -
-
- -
-
- - {% if run_names|length > 0 %} -
-
-
{{report_name}}
-
-
-
- {% for run_name in run_names %} - {{run_name}} - {% endfor %} -
-
-
- {% endif %} - - {% if window_nuc_pct_quilts|length > 0 %} -
-
-
Nucleotide percentages around guides
-
-
- {% for plot_name in window_nuc_pct_quilts %} -
{{report_data['titles'][plot_name]}}
- {{ render_partial('shared/partials/fig_summaries.html', report_data=report_data, plot_name=plot_name) }} - {% endfor %} -
-
- {% endif %} - - {% if nuc_pct_quilts|length > 0 %} -
-
-
Nucleotide percentages in the entire amplicon
-
-
- {% for plot_name in nuc_pct_quilts %} -
{{report_data['titles'][plot_name]}}
- {{ render_partial('shared/partials/fig_summaries.html', report_data=report_data, plot_name=plot_name) }} - {% endfor %} -
-
- {% endif %} - - {% if window_nuc_conv_plots|length > 0 %} -
-
-
Conversion of target bases around guides
-
-
- {% for plot_name in window_nuc_conv_plots %} -
{{report_data['titles'][plot_name]}}
- {{ render_partial('shared/partials/fig_summaries.html', report_data=report_data, plot_name=plot_name) }} - {% endfor %} -
-
- {% endif %} - - {% if nuc_conv_plots|length > 0 %} -
-
-
Conversion of target bases in the entire amplicon
-
-
- {% for plot_name in nuc_conv_plots %} -
{{report_data['titles'][plot_name]}}
- {{ render_partial('shared/partials/fig_summaries.html', report_data=report_data, plot_name=plot_name) }} - {% endfor %} -
-
- {% endif %} - - {% if report_data['names']|length > 0 %} - {% for plot_name in report_data['names'] %} -
-
-
{{report_data['titles'][plot_name]}}
-
-
- {{ render_partial('shared/partials/fig_summaries.html', report_data=report_data, plot_name=plot_name) }} -
-
- {% endfor %} - {% endif %} - - {% if allele_modification_heatmap_plot_names|length > 0 %} - {% for heatmap_plot_name in allele_modification_heatmap_plot_names %} - {% set line_plot_name = allele_modification_line_plot_names[loop.index - 1] %} - {% set modification_type = heatmap_plot_name.split('_')[3] %} -
-
-
{{allele_modification_heatmap_plot_titles[heatmap_plot_name]}}
- -
-
-
-
- {{allele_modification_heatmap_plot_htmls[heatmap_plot_name]}} - - {% for (data_label, data_path) in allele_modification_heatmap_plot_datas[heatmap_plot_name] %} -

Data: {{data_label}}

- {% endfor %} -
-
- {{allele_modification_line_plot_htmls[line_plot_name]}} - - {% for (data_label, data_path) in allele_modification_line_plot_datas[line_plot_name] %} -

Data: {{data_label}}

- {% endfor %} -
-
-
-
- - {% endfor %} - - - - {% endif %} - - {% if compact_plots_to_show|length > 0 %} -
-
-
Summary Plots
-
-
-
- {% for compact_plot in compact_plots_to_show %} - - {% endfor %} -
-
-
- {% endif %} - - -
- -
- -
{# jumbotron_content #} -
{# jumbrotron #} - -
{# column #} - -
-{% endblock %} - -{% block foot %} -{% endblock %} diff --git a/templates/pooledReport.html b/templates/pooledReport.html deleted file mode 100644 index f4550e82..00000000 --- a/templates/pooledReport.html +++ /dev/null @@ -1,101 +0,0 @@ -{% extends "layout.html" %} -{% block head %} - - -{% endblock %} - -{% block content %} -
-
-
- -
-
- - {% if run_names|length > 0 %} -
-
-
{{report_name}}
-
-
-
- {% for region_name in run_names %} - {{region_name}} - {% endfor %} -
-
-
- {% endif %} - - {% if report_data['names']|length > 0 %} - {% for plot_name in report_data['names'] %} -
-
-
{{report_data['titles'][plot_name]}}
-
-
- {{ render_partial('shared/partials/fig_summaries.html', report_data=report_data, plot_name=plot_name) }} -
-
- {% endfor %} - {% endif %} - -
- Download report - Link to report - -
- {# data bit for web version: #} - {# -

Data: {{data_label}}

- #} -
{# jumbotron_content #} -
{# jumbrotron #} - -
{# column #} - -
-
-{% endblock %} - -{% block foot %} -{% endblock %} diff --git a/templates/report.html b/templates/report.html deleted file mode 100644 index fb755d18..00000000 --- a/templates/report.html +++ /dev/null @@ -1,693 +0,0 @@ -{% extends "layout.html" %} -{% block head %} - - -{% endblock %} - -{% block content %} -
-
-
-
-
-
- {% if report_data['report_display_name'] != '' %} -
{{report_data['report_display_name']}}
- {% endif %} -
CRISPResso2 run information
-
    -
  • - -
    • -
  • - -
    • -
-
-
-
-
- {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_1a')}} -
- {{ render_partial('shared/partials/log_params.html', report_data=report_data) }} -
-
-
- -
-
-
Allele assignments
-
    -
  • - -
    • -
  • - -
    • - {% if report_data['figures']['locs']['plot_1d'] %} -
  • - -
    • - {% endif %} -
-
-
-
-
- {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_1b')}} -
-
- {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_1c')}} -
- {% if report_data['figures']['locs']['plot_1d'] %} -
- {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_1d')}} -
- {% endif %} -
-
-
{# end card #} - - {# start global coding sequence report #} - {% if report_data['figures']['locs']['plot_5a'] %} -
-
-
Global frameshift analysis
-
-
- {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_5a')}} -
-
- {% endif %} - - {% if report_data['figures']['locs']['plot_6a'] %} -
-
-
Global frameshift mutagenesis profiles
-
-
- {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_6a')}} -
-
- {% endif %} - - {% if report_data['figures']['locs']['plot_8a'] %} -
-
-
Global splicing analysis
-
-
- {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_8a')}} -
-
- {% endif %} - {# end of global coding sequence analysis #} - - {# start hdr summary #} - {% if report_data['figures']['locs'][report_data.amplicons[0]]['plot_4g'] %} -
-
- {% if report_data.amplicons|length == 1 %} {# if only one amplicon #} -
HDR summary plot
- {% else %} -
HDR summary report (all reads aligned to {{report_data.amplicons[0]}})
- {% endif %} -
-
- {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_4g', amplicon_name=report_data.amplicons[0])}} -
-
- {% endif %} - {# end HDR summary #} - - {# start prime editing report #} - {% if report_data['figures']['locs'][report_data.amplicons[0]]['plot_11a'] %} -
-
- {% if report_data.amplicons|length == 1 %} {# if only one amplicon #} -
Prime editing report
- {% else %} -
Prime editing report (all reads aligned to {{report_data.amplicons[0]}})
- {% endif %} -
-
- {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_11a', amplicon_name=report_data.amplicons[0])}} -
-
- {% endif %} - - {% if report_data['figures']['sgRNA_based_names'][report_data.amplicons[0]] and report_data['figures']['sgRNA_based_names'][report_data.amplicons[0]]['11b']%} -
-
- {% if report_data.amplicons|length == 1 %} {# if only one amplicon #} -
Prime editing summary plots at analysis positions
- {% else %} -
Prime editing summary plots at analysis positions (aligned to {{report_data.amplicons[0]}})
- {% endif %} -
-
- {% for fig_name in report_data['figures']['sgRNA_based_names'][report_data.amplicons[0]]['11b'] %} -
- {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name=fig_name, amplicon_name=report_data.amplicons[0])}} -
- {% endfor %} -
-
- {% endif %} - {# end plot 11b for prime editing #} - - {% if report_data['figures']['locs']['plot_11c'] %} -
-
-
Scaffold insertions
-
-
- {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_11c')}} -
-
- {% endif %} - {# end prime editing section #} - - {% if report_data.amplicons|length == 1 %} -
{# if only one amplicon, just a normal div #} - {% else %} - {# If there is more than one amplicon, print a navigation to show each amplicon #} -

Reads are aligned to each amplicon sequence separately. Quantification and visualization of these reads are shown for each amplicon below:

-
-
-
Amplicons
- -
- {% endif %} {# end if report contains more than one amplicon #} - - - {% if report_data.amplicons|length == 1 %} {# if only one amplicon, just a normal div #} -
- {% else %} -
- {% endif %} - - {% for amplicon_name in report_data.amplicons %} - {% if report_data.amplicons|length == 1 %} {# if only one amplicon, just a normal div #} -
- {% elif loop.index0 == 0 %} {# if more than one amplicon, and the first, this is the active one #} -
-

Reads aligning to {{amplicon_name}}

{# this bit appears in print mode #} - {% else %} {# otherwise inactive tab #} -
-

Reads aligning to {{amplicon_name}}

{# this bit appears in print mode #} - {% endif %} - -
-
- {% if report_data.amplicons|length == 1 %} {# if only one amplicon #} -
Nucleotide composition
- {% else %} -
Nucleotide composition for {{amplicon_name}}
- {% endif %} -
-
- {% if report_data['figures']['locs'][amplicon_name]['plot_2a'] %} -
-
-
- -
-
-
- -
- -
- - {% for (data_label,data_path) in report_data['figures']['datas'][amplicon_name]['plot_2a'] %} -

Data: {{data_label}}

- {% endfor %} - {% endif %} - - {% if report_data['figures']['sgRNA_based_names'][amplicon_name] and report_data['figures']['sgRNA_based_names'][amplicon_name]['2b']%} - {% for fig_name in report_data['figures']['sgRNA_based_names'][amplicon_name]['2b'] %} - {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name=fig_name, amplicon_name=amplicon_name)}} - {% endfor %} - {% endif %} -
-
{# end card #} - -
-
- {% if report_data.amplicons|length == 1 %} {# if only one amplicon #} -
Modification lengths
- {% else %} -
Modification lengths for {{amplicon_name}}
- {% endif %} -
    - {% if report_data['figures']['locs'][amplicon_name]['plot_3a'] %} -
  • - -
    • - {% endif %} - {% if report_data['figures']['locs'][amplicon_name]['plot_3b'] %} -
  • - -
    • - {% endif %} -
-
-
-
- {% if report_data['figures']['locs'][amplicon_name]['plot_3a'] %} -
- {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_3a', amplicon_name=amplicon_name)}} -
- {% endif %} - - {% if report_data['figures']['locs'][amplicon_name]['plot_3b'] %} -
- {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_3b', amplicon_name=amplicon_name)}} -
- {% endif %} -
-
{# end card_body #} -
{# end card #} - -
-
- {% if report_data.amplicons|length == 1 %} {# if only one amplicon #} -
Indel characterization
- {% else %} -
Indel characterization for {{amplicon_name}}
- {% endif %} -
    - {% if report_data['figures']['locs'][amplicon_name]['plot_4a'] %} -
  • - -
    • - {% endif %} - {% if report_data['figures']['locs'][amplicon_name]['plot_4b'] %} -
  • - -
    • - {% endif %} - {% if report_data['figures']['locs'][amplicon_name]['plot_4c'] %} -
  • - -
    • - {% endif %} - {% if report_data['figures']['locs'][amplicon_name]['plot_4d'] %} -
  • - -
    • - {% endif %} - {% if report_data['figures']['locs'][amplicon_name]['plot_4e'] %} -
  • - -
    • - {% endif %} - {% if report_data['figures']['locs'][amplicon_name]['plot_4f'] %} -
  • - -
    • - {% endif %} -
-
{# end card head #} -
-
- {% if report_data['figures']['locs'][amplicon_name]['plot_4a'] %} -
- {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_4a', amplicon_name=amplicon_name)}} -
- {% endif %} - {% if report_data['figures']['locs'][amplicon_name]['plot_4b'] %} -
- {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_4b', amplicon_name=amplicon_name)}} -
- {% endif %} - {% if report_data['figures']['locs'][amplicon_name]['plot_4c'] %} -
- {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_4c', amplicon_name=amplicon_name)}} -
- {% endif %} - - {% if report_data['figures']['locs'][amplicon_name]['plot_4d'] %} -
- {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_4d', amplicon_name=amplicon_name)}} -
- {% endif %} - - {% if report_data['figures']['locs'][amplicon_name]['plot_4e'] %} -
- {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_4e', amplicon_name=amplicon_name)}} -
- {% endif %} - - {% if report_data['figures']['locs'][amplicon_name]['plot_4f'] %} -
- {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_4f', amplicon_name=amplicon_name)}} -
- {% endif %} -
-
{# end card body #} -
{# end card #} - - - {% if report_data['figures']['locs'][amplicon_name]['plot_5'] %} -
-
- {% if report_data.amplicons|length == 1 %} {# if only one amplicon #} -
Frameshift analysis
- {% else %} -
Frameshift analysis for {{amplicon_name}}
- {% endif %} -
-
- {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_5', amplicon_name=amplicon_name)}} -
-
- {% endif %} - - {% if report_data['figures']['locs'][amplicon_name]['plot_6'] %} -
-
- {% if report_data.amplicons|length == 1 %} {# if only one amplicon #} -
Frameshift mutagenesis profiles
- {% else %} -
Frameshift mutagenesis profiles for {{amplicon_name}}
- {% endif %} -
-
- {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_6', amplicon_name=amplicon_name)}} -
-
- {% endif %} - - {% if report_data['figures']['locs'][amplicon_name]['plot_7'] %} -
-
- {% if report_data.amplicons|length == 1 %} {# if only one amplicon #} -
Non-coding mutations
- {% else %} -
Coding mutations for {{amplicon_name}}
- {% endif %} -
-
- {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_7', amplicon_name=amplicon_name)}} -
-
- {% endif %} - - {% if report_data['figures']['locs'][amplicon_name]['plot_8'] %} -
-
- {% if report_data.amplicons|length == 1 %} {# if only one amplicon #} -
Splicing
- {% else %} -
Splicing for {{amplicon_name}}
- {% endif %} -
-
- {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_8', amplicon_name=amplicon_name)}} -
-
- {% endif %} - - {% if report_data['figures']['sgRNA_based_names'][amplicon_name] and report_data['figures']['sgRNA_based_names'][amplicon_name]['9']%} -
-
- {% if report_data.amplicons|length == 1 %} {# if only one amplicon #} -
Allele plots
- {% else %} -
Allele plots for {{amplicon_name}}
- {% endif %} -
-
- {% for fig_name in report_data['figures']['sgRNA_based_names'][amplicon_name]['9'] %} -
- {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name=fig_name, amplicon_name=amplicon_name)}} -
- {% endfor %} -
-
- {% endif %} - - {% if report_data['figures']['locs'][amplicon_name]['plot_10a'] %} -
-
- {% if report_data.amplicons|length == 1 %} {# if only one amplicon #} -
Base editing
- {% else %} -
Base editing for {{amplicon_name}}
- {% endif %} -
    - {% if report_data['figures']['locs'][amplicon_name]['plot_10a'] %} -
  • - -
    • - {% endif %} - {% if report_data['figures']['sgRNA_based_names'][amplicon_name] and report_data['figures']['sgRNA_based_names'][amplicon_name]['10d']%} -
  • - -
    • - {% endif %} - {% if report_data['figures']['sgRNA_based_names'][amplicon_name] and report_data['figures']['sgRNA_based_names'][amplicon_name]['10e']%} -
  • - -
    • - {% endif %} - {% if report_data['figures']['sgRNA_based_names'][amplicon_name] and report_data['figures']['sgRNA_based_names'][amplicon_name]['10f']%} -
  • - -
    • - {% endif %} -
-
-
-
- {% if report_data['figures']['locs'][amplicon_name]['plot_10c'] %} -
-
- {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_10a', amplicon_name=amplicon_name)}} -
-
- - {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_10b', amplicon_name=amplicon_name)}} - {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_10c', amplicon_name=amplicon_name)}} -
-
- {% else %} -
-
- {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_10a', amplicon_name=amplicon_name)}} -
-
- {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_10b', amplicon_name=amplicon_name)}} -
-
- {% endif %} - {% if report_data['figures']['sgRNA_based_names'][amplicon_name] and report_data['figures']['sgRNA_based_names'][amplicon_name]['10d']%} -
- {% for fig_name in report_data['figures']['sgRNA_based_names'][amplicon_name]['10d'] %} -
- {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name=fig_name, amplicon_name=amplicon_name)}} -
- {% endfor %} -
- {% endif %} - {% if report_data['figures']['sgRNA_based_names'][amplicon_name] and report_data['figures']['sgRNA_based_names'][amplicon_name]['10e']%} -
- {% for fig_name in report_data['figures']['sgRNA_based_names'][amplicon_name]['10e'] %} -
- {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name=fig_name, amplicon_name=amplicon_name)}} -
- {% endfor %} -
- {% endif %} - {% if report_data['figures']['sgRNA_based_names'][amplicon_name] and report_data['figures']['sgRNA_based_names'][amplicon_name]['10f']%} -
- {% for fig_name in report_data['figures']['sgRNA_based_names'][amplicon_name]['10f'] %} -
- {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_10f', amplicon_name=amplicon_name)}} -
- {% endfor %} - {% for fig_name in report_data['figures']['sgRNA_based_names'][amplicon_name]['10g'] %} -
- {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_10g', amplicon_name=amplicon_name)}} -
- {% endfor %} -
-
- {% endif %} -
-
{# end card #} - {% endif %} {# end base editing card #} -
{# end this amplicon tab #} - {% endfor %} -
{# tab content #} -
-
{# jumbotron_content #} -
{# jumbrotron #} -
{# column #} -
- -
-{% endblock %} - -{% block foot %} - -{% endblock %} diff --git a/templates/shared/partials/fig_reports.html b/templates/shared/partials/fig_reports.html deleted file mode 100644 index 6f7e448e..00000000 --- a/templates/shared/partials/fig_reports.html +++ /dev/null @@ -1,31 +0,0 @@ -
- {% if amplicon_name is defined %} - {% if 'htmls' in report_data['figures'] and fig_name in report_data['figures']['htmls'][amplicon_name] %} - {{report_data['figures']['htmls'][amplicon_name][fig_name]|safe}} - {% else %} - {% if fig_name in ['plot_1a', 'plot_1b', 'plot_1c', 'plot_3a', 'plot_4a', 'plot_4b', 'plot_4c'] %} - - {% else %} - - {% endif %} - {% endif %} - - {% for (data_label,data_path) in report_data['figures']['datas'][amplicon_name][fig_name] %} -

Data: {{data_label}}

- {% endfor %} - {% else %} - {% if 'htmls' in report_data['figures'] and fig_name in report_data['figures']['htmls'] %} - {{report_data['figures']['htmls'][fig_name]|safe}} - {% else %} - {% if fig_name in ['plot_1a', 'plot_1b', 'plot_1c', 'plot_3a', 'plot_4a', 'plot_4b', 'plot_4c'] %} - - {% else %} - - {% endif %} - {% endif %} - - {% for (data_label,data_path) in report_data['figures']['datas'][fig_name] %} -

Data: {{data_label}}

- {% endfor %} - {% endif %} -
\ No newline at end of file diff --git a/templates/shared/partials/fig_summaries.html b/templates/shared/partials/fig_summaries.html deleted file mode 100644 index e4e3297a..00000000 --- a/templates/shared/partials/fig_summaries.html +++ /dev/null @@ -1,11 +0,0 @@ -
- {% if report_data['htmls'][plot_name] %} - {{report_data['htmls'][plot_name]|safe}} - {% else %} - - {% endif %} - - {% for (data_label,data_path) in report_data['datas'][plot_name] %} -

Data: {{data_label}}

- {% endfor %} -
diff --git a/templates/shared/partials/log_params.html b/templates/shared/partials/log_params.html deleted file mode 100644 index ad035ae3..00000000 --- a/templates/shared/partials/log_params.html +++ /dev/null @@ -1,11 +0,0 @@ -
-

CRISPResso version: {{report_data['run_data']['running_info']['version']}}

-

Run completed: {{report_data['run_data']['running_info']['end_time_string']}}

-

Amplicon sequence: 

{{report_data['run_data']['running_info']['args']['amplicon_seq']}}

- {% if report_data['run_data']['running_info']['args']['guide_seq'] != '' %} -

Guide sequence: 

{{report_data['run_data']['running_info']['args']['guide_seq']}}

- {% endif %} -

Command used: 

{{report_data['run_data']['running_info']['command_used']}}

-

Parameters: 

{{report_data['run_data']['running_info']['args_string']}}

-

Running log

-
diff --git a/templates/wgsReport.html b/templates/wgsReport.html deleted file mode 100644 index 0a5a1277..00000000 --- a/templates/wgsReport.html +++ /dev/null @@ -1,99 +0,0 @@ -{% extends "layout.html" %} -{% block head %} - - -{% endblock %} - -{% block content %} -
-
-
- -
-
- -
-
-
{{report_name}}
-
-
-
- {% for region_name in run_names %} - {{region_name}} - {% endfor %} -
-
-
- - {% if report_data['names']|length > 0 %} - {% for plot_name in report_data['names'] %} -
-
-
{{report_data['titles'][plot_name]}}
-
-
- {{ render_partial('shared/partials/fig_summaries.html', report_data=report_data, plot_name=plot_name) }} -
-
- {% endfor %} - {% endif %} - -
- Download report - Link to report - -
- {# data bit for web version: #} - {# -

Data: {{data_label}}

- #} -
{# jumbotron_content #} -
{# jumbrotron #} - -
{# column #} - -
-
-{% endblock %} - -{% block foot %} -{% endblock %} From 5cd6d2707e6c95a20939531f1be770be4169625b Mon Sep 17 00:00:00 2001 From: Samuel Nichols Date: Fri, 23 Sep 2022 11:48:32 -0600 Subject: [PATCH 18/33] Final style fixes, color circles for style files --- templates/layout.html | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/templates/layout.html b/templates/layout.html index dba520de..d72c7c3a 100644 --- a/templates/layout.html +++ b/templates/layout.html @@ -184,7 +184,7 @@

Analysis of genome editing ou
-
+
{% block help_block %} {% endblock %}
From 2f70855b57de16584ee0fe85f4f30c1a0d13cf97 Mon Sep 17 00:00:00 2001 From: Cole Lyman Date: Wed, 28 Sep 2022 10:21:16 -0600 Subject: [PATCH 19/33] Add spacing around body and footer tags --- templates/layout.html | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/templates/layout.html b/templates/layout.html index d72c7c3a..ff61410f 100644 --- a/templates/layout.html +++ b/templates/layout.html @@ -87,9 +87,9 @@ - + {% if current_user is defined %} -
+
{{ self.help_block() }}
@@ -135,7 +135,7 @@

Analysis of genome editing ou {% else %} {# if doing user sessions #} -

- {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_8a')}} + {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_8a', width='40%')}}
{% endif %} @@ -160,7 +160,7 @@
HDR summary report (all reads aligned to {{report_data.amplicons[0]}})
{% endif %}
- {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_4g', amplicon_name=report_data.amplicons[0])}} + {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_4g', width='40%', amplicon_name=report_data.amplicons[0])}}
{% endif %} @@ -177,7 +177,7 @@
Prime editing report (all reads aligned to {{report_data.amplicons[0]}})
- {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_11a', amplicon_name=report_data.amplicons[0])}} + {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_11a', width='40%', amplicon_name=report_data.amplicons[0])}}
{% endif %} @@ -194,7 +194,7 @@
Prime editing summary plots at analysis positions (aligned to {{report_data.
{% for fig_name in report_data['figures']['sgRNA_based_names'][report_data.amplicons[0]]['11b'] %}
- {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name=fig_name, amplicon_name=report_data.amplicons[0])}} + {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name=fig_name, width='40%', amplicon_name=report_data.amplicons[0])}}
{% endfor %}
@@ -208,7 +208,7 @@
Prime editing summary plots at analysis positions (aligned to {{report_data.
Scaffold insertions
- {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_11c')}} + {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_11c', width='40%')}}
{% endif %} @@ -288,7 +288,7 @@
Nucleotide composition for {{amplicon_name}}
{% if report_data['figures']['sgRNA_based_names'][amplicon_name] and report_data['figures']['sgRNA_based_names'][amplicon_name]['2b']%} {% for fig_name in report_data['figures']['sgRNA_based_names'][amplicon_name]['2b'] %} - {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name=fig_name, amplicon_name=amplicon_name)}} + {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name=fig_name, width='80%', amplicon_name=amplicon_name)}} {% endfor %} {% endif %} @@ -318,13 +318,13 @@
Modification lengths for {{amplicon_name}}
{% if report_data['figures']['locs'][amplicon_name]['plot_3a'] %}
- {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_3a', amplicon_name=amplicon_name)}} + {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_3a', width='40%', amplicon_name=amplicon_name)}}
{% endif %} {% if report_data['figures']['locs'][amplicon_name]['plot_3b'] %}
- {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_3b', amplicon_name=amplicon_name)}} + {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_3b', width='100%', amplicon_name=amplicon_name)}}
{% endif %}
@@ -375,35 +375,35 @@
Indel characterization for {{amplicon_name}}
{% if report_data['figures']['locs'][amplicon_name]['plot_4a'] %}
- {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_4a', amplicon_name=amplicon_name)}} + {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_4a', width='40%', amplicon_name=amplicon_name)}}
{% endif %} {% if report_data['figures']['locs'][amplicon_name]['plot_4b'] %}
- {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_4b', amplicon_name=amplicon_name)}} + {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_4b', width='40%', amplicon_name=amplicon_name)}}
{% endif %} {% if report_data['figures']['locs'][amplicon_name]['plot_4c'] %}
- {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_4c', amplicon_name=amplicon_name)}} + {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_4c', width='40%', amplicon_name=amplicon_name)}}
{% endif %} {% if report_data['figures']['locs'][amplicon_name]['plot_4d'] %}
- {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_4d', amplicon_name=amplicon_name)}} + {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_4d', width='80%', amplicon_name=amplicon_name)}}
{% endif %} {% if report_data['figures']['locs'][amplicon_name]['plot_4e'] %}
- {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_4e', amplicon_name=amplicon_name)}} + {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_4e', width='40%', amplicon_name=amplicon_name)}}
{% endif %} {% if report_data['figures']['locs'][amplicon_name]['plot_4f'] %}
- {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_4f', amplicon_name=amplicon_name)}} + {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_4f', width='40%', amplicon_name=amplicon_name)}}
{% endif %}
@@ -421,7 +421,7 @@
Frameshift analysis for {{amplicon_name}}
{% endif %}
- {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_5', amplicon_name=amplicon_name)}} + {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_5', width='40%', amplicon_name=amplicon_name)}}
{% endif %} @@ -436,7 +436,7 @@
Frameshift mutagenesis profiles for {{amplicon_name}}
{% endif %}
- {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_6', amplicon_name=amplicon_name)}} + {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_6', width='40%', amplicon_name=amplicon_name)}}
{% endif %} @@ -451,7 +451,7 @@
Coding mutations for {{amplicon_name}}
{% endif %}
- {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_7', amplicon_name=amplicon_name)}} + {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_7', width='40%', amplicon_name=amplicon_name)}}
{% endif %} @@ -466,7 +466,7 @@
Splicing for {{amplicon_name}}
{% endif %}
- {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_8', amplicon_name=amplicon_name)}} + {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_8', width='40%', amplicon_name=amplicon_name)}}
{% endif %} @@ -483,7 +483,7 @@
Allele plots for {{amplicon_name}}
{% for fig_name in report_data['figures']['sgRNA_based_names'][amplicon_name]['9'] %}
- {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name=fig_name, amplicon_name=amplicon_name)}} + {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name=fig_name, width='100%', amplicon_name=amplicon_name)}}
{% endfor %}
@@ -526,21 +526,21 @@
Base editing for {{amplicon_name}}
{% if report_data['figures']['locs'][amplicon_name]['plot_10c'] %}
- {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_10a', amplicon_name=amplicon_name)}} + {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_10a', width='80%', amplicon_name=amplicon_name)}}
- - {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_10b', amplicon_name=amplicon_name)}} - {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_10c', amplicon_name=amplicon_name)}} + + {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_10b', width='50%', amplicon_name=amplicon_name)}} + {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_10c', width='50%', amplicon_name=amplicon_name)}}
{% else %}
- {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_10a', amplicon_name=amplicon_name)}} + {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_10a', width='80%', amplicon_name=amplicon_name)}}
- {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_10b', amplicon_name=amplicon_name)}} + {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_10b', width='50%', amplicon_name=amplicon_name)}}
{% endif %} @@ -548,7 +548,7 @@
Base editing for {{amplicon_name}}
{% for fig_name in report_data['figures']['sgRNA_based_names'][amplicon_name]['10d'] %}
- {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name=fig_name, amplicon_name=amplicon_name)}} + {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name=fig_name, width='80%', amplicon_name=amplicon_name)}}
{% endfor %}
@@ -557,7 +557,7 @@
Base editing for {{amplicon_name}}
{% for fig_name in report_data['figures']['sgRNA_based_names'][amplicon_name]['10e'] %}
- {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name=fig_name, amplicon_name=amplicon_name)}} + {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name=fig_name, width='80%', amplicon_name=amplicon_name)}}
{% endfor %}
@@ -566,17 +566,17 @@
Base editing for {{amplicon_name}}
{% for fig_name in report_data['figures']['sgRNA_based_names'][amplicon_name]['10f'] %}
- {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_10f', amplicon_name=amplicon_name)}} + {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name=fig_name, width='80%', amplicon_name=amplicon_name)}}
{% endfor %} {% for fig_name in report_data['figures']['sgRNA_based_names'][amplicon_name]['10g'] %}
- {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_10g', amplicon_name=amplicon_name)}} + {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name=fig_name, width='80%', amplicon_name=amplicon_name)}}
{% endfor %}
+ {% endif %} - {% endif %} {# end card #} {% endif %} {# end base editing card #} diff --git a/templates/shared/partials/fig_reports.html b/templates/shared/partials/fig_reports.html index 6f7e448e..e9057e16 100644 --- a/templates/shared/partials/fig_reports.html +++ b/templates/shared/partials/fig_reports.html @@ -1,13 +1,10 @@
+
{% if amplicon_name is defined %} {% if 'htmls' in report_data['figures'] and fig_name in report_data['figures']['htmls'][amplicon_name] %} {{report_data['figures']['htmls'][amplicon_name][fig_name]|safe}} {% else %} - {% if fig_name in ['plot_1a', 'plot_1b', 'plot_1c', 'plot_3a', 'plot_4a', 'plot_4b', 'plot_4c'] %} - - {% else %} - - {% endif %} + {% endif %} {% for (data_label,data_path) in report_data['figures']['datas'][amplicon_name][fig_name] %} @@ -17,15 +14,12 @@ {% if 'htmls' in report_data['figures'] and fig_name in report_data['figures']['htmls'] %} {{report_data['figures']['htmls'][fig_name]|safe}} {% else %} - {% if fig_name in ['plot_1a', 'plot_1b', 'plot_1c', 'plot_3a', 'plot_4a', 'plot_4b', 'plot_4c'] %} - - {% else %} - - {% endif %} + {% endif %} {% for (data_label,data_path) in report_data['figures']['datas'][fig_name] %}

Data: {{data_label}}

{% endfor %} {% endif %} +
\ No newline at end of file From e7ef285dbc92b309b674c8c3f54b88cb8e07a2a0 Mon Sep 17 00:00:00 2001 From: Samuel Nichols Date: Wed, 28 Sep 2022 11:31:42 -0600 Subject: [PATCH 21/33] Fix hamburger menu and add -bs- to data-target and data-toggle --- templates/batchReport.html | 2 +- templates/layout.html | 2 +- templates/multiReport.html | 2 +- templates/pooledReport.html | 2 +- templates/wgsReport.html | 2 +- 5 files changed, 5 insertions(+), 5 deletions(-) diff --git a/templates/batchReport.html b/templates/batchReport.html index d02c6269..cb9d4aa0 100644 --- a/templates/batchReport.html +++ b/templates/batchReport.html @@ -148,7 +148,7 @@
{{report_data['titles'][plot_name]}}
{# data bit for web version: #} {# -

Data: {{data_label}}

+

Data: {{data_label}}

#} {# jumbotron_content #} {# jumbrotron #} diff --git a/templates/layout.html b/templates/layout.html index ff61410f..1e37522a 100644 --- a/templates/layout.html +++ b/templates/layout.html @@ -143,7 +143,7 @@

Analysis of genome editing ou {{config['BANNER_TEXT']}} - diff --git a/templates/multiReport.html b/templates/multiReport.html index 8e8d83ca..44d66112 100644 --- a/templates/multiReport.html +++ b/templates/multiReport.html @@ -241,7 +241,7 @@

Summary Plots
{% for compact_plot in compact_plots_to_show %} - + {% endfor %}
diff --git a/templates/pooledReport.html b/templates/pooledReport.html index f4550e82..e6817601 100644 --- a/templates/pooledReport.html +++ b/templates/pooledReport.html @@ -86,7 +86,7 @@
{{report_data['titles'][plot_name]}}
{# data bit for web version: #} {# -

Data: {{data_label}}

+

Data: {{data_label}}

#} {# jumbotron_content #} {# jumbrotron #} diff --git a/templates/wgsReport.html b/templates/wgsReport.html index 0a5a1277..2f11c5f1 100644 --- a/templates/wgsReport.html +++ b/templates/wgsReport.html @@ -84,7 +84,7 @@
{{report_data['titles'][plot_name]}}
{# data bit for web version: #} {# -

Data: {{data_label}}

+

Data: {{data_label}}

#} {# jumbotron_content #} {# jumbrotron #} From 1efad706b7c147dd45601111d697534fa993c007 Mon Sep 17 00:00:00 2001 From: Cole Lyman Date: Mon, 3 Oct 2022 15:21:07 -0600 Subject: [PATCH 22/33] Replace tabs with spaces and reindent template files --- templates/layout.html | 442 ++++++------ templates/multiReport.html | 456 ++++++------ templates/report.html | 1348 ++++++++++++++++++------------------ 3 files changed, 1123 insertions(+), 1123 deletions(-) diff --git a/templates/layout.html b/templates/layout.html index 1e37522a..16551f22 100644 --- a/templates/layout.html +++ b/templates/layout.html @@ -1,237 +1,237 @@ - - CRISPResso2 - - - - - - - - - - - - - - - - - - - - - - - {% if current_user is defined %} - - {% else %} - - {% endif %} - - - - - {% block head %}{% endblock %} - - - - - {% if current_user is defined %} -
- {{ self.help_block() }} -
- - {% with messages = get_flashed_messages(with_categories=true) %} - {% if messages %} - {% for category, message in messages %} - {% if category == "error" %} - - {% else %} - - {% endif %} - {% endfor %} - {% endif %} - {% endwith %} - {% endif %} - - {# if default user (normal crispresso mode) #} - {% if current_user == null or not current_user.is_anonymous and current_user.username == "DEFAULTUSER" %} - -
-
-
- {% if current_user is defined %} -
- {% else %} -
- {% endif %} -
-
-

CRISPResso2

-

Analysis of genome editing outcomes from deep sequencing data

-
-
-
-
- - - {% else %} - {# if doing user sessions #} - +
+ {% endif %} + +
+
+
+
+ {% block help_block %} {% endblock %} +
+
+
+
+ + {% block content %}{% endblock %} + + {% if current_user is defined and (not current_user.is_anonymous and current_user.username == "DEFAULTUSER") %} +
+
+ -
-
- {% else %} -
-
- -
-
- {% endif %} + Clement K, Rees H, Canver MC, Gehrke JM, Farouni R, Hsu JY, Cole MA, Liu DR, Joung JK, Bauer DE, Pinello L.
+ CRISPResso2 provides accurate and rapid genome editing sequence analysis.
+ Nat Biotechnol. 2019 Mar; 37(3):224-226. doi: 10.1038/s41587-019-0032-3. PubMed PMID: 30809026. +

+

© Copyright Kendell Clement and Luca Pinello

+

+ + + +

+ + +
+
+ {% else %} +
+
+ +
+
+ {% endif %}
- - - - - {% block foot %}{% endblock %} - + + + + + {% block foot %}{% endblock %} + diff --git a/templates/multiReport.html b/templates/multiReport.html index 44d66112..5def61f1 100644 --- a/templates/multiReport.html +++ b/templates/multiReport.html @@ -1,44 +1,44 @@ {% extends "layout.html" %} {% block head %} {% endblock %} @@ -47,213 +47,213 @@
-
-
+
+
- {% if run_names|length > 0 %} -
-
-
{{report_name}}
-
-
-
- {% for run_name in run_names %} - {{run_name}} - {% endfor %} -
-
-
- {% endif %} + {% if run_names|length > 0 %} +
+
+
{{report_name}}
+
+
+
+ {% for run_name in run_names %} + {{run_name}} + {% endfor %} +
+
+
+ {% endif %} - {% if window_nuc_pct_quilts|length > 0 %} -
-
-
Nucleotide percentages around guides
-
-
- {% for plot_name in window_nuc_pct_quilts %} -
{{report_data['titles'][plot_name]}}
- {{ render_partial('shared/partials/fig_summaries.html', report_data=report_data, plot_name=plot_name) }} - {% endfor %} -
-
- {% endif %} + {% if window_nuc_pct_quilts|length > 0 %} +
+
+
Nucleotide percentages around guides
+
+
+ {% for plot_name in window_nuc_pct_quilts %} +
{{report_data['titles'][plot_name]}}
+ {{ render_partial('shared/partials/fig_summaries.html', report_data=report_data, plot_name=plot_name) }} + {% endfor %} +
+
+ {% endif %} - {% if nuc_pct_quilts|length > 0 %} -
-
-
Nucleotide percentages in the entire amplicon
-
-
- {% for plot_name in nuc_pct_quilts %} -
{{report_data['titles'][plot_name]}}
- {{ render_partial('shared/partials/fig_summaries.html', report_data=report_data, plot_name=plot_name) }} - {% endfor %} -
-
- {% endif %} + {% if nuc_pct_quilts|length > 0 %} +
+
+
Nucleotide percentages in the entire amplicon
+
+
+ {% for plot_name in nuc_pct_quilts %} +
{{report_data['titles'][plot_name]}}
+ {{ render_partial('shared/partials/fig_summaries.html', report_data=report_data, plot_name=plot_name) }} + {% endfor %} +
+
+ {% endif %} - {% if window_nuc_conv_plots|length > 0 %} -
-
-
Conversion of target bases around guides
-
-
- {% for plot_name in window_nuc_conv_plots %} -
{{report_data['titles'][plot_name]}}
- {{ render_partial('shared/partials/fig_summaries.html', report_data=report_data, plot_name=plot_name) }} - {% endfor %} -
-
- {% endif %} + {% if window_nuc_conv_plots|length > 0 %} +
+
+
Conversion of target bases around guides
+
+
+ {% for plot_name in window_nuc_conv_plots %} +
{{report_data['titles'][plot_name]}}
+ {{ render_partial('shared/partials/fig_summaries.html', report_data=report_data, plot_name=plot_name) }} + {% endfor %} +
+
+ {% endif %} - {% if nuc_conv_plots|length > 0 %} -
-
-
Conversion of target bases in the entire amplicon
-
-
- {% for plot_name in nuc_conv_plots %} -
{{report_data['titles'][plot_name]}}
- {{ render_partial('shared/partials/fig_summaries.html', report_data=report_data, plot_name=plot_name) }} - {% endfor %} -
-
- {% endif %} + {% if nuc_conv_plots|length > 0 %} +
+
+
Conversion of target bases in the entire amplicon
+
+
+ {% for plot_name in nuc_conv_plots %} +
{{report_data['titles'][plot_name]}}
+ {{ render_partial('shared/partials/fig_summaries.html', report_data=report_data, plot_name=plot_name) }} + {% endfor %} +
+
+ {% endif %} + + {% if report_data['names']|length > 0 %} + {% for plot_name in report_data['names'] %} +
+
+
{{report_data['titles'][plot_name]}}
+
+
+ {{ render_partial('shared/partials/fig_summaries.html', report_data=report_data, plot_name=plot_name) }} +
+
+ {% endfor %} + {% endif %} - {% if report_data['names']|length > 0 %} - {% for plot_name in report_data['names'] %} -
-
-
{{report_data['titles'][plot_name]}}
-
-
- {{ render_partial('shared/partials/fig_summaries.html', report_data=report_data, plot_name=plot_name) }} -
+ {% if allele_modification_heatmap_plot_names|length > 0 %} + {% for heatmap_plot_name in allele_modification_heatmap_plot_names %} + {% set line_plot_name = allele_modification_line_plot_names[loop.index - 1] %} + {% set modification_type = heatmap_plot_name.split('_')[3] %} +
+
+
{{allele_modification_heatmap_plot_titles[heatmap_plot_name]}}
+ +
+
+
+
+ {{allele_modification_heatmap_plot_htmls[heatmap_plot_name]}} + + {% for (data_label, data_path) in allele_modification_heatmap_plot_datas[heatmap_plot_name] %} +

Data: {{data_label}}

+ {% endfor %}
- {% endfor %} - {% endif %} +
+ {{allele_modification_line_plot_htmls[line_plot_name]}} + + {% for (data_label, data_path) in allele_modification_line_plot_datas[line_plot_name] %} +

Data: {{data_label}}

+ {% endfor %} +
+
+
+
+ + {% endfor %} + + + + {% endif %} - {% if allele_modification_heatmap_plot_names|length > 0 %} - {% for heatmap_plot_name in allele_modification_heatmap_plot_names %} - {% set line_plot_name = allele_modification_line_plot_names[loop.index - 1] %} - {% set modification_type = heatmap_plot_name.split('_')[3] %} -
-
-
{{allele_modification_heatmap_plot_titles[heatmap_plot_name]}}
- -
-
-
-
- {{allele_modification_heatmap_plot_htmls[heatmap_plot_name]}} - - {% for (data_label, data_path) in allele_modification_heatmap_plot_datas[heatmap_plot_name] %} -

Data: {{data_label}}

- {% endfor %} -
-
- {{allele_modification_line_plot_htmls[line_plot_name]}} - - {% for (data_label, data_path) in allele_modification_line_plot_datas[line_plot_name] %} -

Data: {{data_label}}

- {% endfor %} -
-
-
-
- + {% if compact_plots_to_show|length > 0 %} +
+
+
Summary Plots
+
+
+
+ {% for compact_plot in compact_plots_to_show %} + {% endfor %} - - - - {% endif %} - - {% if compact_plots_to_show|length > 0 %} -
-
-
Summary Plots
-
-
-
- {% for compact_plot in compact_plots_to_show %} - - {% endfor %} -
-
-
- {% endif %} +
+
+
+ {% endif %} -
+
-
+
-
{# jumbotron_content #} +
{# jumbotron_content #}
{# jumbrotron #} {# column #} diff --git a/templates/report.html b/templates/report.html index a653e241..3b998cec 100644 --- a/templates/report.html +++ b/templates/report.html @@ -1,51 +1,51 @@ {% extends "layout.html" %} {% block head %} {% endblock %} @@ -53,540 +53,540 @@ {% block content %}
-
-
-
-
- {% if report_data['report_display_name'] != '' %} -
{{report_data['report_display_name']}}
- {% endif %} -
CRISPResso2 run information
-
    -
  • - -
    • -
  • - -
    • -
-
-
-
-
- {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_1a', width='40%')}} -
- {{ render_partial('shared/partials/log_params.html', report_data=report_data) }} -
-
-
- -
-
-
Allele assignments
-
    -
  • - -
    • -
  • - -
    • - {% if report_data['figures']['locs']['plot_1d'] %} -
  • - -
    • - {% endif %} -
-
-
-
-
- {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_1b', width='40%')}} -
-
- {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_1c', width='40%')}} -
- {% if report_data['figures']['locs']['plot_1d'] %} -
- {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_1d', width='40%')}} -
- {% endif %} -
-
-
{# end card #} - - {# start global coding sequence report #} - {% if report_data['figures']['locs']['plot_5a'] %} -
-
-
Global frameshift analysis
-
-
- {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_5a', width='40%')}} -
-
- {% endif %} - - {% if report_data['figures']['locs']['plot_6a'] %} -
-
-
Global frameshift mutagenesis profiles
-
-
- {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_6a', width='40%')}} -
-
- {% endif %} - - {% if report_data['figures']['locs']['plot_8a'] %} -
-
-
Global splicing analysis
-
-
- {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_8a', width='40%')}} -
-
- {% endif %} - {# end of global coding sequence analysis #} - - {# start hdr summary #} - {% if report_data['figures']['locs'][report_data.amplicons[0]]['plot_4g'] %} -
-
- {% if report_data.amplicons|length == 1 %} {# if only one amplicon #} -
HDR summary plot
- {% else %} -
HDR summary report (all reads aligned to {{report_data.amplicons[0]}})
- {% endif %} -
-
- {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_4g', width='40%', amplicon_name=report_data.amplicons[0])}} -
-
- {% endif %} - {# end HDR summary #} - - {# start prime editing report #} - {% if report_data['figures']['locs'][report_data.amplicons[0]]['plot_11a'] %} -
-
- {% if report_data.amplicons|length == 1 %} {# if only one amplicon #} -
Prime editing report
- {% else %} -
Prime editing report (all reads aligned to {{report_data.amplicons[0]}})
- {% endif %} -
-
- {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_11a', width='40%', amplicon_name=report_data.amplicons[0])}} -
-
- {% endif %} - - {% if report_data['figures']['sgRNA_based_names'][report_data.amplicons[0]] and report_data['figures']['sgRNA_based_names'][report_data.amplicons[0]]['11b']%} -
-
- {% if report_data.amplicons|length == 1 %} {# if only one amplicon #} -
Prime editing summary plots at analysis positions
- {% else %} -
Prime editing summary plots at analysis positions (aligned to {{report_data.amplicons[0]}})
- {% endif %} -
-
- {% for fig_name in report_data['figures']['sgRNA_based_names'][report_data.amplicons[0]]['11b'] %} -
- {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name=fig_name, width='40%', amplicon_name=report_data.amplicons[0])}} -
- {% endfor %} -
-
- {% endif %} - {# end plot 11b for prime editing #} - - {% if report_data['figures']['locs']['plot_11c'] %} -
-
-
Scaffold insertions
-
-
- {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_11c', width='40%')}} -
-
- {% endif %} - {# end prime editing section #} - - {% if report_data.amplicons|length == 1 %} -
{# if only one amplicon, just a normal div #} - {% else %} - {# If there is more than one amplicon, print a navigation to show each amplicon #} -

Reads are aligned to each amplicon sequence separately. Quantification and visualization of these reads are shown for each amplicon below:

-
-
-
Amplicons
- -
- {% endif %} {# end if report contains more than one amplicon #} - - - {% if report_data.amplicons|length == 1 %} {# if only one amplicon, just a normal div #} -
- {% else %} -
- {% endif %} - - {% for amplicon_name in report_data.amplicons %} - {% if report_data.amplicons|length == 1 %} {# if only one amplicon, just a normal div #} -
- {% elif loop.index0 == 0 %} {# if more than one amplicon, and the first, this is the active one #} -
-

Reads aligning to {{amplicon_name}}

{# this bit appears in print mode #} - {% else %} {# otherwise inactive tab #} -
-

Reads aligning to {{amplicon_name}}

{# this bit appears in print mode #} - {% endif %} - -
-
- {% if report_data.amplicons|length == 1 %} {# if only one amplicon #} -
Nucleotide composition
- {% else %} -
Nucleotide composition for {{amplicon_name}}
- {% endif %} -
-
- {% if report_data['figures']['locs'][amplicon_name]['plot_2a'] %} -
-
-
- -
-
-
- -
- -
- - {% for (data_label,data_path) in report_data['figures']['datas'][amplicon_name]['plot_2a'] %} -

Data: {{data_label}}

- {% endfor %} - {% endif %} - - {% if report_data['figures']['sgRNA_based_names'][amplicon_name] and report_data['figures']['sgRNA_based_names'][amplicon_name]['2b']%} - {% for fig_name in report_data['figures']['sgRNA_based_names'][amplicon_name]['2b'] %} - {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name=fig_name, width='80%', amplicon_name=amplicon_name)}} - {% endfor %} - {% endif %} -
-
{# end card #} - -
-
- {% if report_data.amplicons|length == 1 %} {# if only one amplicon #} -
Modification lengths
- {% else %} -
Modification lengths for {{amplicon_name}}
- {% endif %} -
    - {% if report_data['figures']['locs'][amplicon_name]['plot_3a'] %} -
  • - -
    • - {% endif %} - {% if report_data['figures']['locs'][amplicon_name]['plot_3b'] %} -
  • - -
    • - {% endif %} -
-
-
-
- {% if report_data['figures']['locs'][amplicon_name]['plot_3a'] %} -
- {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_3a', width='40%', amplicon_name=amplicon_name)}} -
- {% endif %} - - {% if report_data['figures']['locs'][amplicon_name]['plot_3b'] %} -
- {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_3b', width='100%', amplicon_name=amplicon_name)}} -
- {% endif %} -
-
{# end card_body #} -
{# end card #} - -
-
- {% if report_data.amplicons|length == 1 %} {# if only one amplicon #} -
Indel characterization
- {% else %} -
Indel characterization for {{amplicon_name}}
- {% endif %} -
    - {% if report_data['figures']['locs'][amplicon_name]['plot_4a'] %} -
  • - -
    • - {% endif %} - {% if report_data['figures']['locs'][amplicon_name]['plot_4b'] %} -
  • - -
    • - {% endif %} - {% if report_data['figures']['locs'][amplicon_name]['plot_4c'] %} -
  • - -
    • - {% endif %} - {% if report_data['figures']['locs'][amplicon_name]['plot_4d'] %} -
  • - -
    • - {% endif %} - {% if report_data['figures']['locs'][amplicon_name]['plot_4e'] %} -
  • - -
    • - {% endif %} - {% if report_data['figures']['locs'][amplicon_name]['plot_4f'] %} -
  • - -
    • - {% endif %} -
-
{# end card head #} -
-
- {% if report_data['figures']['locs'][amplicon_name]['plot_4a'] %} -
- {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_4a', width='40%', amplicon_name=amplicon_name)}} -
- {% endif %} - {% if report_data['figures']['locs'][amplicon_name]['plot_4b'] %} -
- {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_4b', width='40%', amplicon_name=amplicon_name)}} -
- {% endif %} - {% if report_data['figures']['locs'][amplicon_name]['plot_4c'] %} -
- {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_4c', width='40%', amplicon_name=amplicon_name)}} -
- {% endif %} - - {% if report_data['figures']['locs'][amplicon_name]['plot_4d'] %} -
- {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_4d', width='80%', amplicon_name=amplicon_name)}} -
- {% endif %} - - {% if report_data['figures']['locs'][amplicon_name]['plot_4e'] %} -
- {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_4e', width='40%', amplicon_name=amplicon_name)}} -
- {% endif %} - - {% if report_data['figures']['locs'][amplicon_name]['plot_4f'] %} -
- {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_4f', width='40%', amplicon_name=amplicon_name)}} -
- {% endif %} -
-
{# end card body #} -
{# end card #} - - - {% if report_data['figures']['locs'][amplicon_name]['plot_5'] %} -
-
- {% if report_data.amplicons|length == 1 %} {# if only one amplicon #} -
Frameshift analysis
- {% else %} -
Frameshift analysis for {{amplicon_name}}
- {% endif %} -
-
- {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_5', width='40%', amplicon_name=amplicon_name)}} -
-
- {% endif %} - - {% if report_data['figures']['locs'][amplicon_name]['plot_6'] %} -
-
- {% if report_data.amplicons|length == 1 %} {# if only one amplicon #} -
Frameshift mutagenesis profiles
- {% else %} -
Frameshift mutagenesis profiles for {{amplicon_name}}
- {% endif %} -
-
- {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_6', width='40%', amplicon_name=amplicon_name)}} -
-
- {% endif %} - - {% if report_data['figures']['locs'][amplicon_name]['plot_7'] %} -
-
- {% if report_data.amplicons|length == 1 %} {# if only one amplicon #} -
Non-coding mutations
- {% else %} -
Coding mutations for {{amplicon_name}}
- {% endif %} -
-
- {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_7', width='40%', amplicon_name=amplicon_name)}} -
-
- {% endif %} - - {% if report_data['figures']['locs'][amplicon_name]['plot_8'] %} -
-
- {% if report_data.amplicons|length == 1 %} {# if only one amplicon #} -
Splicing
- {% else %} -
Splicing for {{amplicon_name}}
- {% endif %} -
-
- {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_8', width='40%', amplicon_name=amplicon_name)}} -
-
- {% endif %} - - {% if report_data['figures']['sgRNA_based_names'][amplicon_name] and report_data['figures']['sgRNA_based_names'][amplicon_name]['9']%} -
-
- {% if report_data.amplicons|length == 1 %} {# if only one amplicon #} -
Allele plots
- {% else %} -
Allele plots for {{amplicon_name}}
- {% endif %} -
-
- {% for fig_name in report_data['figures']['sgRNA_based_names'][amplicon_name]['9'] %} -
- {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name=fig_name, width='100%', amplicon_name=amplicon_name)}} -
- {% endfor %} -
-
- {% endif %} - - {% if report_data['figures']['locs'][amplicon_name]['plot_10a'] %} -
-
- {% if report_data.amplicons|length == 1 %} {# if only one amplicon #} -
Base editing
- {% else %} -
Base editing for {{amplicon_name}}
- {% endif %} -
    - {% if report_data['figures']['locs'][amplicon_name]['plot_10a'] %} -
  • - -
    • - {% endif %} - {% if report_data['figures']['sgRNA_based_names'][amplicon_name] and report_data['figures']['sgRNA_based_names'][amplicon_name]['10d']%} -
  • - -
    • - {% endif %} - {% if report_data['figures']['sgRNA_based_names'][amplicon_name] and report_data['figures']['sgRNA_based_names'][amplicon_name]['10e']%} -
  • - -
    • - {% endif %} - {% if report_data['figures']['sgRNA_based_names'][amplicon_name] and report_data['figures']['sgRNA_based_names'][amplicon_name]['10f']%} -
  • - -
    • - {% endif %} -
-
-
-
- {% if report_data['figures']['locs'][amplicon_name]['plot_10c'] %} -
-
- {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_10a', width='80%', amplicon_name=amplicon_name)}} -
-
- - {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_10b', width='50%', amplicon_name=amplicon_name)}} - {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_10c', width='50%', amplicon_name=amplicon_name)}} -
-
- {% else %} -
-
- {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_10a', width='80%', amplicon_name=amplicon_name)}} -
-
- {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_10b', width='50%', amplicon_name=amplicon_name)}} -
-
- {% endif %} - {% if report_data['figures']['sgRNA_based_names'][amplicon_name] and report_data['figures']['sgRNA_based_names'][amplicon_name]['10d']%} -
- {% for fig_name in report_data['figures']['sgRNA_based_names'][amplicon_name]['10d'] %} -
- {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name=fig_name, width='80%', amplicon_name=amplicon_name)}} -
- {% endfor %} -
- {% endif %} - {% if report_data['figures']['sgRNA_based_names'][amplicon_name] and report_data['figures']['sgRNA_based_names'][amplicon_name]['10e']%} -
- {% for fig_name in report_data['figures']['sgRNA_based_names'][amplicon_name]['10e'] %} -
- {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name=fig_name, width='80%', amplicon_name=amplicon_name)}} -
- {% endfor %} -
- {% endif %} - {% if report_data['figures']['sgRNA_based_names'][amplicon_name] and report_data['figures']['sgRNA_based_names'][amplicon_name]['10f']%} -
- {% for fig_name in report_data['figures']['sgRNA_based_names'][amplicon_name]['10f'] %} -
- {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name=fig_name, width='80%', amplicon_name=amplicon_name)}} -
- {% endfor %} - {% for fig_name in report_data['figures']['sgRNA_based_names'][amplicon_name]['10g'] %} -
- {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name=fig_name, width='80%', amplicon_name=amplicon_name)}} -
- {% endfor %} -
- {% endif %} -
-
-
{# end card #} - {% endif %} {# end base editing card #} -
{# end this amplicon tab #} - {% endfor %} -
{# tab content #} -
-
{# jumbotron_content #} -
{# jumbrotron #} -
{# column #} +
+
+
+
+ {% if report_data['report_display_name'] != '' %} +
{{report_data['report_display_name']}}
+ {% endif %} +
CRISPResso2 run information
+
    +
  • + +
    • +
  • + +
    • +
+
+
+
+
+ {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_1a', width='40%')}} +
+ {{ render_partial('shared/partials/log_params.html', report_data=report_data) }} +
+
+
+ +
+
+
Allele assignments
+
    +
  • + +
    • +
  • + +
    • + {% if report_data['figures']['locs']['plot_1d'] %} +
  • + +
    • + {% endif %} +
+
+
+
+
+ {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_1b', width='40%')}} +
+
+ {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_1c', width='40%')}} +
+ {% if report_data['figures']['locs']['plot_1d'] %} +
+ {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_1d', width='40%')}} +
+ {% endif %} +
+
+
{# end card #} + + {# start global coding sequence report #} + {% if report_data['figures']['locs']['plot_5a'] %} +
+
+
Global frameshift analysis
+
+
+ {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_5a', width='40%')}} +
+
+ {% endif %} + + {% if report_data['figures']['locs']['plot_6a'] %} +
+
+
Global frameshift mutagenesis profiles
+
+
+ {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_6a', width='40%')}} +
+
+ {% endif %} + + {% if report_data['figures']['locs']['plot_8a'] %} +
+
+
Global splicing analysis
+
+
+ {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_8a', width='40%')}} +
+
+ {% endif %} + {# end of global coding sequence analysis #} + + {# start hdr summary #} + {% if report_data['figures']['locs'][report_data.amplicons[0]]['plot_4g'] %} +
+
+ {% if report_data.amplicons|length == 1 %} {# if only one amplicon #} +
HDR summary plot
+ {% else %} +
HDR summary report (all reads aligned to {{report_data.amplicons[0]}})
+ {% endif %} +
+
+ {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_4g', width='40%', amplicon_name=report_data.amplicons[0])}} +
+
+ {% endif %} + {# end HDR summary #} + + {# start prime editing report #} + {% if report_data['figures']['locs'][report_data.amplicons[0]]['plot_11a'] %} +
+
+ {% if report_data.amplicons|length == 1 %} {# if only one amplicon #} +
Prime editing report
+ {% else %} +
Prime editing report (all reads aligned to {{report_data.amplicons[0]}})
+ {% endif %} +
+
+ {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_11a', width='40%', amplicon_name=report_data.amplicons[0])}} +
+
+ {% endif %} + + {% if report_data['figures']['sgRNA_based_names'][report_data.amplicons[0]] and report_data['figures']['sgRNA_based_names'][report_data.amplicons[0]]['11b']%} +
+
+ {% if report_data.amplicons|length == 1 %} {# if only one amplicon #} +
Prime editing summary plots at analysis positions
+ {% else %} +
Prime editing summary plots at analysis positions (aligned to {{report_data.amplicons[0]}})
+ {% endif %} +
+
+ {% for fig_name in report_data['figures']['sgRNA_based_names'][report_data.amplicons[0]]['11b'] %} +
+ {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name=fig_name, width='40%', amplicon_name=report_data.amplicons[0])}} +
+ {% endfor %} +
+
+ {% endif %} + {# end plot 11b for prime editing #} + + {% if report_data['figures']['locs']['plot_11c'] %} +
+
+
Scaffold insertions
+
+
+ {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_11c', width='40%')}} +
+
+ {% endif %} + {# end prime editing section #} + + {% if report_data.amplicons|length == 1 %} +
{# if only one amplicon, just a normal div #} + {% else %} + {# If there is more than one amplicon, print a navigation to show each amplicon #} +

Reads are aligned to each amplicon sequence separately. Quantification and visualization of these reads are shown for each amplicon below:

+
+
+
Amplicons
+ +
+ {% endif %} {# end if report contains more than one amplicon #} + + + {% if report_data.amplicons|length == 1 %} {# if only one amplicon, just a normal div #} +
+ {% else %} +
+ {% endif %} + + {% for amplicon_name in report_data.amplicons %} + {% if report_data.amplicons|length == 1 %} {# if only one amplicon, just a normal div #} +
+ {% elif loop.index0 == 0 %} {# if more than one amplicon, and the first, this is the active one #} +
+

Reads aligning to {{amplicon_name}}

{# this bit appears in print mode #} + {% else %} {# otherwise inactive tab #} +
+

Reads aligning to {{amplicon_name}}

{# this bit appears in print mode #} + {% endif %} + +
+
+ {% if report_data.amplicons|length == 1 %} {# if only one amplicon #} +
Nucleotide composition
+ {% else %} +
Nucleotide composition for {{amplicon_name}}
+ {% endif %} +
+
+ {% if report_data['figures']['locs'][amplicon_name]['plot_2a'] %} +
+
+
+ +
+
+
+ +
+ +
+ + {% for (data_label,data_path) in report_data['figures']['datas'][amplicon_name]['plot_2a'] %} +

Data: {{data_label}}

+ {% endfor %} + {% endif %} + + {% if report_data['figures']['sgRNA_based_names'][amplicon_name] and report_data['figures']['sgRNA_based_names'][amplicon_name]['2b']%} + {% for fig_name in report_data['figures']['sgRNA_based_names'][amplicon_name]['2b'] %} + {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name=fig_name, width='80%', amplicon_name=amplicon_name)}} + {% endfor %} + {% endif %} +
+
{# end card #} + +
+
+ {% if report_data.amplicons|length == 1 %} {# if only one amplicon #} +
Modification lengths
+ {% else %} +
Modification lengths for {{amplicon_name}}
+ {% endif %} +
    + {% if report_data['figures']['locs'][amplicon_name]['plot_3a'] %} +
  • + +
    • + {% endif %} + {% if report_data['figures']['locs'][amplicon_name]['plot_3b'] %} +
  • + +
    • + {% endif %} +
+
+
+
+ {% if report_data['figures']['locs'][amplicon_name]['plot_3a'] %} +
+ {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_3a', width='40%', amplicon_name=amplicon_name)}} +
+ {% endif %} + + {% if report_data['figures']['locs'][amplicon_name]['plot_3b'] %} +
+ {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_3b', width='100%', amplicon_name=amplicon_name)}} +
+ {% endif %} +
+
{# end card_body #} +
{# end card #} + +
+
+ {% if report_data.amplicons|length == 1 %} {# if only one amplicon #} +
Indel characterization
+ {% else %} +
Indel characterization for {{amplicon_name}}
+ {% endif %} +
    + {% if report_data['figures']['locs'][amplicon_name]['plot_4a'] %} +
  • + +
    • + {% endif %} + {% if report_data['figures']['locs'][amplicon_name]['plot_4b'] %} +
  • + +
    • + {% endif %} + {% if report_data['figures']['locs'][amplicon_name]['plot_4c'] %} +
  • + +
    • + {% endif %} + {% if report_data['figures']['locs'][amplicon_name]['plot_4d'] %} +
  • + +
    • + {% endif %} + {% if report_data['figures']['locs'][amplicon_name]['plot_4e'] %} +
  • + +
    • + {% endif %} + {% if report_data['figures']['locs'][amplicon_name]['plot_4f'] %} +
  • + +
    • + {% endif %} +
+
{# end card head #} +
+
+ {% if report_data['figures']['locs'][amplicon_name]['plot_4a'] %} +
+ {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_4a', width='40%', amplicon_name=amplicon_name)}} +
+ {% endif %} + {% if report_data['figures']['locs'][amplicon_name]['plot_4b'] %} +
+ {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_4b', width='40%', amplicon_name=amplicon_name)}} +
+ {% endif %} + {% if report_data['figures']['locs'][amplicon_name]['plot_4c'] %} +
+ {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_4c', width='40%', amplicon_name=amplicon_name)}} +
+ {% endif %} + + {% if report_data['figures']['locs'][amplicon_name]['plot_4d'] %} +
+ {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_4d', width='80%', amplicon_name=amplicon_name)}} +
+ {% endif %} + + {% if report_data['figures']['locs'][amplicon_name]['plot_4e'] %} +
+ {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_4e', width='40%', amplicon_name=amplicon_name)}} +
+ {% endif %} + + {% if report_data['figures']['locs'][amplicon_name]['plot_4f'] %} +
+ {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_4f', width='40%', amplicon_name=amplicon_name)}} +
+ {% endif %} +
+
{# end card body #} +
{# end card #} + + + {% if report_data['figures']['locs'][amplicon_name]['plot_5'] %} +
+
+ {% if report_data.amplicons|length == 1 %} {# if only one amplicon #} +
Frameshift analysis
+ {% else %} +
Frameshift analysis for {{amplicon_name}}
+ {% endif %} +
+
+ {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_5', width='40%', amplicon_name=amplicon_name)}} +
+
+ {% endif %} + + {% if report_data['figures']['locs'][amplicon_name]['plot_6'] %} +
+
+ {% if report_data.amplicons|length == 1 %} {# if only one amplicon #} +
Frameshift mutagenesis profiles
+ {% else %} +
Frameshift mutagenesis profiles for {{amplicon_name}}
+ {% endif %} +
+
+ {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_6', width='40%', amplicon_name=amplicon_name)}} +
+
+ {% endif %} + + {% if report_data['figures']['locs'][amplicon_name]['plot_7'] %} +
+
+ {% if report_data.amplicons|length == 1 %} {# if only one amplicon #} +
Non-coding mutations
+ {% else %} +
Coding mutations for {{amplicon_name}}
+ {% endif %} +
+
+ {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_7', width='40%', amplicon_name=amplicon_name)}} +
+
+ {% endif %} + + {% if report_data['figures']['locs'][amplicon_name]['plot_8'] %} +
+
+ {% if report_data.amplicons|length == 1 %} {# if only one amplicon #} +
Splicing
+ {% else %} +
Splicing for {{amplicon_name}}
+ {% endif %} +
+
+ {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_8', width='40%', amplicon_name=amplicon_name)}} +
+
+ {% endif %} + + {% if report_data['figures']['sgRNA_based_names'][amplicon_name] and report_data['figures']['sgRNA_based_names'][amplicon_name]['9']%} +
+
+ {% if report_data.amplicons|length == 1 %} {# if only one amplicon #} +
Allele plots
+ {% else %} +
Allele plots for {{amplicon_name}}
+ {% endif %} +
+
+ {% for fig_name in report_data['figures']['sgRNA_based_names'][amplicon_name]['9'] %} +
+ {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name=fig_name, width='100%', amplicon_name=amplicon_name)}} +
+ {% endfor %} +
+
+ {% endif %} + + {% if report_data['figures']['locs'][amplicon_name]['plot_10a'] %} +
+
+ {% if report_data.amplicons|length == 1 %} {# if only one amplicon #} +
Base editing
+ {% else %} +
Base editing for {{amplicon_name}}
+ {% endif %} +
    + {% if report_data['figures']['locs'][amplicon_name]['plot_10a'] %} +
  • + +
    • + {% endif %} + {% if report_data['figures']['sgRNA_based_names'][amplicon_name] and report_data['figures']['sgRNA_based_names'][amplicon_name]['10d']%} +
  • + +
    • + {% endif %} + {% if report_data['figures']['sgRNA_based_names'][amplicon_name] and report_data['figures']['sgRNA_based_names'][amplicon_name]['10e']%} +
  • + +
    • + {% endif %} + {% if report_data['figures']['sgRNA_based_names'][amplicon_name] and report_data['figures']['sgRNA_based_names'][amplicon_name]['10f']%} +
  • + +
    • + {% endif %} +
+
+
+
+ {% if report_data['figures']['locs'][amplicon_name]['plot_10c'] %} +
+
+ {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_10a', width='80%', amplicon_name=amplicon_name)}} +
+
+ + {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_10b', width='50%', amplicon_name=amplicon_name)}} + {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_10c', width='50%', amplicon_name=amplicon_name)}} +
+
+ {% else %} +
+
+ {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_10a', width='80%', amplicon_name=amplicon_name)}} +
+
+ {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_10b', width='50%', amplicon_name=amplicon_name)}} +
+
+ {% endif %} + {% if report_data['figures']['sgRNA_based_names'][amplicon_name] and report_data['figures']['sgRNA_based_names'][amplicon_name]['10d']%} +
+ {% for fig_name in report_data['figures']['sgRNA_based_names'][amplicon_name]['10d'] %} +
+ {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name=fig_name, width='80%', amplicon_name=amplicon_name)}} +
+ {% endfor %} +
+ {% endif %} + {% if report_data['figures']['sgRNA_based_names'][amplicon_name] and report_data['figures']['sgRNA_based_names'][amplicon_name]['10e']%} +
+ {% for fig_name in report_data['figures']['sgRNA_based_names'][amplicon_name]['10e'] %} +
+ {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name=fig_name, width='80%', amplicon_name=amplicon_name)}} +
+ {% endfor %} +
+ {% endif %} + {% if report_data['figures']['sgRNA_based_names'][amplicon_name] and report_data['figures']['sgRNA_based_names'][amplicon_name]['10f']%} +
+ {% for fig_name in report_data['figures']['sgRNA_based_names'][amplicon_name]['10f'] %} +
+ {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name=fig_name, width='80%', amplicon_name=amplicon_name)}} +
+ {% endfor %} + {% for fig_name in report_data['figures']['sgRNA_based_names'][amplicon_name]['10g'] %} +
+ {{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name=fig_name, width='80%', amplicon_name=amplicon_name)}} +
+ {% endfor %} +
+ {% endif %} +
+
+
{# end card #} + {% endif %} {# end base editing card #} +
{# end this amplicon tab #} + {% endfor %} +
{# tab content #} +
+
{# jumbotron_content #} +
{# jumbrotron #} +
{# column #}
@@ -594,100 +594,100 @@
Base editing for {{amplicon_name}}
{% block foot %} + function updateZoom(e) { + /*prevent any other actions that may occur when moving over the image:*/ + // e.preventDefault(); + var img = e.target.imgObj + var view = e.target.viewObj + var lens = e.target.lensObj + + if (!lens.hasWidthSet) + { + view_height = $('#'+view.id).height() + view_width = $('#'+view.id).width() + img_height = $('#'+img.id).height() + img_width = $('#'+img.id).width() + lens_height = $('#'+lens.id).height() + lens_width = $('#'+lens.id).width() + + new_width = img_height * view_width/view_height //make up for loss of precision + $('#'+lens.id).outerWidth(new_width) + lens.hasWidthSet = true + + cx = view_width / new_width + + view.view_height = view_height + view.view_width = view_width + img.img_height = img_height + img.img_width = img_width + lens.lens_height = lens_height + lens.lens_width = new_width + + } + + var pos, x, y; + /*get the cursor's x and y positions:*/ + pos = getCursorPos(e,img); + /*calculate the position of the lens:*/ + x = pos.x - (lens.lens_width / 2); + /*prevent the lens from being positioned outside the image:*/ + if (x > img.img_width - lens.lens_width) {x = img.img_width - lens.lens_width;; + } + if (x < 0) {x = 0;} + lens.style.left = x + "px"; + view.style.backgroundPosition = "-" + (x * cx) + "px 0px"; + } + + function getCursorPos(e,img) { + var a, x = 0, y = 0; + e = e || window.event; + /*get the x and y positions of the image:*/ + a = img.getBoundingClientRect(); + /*calculate the cursor's x and y coordinates, relative to the image:*/ + x = e.pageX - a.left; + y = e.pageY - a.top; + /*consider any page scrolling:*/ + x = x - window.pageXOffset; + y = y - window.pageYOffset; + return {x : x, y : y}; + } + + var passiveSupported = false; + try { + var options = { + get passive() { // This function will be called when the browser + // attempts to access the passive property. + passiveSupported = true; + } + }; + + window.addEventListener("test", options, options); + window.removeEventListener("test", options, options); + } catch(err) { + passiveSupported = false; + } + + {% for amplicon_name in report_data.amplicons %} + {% if report_data['figures']['locs'][amplicon_name]['plot_2a'] %} + view = document.getElementById('zoomview_nucs_{{amplicon_name}}'); + img = document.getElementById('tozoom_nucs_{{amplicon_name}}'); + lens = document.getElementById('zoomlens_nucs_{{amplicon_name}}') + + img.viewObj = view + img.lensObj = lens + img.imgObj = img + + lens.viewObj = view + lens.lensObj = lens + lens.imgObj = img + + lens.addEventListener("mousemove", updateZoom, passiveSupported? { passive: true } : false); + img.addEventListener("mousemove", updateZoom, passiveSupported? { passive: true } : false); + /*and also for touch screens:*/ + lens.addEventListener("touchmove", updateZoom, passiveSupported? { passive: true } : false); + img.addEventListener("touchmove", updateZoom, passiveSupported? { passive: true } : false); + + {% endif %} + {% endfor %} + {% endblock %} From e80a13932ef1651db312ee4d0cf31290dbc8df6f Mon Sep 17 00:00:00 2001 From: Samuel Nichols Date: Tue, 4 Oct 2022 10:36:52 -0600 Subject: [PATCH 23/33] Indentation and parenthesis --- templates/batchReport.html | 2 +- templates/layout.html | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/templates/batchReport.html b/templates/batchReport.html index cb9d4aa0..58a41e97 100644 --- a/templates/batchReport.html +++ b/templates/batchReport.html @@ -148,7 +148,7 @@
{{report_data['titles'][plot_name]}}
{# data bit for web version: #} {# -

Data: {{data_label}}

+

Data: {{data_label}}

#} {# jumbotron_content #} {# jumbrotron #} diff --git a/templates/layout.html b/templates/layout.html index 16551f22..b74ab9bc 100644 --- a/templates/layout.html +++ b/templates/layout.html @@ -113,7 +113,7 @@ {% endif %} {# if default user (normal crispresso mode) #} - {% if current_user == null or not current_user.is_anonymous and current_user.username == "DEFAULTUSER" %} + {% if current_user == null or (not current_user.is_anonymous and current_user.username == "DEFAULTUSER") %}
From dcf739175ff8db098d63b9b000afd0bdb59e6dff Mon Sep 17 00:00:00 2001 From: Samuel Nichols Date: Mon, 6 Feb 2023 16:24:45 -0700 Subject: [PATCH 24/33] Adding styling for print-only and screen only --- templates/layout.html | 14 +++- templates/report.html | 96 ++++++++++++++--------- templates/shared/partials/log_params.html | 16 +++- 3 files changed, 86 insertions(+), 40 deletions(-) diff --git a/templates/layout.html b/templates/layout.html index dba520de..4a10539a 100644 --- a/templates/layout.html +++ b/templates/layout.html @@ -66,6 +66,16 @@ display:none } } + + @media screen + { + .print-only{ + display: none !important; + } + .screen-only{ + display: block; + } + } @@ -197,9 +207,9 @@

Analysis of genome editing ou {% if current_user is defined and (not current_user.is_anonymous and current_user.username == "DEFAULTUSER") %}
-