From 7c6dfcd30cdcfc43a159d2f3d506f8ed5a67c2d3 Mon Sep 17 00:00:00 2001 From: Samuel Nichols Date: Tue, 13 Sep 2022 11:01:52 -0600 Subject: [PATCH] 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 %}