From 3fb59cff66e4f8082c46f4d8594e4abf5b277333 Mon Sep 17 00:00:00 2001 From: Samuel Nichols Date: Mon, 14 Aug 2023 14:35:27 -0600 Subject: [PATCH 1/6] Reports, add reports to packages, colors, ordered pandas sort (#28) * Sort by #Reads instead of %Reads to avoid floating point errors * Fix x-axis spacing on some reports * Add break to header matching loop to prevent match statements being printed after failure * Check all headers and only error if there are unmatched values * Fix indent * Remove missing_header variable * Fix tick marks * Squashed 'CRISPResso2/CRISPRessoReports/' changes from 7d9b4e5..e18807d * X-axis tick fix on fig 6a * Fix function name from styles to config * Squashed 'CRISPResso2/CRISPRessoReports/' changes from e18807d..e9da7bf git-subtree-dir: CRISPResso2/CRISPRessoReports git-subtree-split: e9da7bff794058e1fcdb3dc9ced79871c6a30e18 * Add CRISPRessoReports to packages * Colors only with pro --- CRISPResso2/CRISPRessoAggregateCORE.py | 2 +- CRISPResso2/CRISPRessoBatchCORE.py | 9 +- CRISPResso2/CRISPRessoCORE.py | 33 +- CRISPResso2/CRISPRessoCompareCORE.py | 2 +- CRISPResso2/CRISPRessoMetaCORE.py | 2 +- CRISPResso2/CRISPRessoPlot.py | 110 ++- CRISPResso2/CRISPRessoPooledCORE.py | 16 +- CRISPResso2/CRISPRessoPooledWGSCompareCORE.py | 2 +- .../.github/workflows/.pylintrc | 7 + .../.github/workflows/pylint.yml | 26 + .../CRISPRessoReport.py | 345 ++++--- CRISPResso2/CRISPRessoReports/README.md | 50 + CRISPResso2/CRISPRessoReports/__init__.py | 0 .../templates/CRISPResso_justcup.png | Bin .../templates/batchReport.html | 163 ++++ .../templates/favicon.ico | Bin .../CRISPRessoReports/templates/layout.html | 238 +++++ .../templates/multiReport.html | 52 +- .../templates/pooledReport.html | 101 +++ .../CRISPRessoReports/templates/report.html | 720 +++++++++++++++ .../shared/partials/fig_reports.html | 35 + .../shared/partials/fig_summaries.html | 15 + .../templates/shared/partials/log_params.html | 23 + .../templates/wgsReport.html | 99 ++ CRISPResso2/CRISPRessoShared.py | 89 +- CRISPResso2/CRISPRessoWGSCORE.py | 2 +- CRISPResso2/default_style.json | 13 + CRISPResso2/templates/layout.html | 104 --- CRISPResso2/templates/report.html | 854 ------------------ MANIFEST.in | 2 +- setup.py | 3 +- 31 files changed, 1919 insertions(+), 1198 deletions(-) create mode 100644 CRISPResso2/CRISPRessoReports/.github/workflows/.pylintrc create mode 100644 CRISPResso2/CRISPRessoReports/.github/workflows/pylint.yml rename CRISPResso2/{ => CRISPRessoReports}/CRISPRessoReport.py (70%) create mode 100644 CRISPResso2/CRISPRessoReports/README.md create mode 100644 CRISPResso2/CRISPRessoReports/__init__.py rename CRISPResso2/{ => CRISPRessoReports}/templates/CRISPResso_justcup.png (100%) create mode 100644 CRISPResso2/CRISPRessoReports/templates/batchReport.html rename CRISPResso2/{ => CRISPRessoReports}/templates/favicon.ico (100%) create mode 100644 CRISPResso2/CRISPRessoReports/templates/layout.html rename CRISPResso2/{ => CRISPRessoReports}/templates/multiReport.html (75%) create mode 100644 CRISPResso2/CRISPRessoReports/templates/pooledReport.html create mode 100644 CRISPResso2/CRISPRessoReports/templates/report.html create mode 100644 CRISPResso2/CRISPRessoReports/templates/shared/partials/fig_reports.html create mode 100644 CRISPResso2/CRISPRessoReports/templates/shared/partials/fig_summaries.html create mode 100644 CRISPResso2/CRISPRessoReports/templates/shared/partials/log_params.html create mode 100644 CRISPResso2/CRISPRessoReports/templates/wgsReport.html create mode 100644 CRISPResso2/default_style.json delete mode 100644 CRISPResso2/templates/layout.html delete mode 100644 CRISPResso2/templates/report.html diff --git a/CRISPResso2/CRISPRessoAggregateCORE.py b/CRISPResso2/CRISPRessoAggregateCORE.py index 748a0794..689bef98 100644 --- a/CRISPResso2/CRISPRessoAggregateCORE.py +++ b/CRISPResso2/CRISPRessoAggregateCORE.py @@ -18,7 +18,7 @@ from datetime import datetime from CRISPResso2 import CRISPRessoShared from CRISPResso2 import CRISPRessoPlot -from CRISPResso2 import CRISPRessoReport +from CRISPResso2.CRISPRessoReports import CRISPRessoReport from CRISPResso2.CRISPRessoMultiProcessing import get_max_processes, run_plot diff --git a/CRISPResso2/CRISPRessoBatchCORE.py b/CRISPResso2/CRISPRessoBatchCORE.py index c265a9d1..b6c51c2d 100644 --- a/CRISPResso2/CRISPRessoBatchCORE.py +++ b/CRISPResso2/CRISPRessoBatchCORE.py @@ -16,7 +16,7 @@ from CRISPResso2 import CRISPRessoShared from CRISPResso2 import CRISPRessoPlot from CRISPResso2 import CRISPRessoMultiProcessing -from CRISPResso2 import CRISPRessoReport +from CRISPResso2.CRISPRessoReports import CRISPRessoReport import logging @@ -91,6 +91,7 @@ def main(): crispresso_options_for_batch = list(crispresso_options-options_to_ignore) CRISPRessoShared.check_file(args.batch_settings) + config = CRISPRessoShared.check_custom_config(args) if args.zip_output and not args.place_report_in_output_folder: warn('Invalid arguement combination: If zip_output is True then place_report_in_output_folder must also be True. Setting place_report_in_output_folder to True.') @@ -596,6 +597,7 @@ def main(): 'save_also_png': save_png, 'sgRNA_intervals': sub_sgRNA_intervals, 'quantification_window_idxs': include_idxs, + 'custom_colors': config['colors'], } debug('Plotting nucleotide percentage quilt for amplicon {0}, sgRNA {1}'.format(amplicon_name, sgRNA)) plot( @@ -620,6 +622,7 @@ def main(): 'save_also_png': save_png, 'sgRNA_intervals': sub_sgRNA_intervals, 'quantification_window_idxs': include_idxs, + 'custom_colors': config['colors'] } debug('Plotting nucleotide conversion map for amplicon {0}, sgRNA {1}'.format(amplicon_name, sgRNA)) plot( @@ -646,6 +649,7 @@ def main(): 'save_also_png': save_png, 'sgRNA_intervals': consensus_sgRNA_intervals, 'quantification_window_idxs': include_idxs, + 'custom_colors': config['colors'], } debug('Plotting nucleotide quilt for {0}'.format(amplicon_name)) plot( @@ -669,6 +673,7 @@ def main(): 'save_also_png': save_png, 'sgRNA_intervals': consensus_sgRNA_intervals, 'quantification_window_idxs': include_idxs, + 'custom_colors': config['colors'] } debug('Plotting nucleotide conversion map for {0}'.format(amplicon_name)) plot( @@ -692,6 +697,7 @@ def main(): 'mod_pct_df': modification_percentage_summary_df, 'fig_filename_root': this_nuc_pct_quilt_plot_name, 'save_also_png': save_png, + 'custom_colors': config['colors'], } debug('Plotting nucleotide quilt for {0}'.format(amplicon_name)) plot( @@ -710,6 +716,7 @@ def main(): 'conversion_nuc_from': args.conversion_nuc_from, 'conversion_nuc_to': args.conversion_nuc_to, 'save_also_png': save_png, + 'custom_colors': config['colors'] } debug('Plotting BE nucleotide conversion map for {0}'.format(amplicon_name)) plot( diff --git a/CRISPResso2/CRISPRessoCORE.py b/CRISPResso2/CRISPRessoCORE.py index 8377978d..1f5374fb 100644 --- a/CRISPResso2/CRISPRessoCORE.py +++ b/CRISPResso2/CRISPRessoCORE.py @@ -28,7 +28,7 @@ from CRISPResso2 import CRISPRessoCOREResources -from CRISPResso2 import CRISPRessoReport +from CRISPResso2.CRISPRessoReports import CRISPRessoReport from CRISPResso2 import CRISPRessoShared from CRISPResso2 import CRISPRessoPlot from CRISPResso2 import CRISPResso2Align @@ -3363,6 +3363,7 @@ def save_count_vectors_to_file(vectors, vectorNames, refSeq, filename): info('Making Plots...') ############################################################################################################################################### save_png = True + config = CRISPRessoShared.check_custom_config(args) if args.suppress_report: save_png = False @@ -3407,6 +3408,7 @@ def count_alternate_alleles(sub_base_vectors, ref_name, ref_sequence, ref_total_ else: process_pool = None process_futures = None + plot = partial( CRISPRessoMultiProcessing.run_plot, num_processes=n_processes, @@ -3592,6 +3594,7 @@ def count_alternate_alleles(sub_base_vectors, ref_name, ref_sequence, ref_total_ 'sgRNA_names': sgRNA_names, 'sgRNA_mismatches': sgRNA_mismatches, 'quantification_window_idxs': include_idxs_list, + 'custom_colors': config["colors"], } debug('Plotting nucleotide quilt across amplicon') plot(CRISPRessoPlot.plot_nucleotide_quilt, plot_2a_input) @@ -3638,6 +3641,7 @@ def count_alternate_alleles(sub_base_vectors, ref_name, ref_sequence, ref_total_ 'sgRNA_names': sgRNA_names, 'sgRNA_mismatches': sgRNA_mismatches, 'quantification_window_idxs': new_include_idx, + 'custom_colors': config["colors"], } debug('Plotting nucleotide distribuition around {0} for {1}'.format(sgRNA_legend, ref_name)) plot(CRISPRessoPlot.plot_nucleotide_quilt, plot_2b_input) @@ -3815,6 +3819,7 @@ def count_alternate_alleles(sub_base_vectors, ref_name, ref_sequence, ref_total_ ), }, 'plot_root': plot_root, + 'custom_colors': config["colors"], 'save_also_png': save_png, } debug('Plotting amplication modifications for {0}'.format(ref_name)) @@ -3844,12 +3849,13 @@ def count_alternate_alleles(sub_base_vectors, ref_name, ref_sequence, ref_total_ 'Mutation position distribution', ref_name, ), 'plot_root': plot_root, + 'custom_colors': config["colors"], 'save_also_png': save_png, } debug('Plotting modification frequency for {0}'.format(ref_name)) plot(CRISPRessoPlot.plot_modification_frequency, plot_4b_input) crispresso2_info['results']['refs'][ref_name]['plot_4b_root'] = os.path.basename(plot_root) - crispresso2_info['results']['refs'][ref_name]['plot_4b_caption'] = "Figure 4b: Frequency of insertions (red), deletions (purple), and substitutions (green) across the entire amplicon, including modifications outside of the quantification window." + crispresso2_info['results']['refs'][ref_name]['plot_4b_caption'] = "Figure 4b: Frequency of insertions, deletions, and substitutions across the entire amplicon, including modifications outside of the quantification window." crispresso2_info['results']['refs'][ref_name]['plot_4b_data'] = [('Modification frequency', os.path.basename(mod_count_filename))] plot_root = _jp( @@ -3872,6 +3878,7 @@ def count_alternate_alleles(sub_base_vectors, ref_name, ref_sequence, ref_total_ ), 'ref_name': ref_name, 'plot_root': plot_root, + 'custom_colors': config["colors"], 'save_also_png': save_png, } debug('Plotting quantification window locations for {0}'.format(ref_name)) @@ -3880,7 +3887,7 @@ def count_alternate_alleles(sub_base_vectors, ref_name, ref_sequence, ref_total_ plot_4c_input, ) crispresso2_info['results']['refs'][ref_name]['plot_4c_root'] = os.path.basename(plot_root) - crispresso2_info['results']['refs'][ref_name]['plot_4c_caption'] = "Figure 4c: Frequency of insertions (red), deletions (purple), and substitutions (green) across the entire amplicon, considering only modifications that overlap with the quantification window." + crispresso2_info['results']['refs'][ref_name]['plot_4c_caption'] = "Figure 4c: Frequency of insertions, deletions, and substitutions across the entire amplicon, considering only modifications that overlap with the quantification window." crispresso2_info['results']['refs'][ref_name]['plot_4c_data'] = [('Modification frequency in quantification window', os.path.basename(quant_window_mod_count_filename))] #Position dependent indels plot @@ -3928,6 +3935,7 @@ def count_alternate_alleles(sub_base_vectors, ref_name, ref_sequence, ref_total_ 'n_total': N_TOTAL, 'ref_len': ref_len, 'ref_name': ref_names[0], + 'custom_colors': config["colors"], 'save_also_png': save_png, } if ref_name == ref_names[0]: @@ -3997,6 +4005,7 @@ def count_alternate_alleles(sub_base_vectors, ref_name, ref_sequence, ref_total_ 'quantification_window_idxs': include_idxs_list, 'sgRNA_names': sgRNA_names, 'sgRNA_mismatches': sgRNA_mismatches, + 'custom_colors': config["colors"], } debug('Plotting HDR nucleotide quilt') plot(CRISPRessoPlot.plot_nucleotide_quilt, plot_4g_input) @@ -4097,12 +4106,13 @@ def count_alternate_alleles(sub_base_vectors, ref_name, ref_sequence, ref_total_ ref_name, ), 'plot_root': plot_root, + 'custom_colors': config["colors"], 'save_also_png': save_png, } debug('Plotting non-coding mutation positions for {0}'.format(ref_name)) plot(CRISPRessoPlot.plot_non_coding_mutations, plot_7_input) crispresso2_info['results']['refs'][ref_name]['plot_7_root'] = os.path.basename(plot_root) - crispresso2_info['results']['refs'][ref_name]['plot_7_caption'] = "Figure 7: Reads with insertions (red), deletions (purple), and substitutions (green) mapped to reference amplicon position exclusively in noncoding region/s (that is, without mutations affecting coding sequences). The predicted cleavage site is indicated by a vertical dashed line. Only sequence positions directly adjacent to insertions or directly affected by deletions or substitutions are plotted." + crispresso2_info['results']['refs'][ref_name]['plot_7_caption'] = "Figure 7: Reads with insertions, deletions, and substitutions mapped to reference amplicon position exclusively in noncoding region/s (that is, without mutations affecting coding sequences). The predicted cleavage site is indicated by a vertical dashed line. Only sequence positions directly adjacent to insertions or directly affected by deletions or substitutions are plotted." crispresso2_info['results']['refs'][ref_name]['plot_7_data'] = [] plot_root = _jp('8.'+ref_plot_name+'Potential_splice_sites_pie_chart') @@ -4136,6 +4146,7 @@ def count_alternate_alleles(sub_base_vectors, ref_name, ref_sequence, ref_total_ 'fig_filename_root': fig_filename_root, 'save_also_png': save_png, 'quantification_window_idxs': include_idxs_list, + 'custom_colors': config['colors'] } debug('Plotting substitutions across reference for {0}'.format(ref_name)) plot(CRISPRessoPlot.plot_subs_across_ref, plot_10a_input) @@ -4153,7 +4164,8 @@ def count_alternate_alleles(sub_base_vectors, ref_name, ref_sequence, ref_total_ 'Substitution frequency\nin entire amplicon', ref_name, ), 'fig_filename_root': fig_filename_root, - 'save_also_png': save_png + 'save_also_png': save_png, + 'custom_colors': config['colors'] } debug('Plotting substitution frequency barplot for {0}'.format(ref_name)) plot(CRISPRessoPlot.plot_sub_freqs, plot_10b_input) @@ -4167,7 +4179,8 @@ def count_alternate_alleles(sub_base_vectors, ref_name, ref_sequence, ref_total_ 'alt_nuc_counts': alt_nuc_counts, 'plot_title': get_plot_title_with_ref_name('Substitution frequency\nin quantification window', ref_name), 'fig_filename_root': fig_filename_root, - 'save_also_png': save_png + 'save_also_png': save_png, + 'custom_colors': config['colors'] } debug('Plotting substitution frequency barplot in quantification window for {0}'.format(ref_name)) plot(CRISPRessoPlot.plot_sub_freqs, plot_10c_input) @@ -4258,6 +4271,7 @@ def count_alternate_alleles(sub_base_vectors, ref_name, ref_sequence, ref_total_ 'sgRNA_names': sgRNA_names, 'sgRNA_mismatches': sgRNA_mismatches, 'annotate_wildtype_allele': args.annotate_wildtype_allele, + 'custom_colors': config["colors"], } debug('Plotting allele distribution around cut for {0}'.format(ref_name)) plot(CRISPRessoPlot.plot_alleles_table, plot_9_input) @@ -4344,6 +4358,7 @@ def count_alternate_alleles(sub_base_vectors, ref_name, ref_sequence, ref_total_ 'conversion_nuc_from': args.conversion_nuc_from, 'fig_filename_root': fig_filename_root, 'save_also_png': save_png, + 'custom_colors': config['colors'], } debug('Plotting conversion at {0}s around the {1} for {2}'.format(args.conversion_nuc_from, sgRNA_legend, ref_name)) plot( @@ -4363,6 +4378,7 @@ def count_alternate_alleles(sub_base_vectors, ref_name, ref_sequence, ref_total_ 'conversion_nuc_from': args.conversion_nuc_from, 'fig_filename_root': fig_filename_root, 'save_also_png': save_png, + 'custom_colors': config['colors'] } debug('Plotting non-reference conversion at {0}s around the {1} for {2}'.format(args.conversion_nuc_from, sgRNA_legend, ref_name)) plot( @@ -4384,7 +4400,8 @@ def count_alternate_alleles(sub_base_vectors, ref_name, ref_sequence, ref_total_ ), 'conversion_nuc_from': args.conversion_nuc_from, 'fig_filename_root': fig_filename_root, - 'save_also_png': save_png + 'save_also_png': save_png, + 'custom_colors': config['colors'] } debug('Plotting scaled non-reference conversion at {0}s around the {1} for {2}'.format(args.conversion_nuc_from, sgRNA_legend, ref_name)) plot( @@ -4576,6 +4593,7 @@ def get_scaffold_len(row, scaffold_start_loc, scaffold_seq): 'sgRNA_names': sgRNA_names, 'sgRNA_mismatches': sgRNA_mismatches, 'quantification_window_idxs': include_idxs_list, + 'custom_colors': config['colors'] } info('Plotting prime editing nucleotide percentage quilt', {'percent_complete': 96}) plot(CRISPRessoPlot.plot_nucleotide_quilt, plot_11a_input) @@ -4634,6 +4652,7 @@ def get_scaffold_len(row, scaffold_start_loc, scaffold_seq): 'sgRNA_names': sgRNA_names, 'sgRNA_mismatches': sgRNA_mismatches, 'quantification_window_idxs': new_include_idx, + 'custom_colors': config['colors'] } info('Plotting nucleotide quilt', {'percent_complete': 97}) plot(CRISPRessoPlot.plot_nucleotide_quilt, plot_11b_input) diff --git a/CRISPResso2/CRISPRessoCompareCORE.py b/CRISPResso2/CRISPRessoCompareCORE.py index 64c77c53..fa3e0f7f 100644 --- a/CRISPResso2/CRISPRessoCompareCORE.py +++ b/CRISPResso2/CRISPRessoCompareCORE.py @@ -11,7 +11,7 @@ import argparse from CRISPResso2 import CRISPRessoShared from CRISPResso2 import CRISPRessoPlot -from CRISPResso2 import CRISPRessoReport +from CRISPResso2.CRISPRessoReports import CRISPRessoReport import logging diff --git a/CRISPResso2/CRISPRessoMetaCORE.py b/CRISPResso2/CRISPRessoMetaCORE.py index 87235ab6..40695b66 100644 --- a/CRISPResso2/CRISPRessoMetaCORE.py +++ b/CRISPResso2/CRISPRessoMetaCORE.py @@ -15,7 +15,7 @@ from CRISPResso2 import CRISPRessoShared from CRISPResso2 import CRISPRessoPlot from CRISPResso2 import CRISPRessoMultiProcessing -from CRISPResso2 import CRISPRessoReport +from CRISPResso2.CRISPRessoReports import CRISPRessoReport import logging diff --git a/CRISPResso2/CRISPRessoPlot.py b/CRISPResso2/CRISPRessoPlot.py index 6ac35e86..c4287c64 100644 --- a/CRISPResso2/CRISPRessoPlot.py +++ b/CRISPResso2/CRISPRessoPlot.py @@ -72,13 +72,30 @@ def get_nuc_color(nuc, alpha): return (charSum, (1-charSum), (2*charSum*(1-charSum))) -def get_color_lookup(nucs, alpha): - colorLookup = {} - for nuc in nucs: - colorLookup[nuc] = get_nuc_color(nuc, alpha) - return colorLookup +def get_color_lookup(nucs, alpha, custom_colors=None): + if custom_colors is None: + colorLookup = {} + for nuc in nucs: + colorLookup[nuc] = get_nuc_color(nuc, alpha) + return colorLookup + else: + get_color = lambda x, y, z: (x / 255.0, y / 255.0, z / 255.0, alpha) + colors = {} + for nuc in nucs: + if nuc == 'INS': + rgb = (193, 129, 114) + else: + rgb = hex_to_rgb(custom_colors[nuc]) + colors[nuc] = get_color(rgb[0], rgb[1], rgb[2]) + return colors + -def plot_nucleotide_quilt(nuc_pct_df,mod_pct_df,fig_filename_root,save_also_png=False,sgRNA_intervals=None,min_text_pct=0.5,max_text_pct=0.95,quantification_window_idxs=None,sgRNA_names=None,sgRNA_mismatches=None,shade_unchanged=True,group_column='Batch'): +def hex_to_rgb(value): + value = value.lstrip('#') + lv = len(value) + return tuple(int(value[i:i + lv // 3], 16) for i in range(0, lv, lv // 3)) + +def plot_nucleotide_quilt(nuc_pct_df,mod_pct_df,fig_filename_root, custom_colors, save_also_png=False,sgRNA_intervals=None,min_text_pct=0.5,max_text_pct=0.95,quantification_window_idxs=None,sgRNA_names=None,sgRNA_mismatches=None,shade_unchanged=True,group_column='Batch'): """ Plots a nucleotide quilt with each square showing the percentage of each base at that position in the reference nuc_pct_df: dataframe with percents of each base (ACTGN-) at each position @@ -111,8 +128,9 @@ def plot_nucleotide_quilt(nuc_pct_df,mod_pct_df,fig_filename_root,save_also_png= samplesList.append(nuc_pct_df.iloc[sample_row_start, 0]) # make a color map of fixed colors - color_lookup = get_color_lookup(['A', 'T', 'C', 'G', 'N', 'INS', '-'], alpha=1) - unchanged_color_lookup = get_color_lookup(['A', 'T', 'C', 'G', 'N', 'INS', '-'], alpha=0.3) + color_lookup = get_color_lookup(['A', 'T', 'C', 'G', 'N', 'INS', '-'], alpha=1, custom_colors=custom_colors) + unchanged_color_lookup = get_color_lookup(['A', 'T', 'C', 'G', 'N', 'INS', '-'], alpha=0.3, + custom_colors=custom_colors) #fig = plt.figure(figsize=(amp_len/2.0,nSamples*2)) #fig = plt.figure(figsize=(amp_len,nSamples)) @@ -497,6 +515,7 @@ def plot_amplicon_modifications( y_max, plot_titles, plot_root, + custom_colors, save_also_png=False, ): fig, ax = plt.subplots(figsize=(10, 10)) @@ -535,9 +554,9 @@ def plot_amplicon_modifications( ax.plot( all_indelsub_count_vectors, - 'r', lw=3, label=plot_titles['combined'], + color=custom_colors['Deletion'] ) if cut_points: @@ -648,6 +667,7 @@ def plot_modification_frequency( y_max, plot_title, plot_root, + custom_colors, save_also_png=False, ): fig, ax = plt.subplots(figsize=(10, 10)) @@ -685,13 +705,13 @@ def plot_modification_frequency( ax.add_patch(p) ax.plot( - all_insertion_count_vectors, 'r', lw=3, label='Insertions', + all_insertion_count_vectors, lw=3, label='Insertions', color=custom_colors['Insertion'] ) ax.plot( - all_deletion_count_vectors, 'm', lw=3, label='Deletions', + all_deletion_count_vectors, lw=3, label='Deletions', color=custom_colors['Deletion'] ) ax.plot( - all_substitution_count_vectors, 'g', lw=3, label='Substitutions', + all_substitution_count_vectors, lw=3, label='Substitutions', color=custom_colors['Substitution'] ) y_max = max( @@ -816,6 +836,7 @@ def plot_quantification_window_locations( ref_name, plot_title, plot_root, + custom_colors, save_also_png, ): fig, ax = plt.subplots(figsize=(10, 10)) @@ -859,11 +880,9 @@ def plot_quantification_window_locations( ) ax.add_patch(p) - ax.plot(insertion_count_vectors, 'r', linewidth=3, label='Insertions') - ax.plot(deletion_count_vectors, 'm', linewidth=3, label='Deletions') - ax.plot( - substitution_count_vectors, 'g', linewidth=3, label='Substitutions', - ) + ax.plot(insertion_count_vectors, linewidth=3, label='Insertions', color=custom_colors['Insertion']) + ax.plot(deletion_count_vectors, linewidth=3, label='Deletions', color=custom_colors['Deletion']) + ax.plot(substitution_count_vectors, linewidth=3, label='Substitutions', color=custom_colors['Substitution']) if cut_points: added_legend = False @@ -1089,6 +1108,7 @@ def plot_global_modifications_reference( ref_name, plot_title, plot_root, + custom_colors, save_also_png=False, ): fig, ax = plt.subplots(figsize=(10, 10)) @@ -1103,13 +1123,13 @@ def plot_global_modifications_reference( 1, ) * 1.1 - ax.plot(ref1_all_insertion_positions, 'r', linewidth=3, label='Insertions') - ax.plot(ref1_all_deletion_positions, 'm', linewidth=3, label='Deletions') + ax.plot(ref1_all_insertion_positions, linewidth=3, label='Insertions', color=custom_colors['Insertion']) + ax.plot(ref1_all_deletion_positions, linewidth=3, label='Deletions', color=custom_colors['Deletion']) ax.plot( ref1_all_substitution_positions, - 'g', linewidth=3, label='Substitutions', + color=custom_colors['Substitution'] ) ref1_cut_points = ref1['sgRNA_cut_points'] @@ -1405,10 +1425,10 @@ def plot_frameshift_frequency( ax1.bar(x - 0.1, y) ax1.set_xlim(-30.5, 30.5) ax1.set_frame_on(False) - ax1.set_xticks([idx for idx in range(-30, 31) if idx % 3]) + ax1.set_xticks([idx for idx in range(-30, 31) if idx % 3 == 0]) ax1.tick_params( which='both', # both major and minor ticks are affected - bottom=False, # ticks along the bottom edge are off + bottom=True, # ticks along the bottom edge are off top=False, # ticks along the top edge are off labelbottom=True, # labels along the bottom edge are off ) @@ -1416,7 +1436,7 @@ def plot_frameshift_frequency( xmin, xmax = ax1.get_xaxis().get_view_interval() ymin, ymax = ax1.get_yaxis().get_view_interval() ax1.set_xticklabels( - map(str, [idx for idx in range(-30, 31) if idx % 3]), + map(str, [idx for idx in range(-30, 31) if idx % 3 == 0]), rotation='vertical', ) ax1.set_title(plot_titles['fs']) @@ -1448,7 +1468,7 @@ def plot_frameshift_frequency( ax2.set_xticks([idx for idx in range(-30, 31) if (idx % 3 == 0)]) ax2.tick_params( which='both', # both major and minor ticks are affected - bottom=False, # ticks along the bottom edge are off + bottom=True, # ticks along the bottom edge are off top=False, # ticks along the top edge are off labelbottom=True, # labels along the bottom edge are off ) @@ -1536,10 +1556,11 @@ def plot_global_frameshift_in_frame_mutations( ax1.bar(x - 0.1, y) ax1.set_xlim(-30.5, 30.5) ax1.set_frame_on(False) - ax1.set_xticks([idx for idx in range(-30, 31) if idx % 3]) + ax1.set_xticks([idx for idx in range(-30, 31) if idx % 3 == 0]) ax1.tick_params( which='both', # both major and minor ticks are affected - bottom=False, # ticks along the bottom edge are off + left=True, + bottom=True, # ticks along the bottom edge are off top=False, # ticks along the top edge are off labelbottom=True, # labels along the bottom edge are off ) @@ -1547,7 +1568,7 @@ def plot_global_frameshift_in_frame_mutations( xmin, xmax = ax1.get_xaxis().get_view_interval() ymin, ymax = ax1.get_yaxis().get_view_interval() ax1.set_xticklabels( - map(str, [idx for idx in range(-30, 31) if idx % 3]), + map(str, [idx for idx in range(-30, 31) if idx % 3 == 0]), rotation='vertical', ) ax1.set_title('Global Frameshift profile') @@ -1659,26 +1680,27 @@ def plot_non_coding_mutations( sgRNA_intervals, plot_title, plot_root, + custom_colors, save_also_png=False, ): fig, ax = plt.subplots(figsize=(10, 10)) ax.plot( insertion_count_vectors_noncoding, - 'r', linewidth=3, label='Insertions', + color=custom_colors['Insertion'] ) ax.plot( deletion_count_vectors_noncoding, - 'm', linewidth=3, label='Deletions', + color=custom_colors['Deletion'] ) ax.plot( substitution_count_vectors_noncoding, - 'g', linewidth=3, label='Substitutions', + color=custom_colors['Substitution'] ) y_max = max( @@ -1974,7 +1996,7 @@ def add_sgRNA_to_ax(ax,sgRNA_intervals,sgRNA_y_start,sgRNA_y_height,amp_len,x_of else: ax.text(x_offset+min_sgRNA_x, this_sgRNA_y_start + this_sgRNA_y_height/2, 'sgRNA ', horizontalalignment='right', verticalalignment='center', fontsize=font_size) -def plot_conversion_map(nuc_pct_df,fig_filename_root,conversion_nuc_from,conversion_nuc_to,save_also_png,plotPct = 0.9,min_text_pct=0.3,max_text_pct=0.9,conversion_scale_max=None,sgRNA_intervals=None,quantification_window_idxs=None,sgRNA_names=None,sgRNA_mismatches=None): +def plot_conversion_map(nuc_pct_df,fig_filename_root,conversion_nuc_from,conversion_nuc_to,save_also_png,custom_colors,plotPct = 0.9,min_text_pct=0.3,max_text_pct=0.9,conversion_scale_max=None,sgRNA_intervals=None,quantification_window_idxs=None,sgRNA_names=None,sgRNA_mismatches=None): """ Plots a heatmap of conversion across several sequences :param nuc_pct_df combined df of multiple batches @@ -2034,7 +2056,9 @@ def plot_conversion_map(nuc_pct_df,fig_filename_root,conversion_nuc_from,convers plt.clf() # make a color map of fixed colors (for coloring reference in this example) - color_lookup = get_color_lookup(['A', 'T', 'C', 'G'], alpha=1) + color_lookup = get_color_lookup(['A', 'T', 'C', 'G', 'N', 'INS', '-'], alpha=1, custom_colors=custom_colors) + unchanged_color_lookup = get_color_lookup(['A', 'T', 'C', 'G', 'N', 'INS', '-'], alpha=0.3, + custom_colors=custom_colors) # fig = plt.figure(figsize=(amp_len/2.0,nSamples*2)) fig, ax = plt.subplots(figsize=((amp_len+10)/2.0, (nSamples+1)*2)) @@ -2144,7 +2168,7 @@ def plot_conversion_map(nuc_pct_df,fig_filename_root,conversion_nuc_from,convers plt.close(fig) -def plot_subs_across_ref(ref_len, ref_seq, ref_name, ref_count, all_substitution_base_vectors, plot_title, fig_filename_root, save_also_png, quantification_window_idxs=None): +def plot_subs_across_ref(ref_len, ref_seq, ref_name, ref_count, all_substitution_base_vectors, plot_title, fig_filename_root, save_also_png, custom_colors, quantification_window_idxs=None): """ Plots substitutions across the reference sequece - each position on the x axis reprsents a nucleotide in the reference bars at each x posion show the number of times the reference nucleotide was substituted for another reference @@ -2153,8 +2177,7 @@ def plot_subs_across_ref(ref_len, ref_seq, ref_name, ref_count, all_substitution fig, ax = plt.subplots(figsize=(16, 8)) ind = np.arange(ref_len) - alph = ['A', 'C', 'G', 'T', 'N'] - color_lookup = get_color_lookup(alph, alpha=1) + color_lookup = get_color_lookup(['A', 'T', 'C', 'G', 'N', 'INS', '-'], alpha=1, custom_colors=custom_colors) pA = ax.bar(ind, all_substitution_base_vectors[ref_name+"_A"], color=color_lookup['A']) pC = ax.bar(ind, all_substitution_base_vectors[ref_name+"_C"], color=color_lookup['C'], bottom=all_substitution_base_vectors[ref_name+"_A"]) @@ -2210,7 +2233,7 @@ def plot_subs_across_ref(ref_len, ref_seq, ref_name, ref_count, all_substitution fig.savefig(fig_filename_root + '.png', bbox_extra_artists=(lgd,), bbox_inches='tight') plt.close(fig) -def plot_sub_freqs(alt_nuc_counts, plot_title, fig_filename_root, save_also_png): +def plot_sub_freqs(alt_nuc_counts, plot_title, fig_filename_root, save_also_png, custom_colors): """ Plots histogram of substitution frequencies for each nucleotide (from nuc X to nuc Y) input: @@ -2220,8 +2243,7 @@ def plot_sub_freqs(alt_nuc_counts, plot_title, fig_filename_root, save_also_png) #plot all substitution rates fig, ax = plt.subplots(figsize=(8.3, 8)) - alph = ['A', 'C', 'G', 'T', 'N'] - color_lookup = get_color_lookup(alph, alpha=1) + color_lookup = get_color_lookup(['A', 'T', 'C', 'G', 'N', 'INS', '-'], alpha=1, custom_colors=custom_colors) ax.bar([1, 2, 3], [alt_nuc_counts['A']['C'], alt_nuc_counts['A']['G'], alt_nuc_counts['A']['T']], color=color_lookup['A']) ax.bar([5, 6, 7], [alt_nuc_counts['C']['A'], alt_nuc_counts['C']['G'], alt_nuc_counts['C']['T']], color=color_lookup['C']) @@ -2295,14 +2317,14 @@ def plot_log_nuc_freqs(df_nuc_freq,tot_aln_reads,plot_title,fig_filename_root,sa plt.close(fig) -def plot_conversion_at_sel_nucs(df_subs, ref_name, ref_sequence, plot_title, conversion_nuc_from, fig_filename_root, save_also_png): +def plot_conversion_at_sel_nucs(df_subs, ref_name, ref_sequence, plot_title, conversion_nuc_from, fig_filename_root, save_also_png, custom_colors): ''' Plots the conversion at selected nucleotides Looks for the 'conversion_nuc_from' in the ref_sequence and sets those as 'selected nucleotides' At selected nucleotides, the proportion of each base is shown as a barplot ''' nucs = list(df_subs.index) - color_lookup = get_color_lookup(nucs, alpha=1) + color_lookup = get_color_lookup(['A', 'T', 'C', 'G', 'N', 'INS', '-'], alpha=1, custom_colors=custom_colors) amp_len = len(ref_sequence) fig = plt.figure(figsize=(amp_len, 6)) @@ -2357,14 +2379,14 @@ def plot_conversion_at_sel_nucs(df_subs, ref_name, ref_sequence, plot_title, con fig.savefig(fig_filename_root+'.png', bbox_inches='tight', pad_inches=0.1) plt.close(fig) -def plot_conversion_at_sel_nucs_not_include_ref(df_subs, ref_name, ref_sequence, plot_title, conversion_nuc_from, fig_filename_root, save_also_png): +def plot_conversion_at_sel_nucs_not_include_ref(df_subs, ref_name, ref_sequence, plot_title, conversion_nuc_from, fig_filename_root, save_also_png, custom_colors): ''' Plots the conversion at selected nucleotides but ignores non-substitutions (for example at nucs that are 'C' in the reference, bars show the proportion of A T G (not C)) Looks for the 'conversion_nuc_from' in the ref_sequence and sets those as 'selected nucleotides' At selected nucleotides, the proportion of each substitution is shown as a barplot ''' nucs = list(df_subs.index) - color_lookup = get_color_lookup(nucs, alpha=1) + color_lookup = get_color_lookup(['A', 'T', 'C', 'G', 'N', 'INS', '-'], alpha=1, custom_colors=custom_colors) amp_len = len(ref_sequence) fig = plt.figure(figsize=(amp_len, 6)) @@ -2429,14 +2451,14 @@ def plot_conversion_at_sel_nucs_not_include_ref(df_subs, ref_name, ref_sequence, fig.savefig(fig_filename_root+'.png', bbox_inches='tight', pad_inches=0.1) plt.close(fig) -def plot_conversion_at_sel_nucs_not_include_ref_scaled(df_subs, ref_name, ref_sequence, plot_title, conversion_nuc_from, fig_filename_root, save_also_png): +def plot_conversion_at_sel_nucs_not_include_ref_scaled(df_subs, ref_name, ref_sequence, plot_title, conversion_nuc_from, fig_filename_root, save_also_png, custom_colors): ''' Plots the conversion at selected nucleotides not including reference base, scaled by number of events Looks for the 'conversion_nuc_from' in the ref_sequence and sets those as 'selected nucleotides' At selected nucleotides, the count of each base is shown as a barplot ''' nucs = list(df_subs.index) - color_lookup = get_color_lookup(nucs, alpha=1) + color_lookup = get_color_lookup(['A', 'T', 'C', 'G', 'N', 'INS', '-'], alpha=1, custom_colors=custom_colors) nucs.remove(conversion_nuc_from) amp_len = len(ref_sequence) diff --git a/CRISPResso2/CRISPRessoPooledCORE.py b/CRISPResso2/CRISPRessoPooledCORE.py index 8d9e7e35..56031988 100644 --- a/CRISPResso2/CRISPRessoPooledCORE.py +++ b/CRISPResso2/CRISPRessoPooledCORE.py @@ -18,7 +18,7 @@ import zipfile from CRISPResso2 import CRISPRessoShared from CRISPResso2 import CRISPRessoMultiProcessing -from CRISPResso2 import CRISPRessoReport +from CRISPResso2.CRISPRessoReports import CRISPRessoReport from CRISPResso2 import CRISPRessoPlot import traceback @@ -663,8 +663,8 @@ def main(): lowercase_default_amplicon_headers = {h.lower(): h for h in default_input_amplicon_headers} headers = [] + unmatched_headers = [] has_header = False - has_unmatched_header_el = False for head in header_els: # Header based on header provided # Look up long name (e.g. qwc -> quantification_window_coordinates) @@ -678,21 +678,23 @@ def main(): match = difflib.get_close_matches(long_head, lowercase_default_amplicon_headers, n=1) if not match: - has_unmatched_header_el = True - warn(f'Unable to find matches for header value "{head}". Using the default header values and order.') + unmatched_headers.append(head) else: has_header = True headers.append(lowercase_default_amplicon_headers[match[0]]) if args.debug: info(f'Matching header {head} with {lowercase_default_amplicon_headers[match[0]]}.') - if not has_header or has_unmatched_header_el: + if len(headers) > 5 and not has_header: + raise CRISPRessoShared.BadParameterException('Incorrect number of columns provided without header.') + elif has_header and len(unmatched_headers) > 0: + raise CRISPRessoShared.BadParameterException('Unable to match headers: ' + str(unmatched_headers)) + + if not has_header: # Default header headers = [] for i in range(len(header_els)): headers.append(default_input_amplicon_headers[i]) - if len(headers) > 5: - raise CRISPRessoShared.BadParameterException('Incorrect number of columns provided without header.') if args.debug: info(f'Header variable names in order: {headers}') diff --git a/CRISPResso2/CRISPRessoPooledWGSCompareCORE.py b/CRISPResso2/CRISPRessoPooledWGSCompareCORE.py index 15f28624..bfddca5c 100644 --- a/CRISPResso2/CRISPRessoPooledWGSCompareCORE.py +++ b/CRISPResso2/CRISPRessoPooledWGSCompareCORE.py @@ -11,7 +11,7 @@ import sys from CRISPResso2 import CRISPRessoShared from CRISPResso2 import CRISPRessoMultiProcessing -from CRISPResso2 import CRISPRessoReport +from CRISPResso2.CRISPRessoReports import CRISPRessoReport import traceback diff --git a/CRISPResso2/CRISPRessoReports/.github/workflows/.pylintrc b/CRISPResso2/CRISPRessoReports/.github/workflows/.pylintrc new file mode 100644 index 00000000..1b892797 --- /dev/null +++ b/CRISPResso2/CRISPRessoReports/.github/workflows/.pylintrc @@ -0,0 +1,7 @@ +[FORMAT] +max-line-length=150 +max-args=15 +max-locals=40 + +[MESSAGES CONTROL] +disable = E0401, W0719 diff --git a/CRISPResso2/CRISPRessoReports/.github/workflows/pylint.yml b/CRISPResso2/CRISPRessoReports/.github/workflows/pylint.yml new file mode 100644 index 00000000..5b7e7e11 --- /dev/null +++ b/CRISPResso2/CRISPRessoReports/.github/workflows/pylint.yml @@ -0,0 +1,26 @@ +name: Pylint + +on: + push: + branches: + - '*' + +jobs: + build: + runs-on: ubuntu-latest + strategy: + matrix: + python-version: ["3.10"] + steps: + - uses: actions/checkout@v3 + - name: Set up Python ${{ matrix.python-version }} + uses: actions/setup-python@v3 + with: + python-version: ${{ matrix.python-version }} + - name: Install dependencies + run: | + python -m pip install --upgrade pip + pip install pylint + - name: Analysing the code with pylint + run: | + pylint --fail-under=9 $(git ls-files '*.py') --rcfile=/home/runner/work/CRISPRessoReports/CRISPRessoReports/.github/workflows/.pylintrc diff --git a/CRISPResso2/CRISPRessoReport.py b/CRISPResso2/CRISPRessoReports/CRISPRessoReport.py similarity index 70% rename from CRISPResso2/CRISPRessoReport.py rename to CRISPResso2/CRISPRessoReports/CRISPRessoReport.py index 2b21db07..e6616ae1 100644 --- a/CRISPResso2/CRISPRessoReport.py +++ b/CRISPResso2/CRISPRessoReports/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 @@ -24,118 +56,127 @@ def make_report_from_folder(crispresso_report_file, crispresso_folder, _ROOT): 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 - fig_names = {} #all except for the figure 1 (which is common to all amplicons) - fig_locs = {} - fig_titles = {} - fig_captions = {} - fig_datas = {} - sgRNA_based_fig_names = {} -# print('crispresso_report file: ' + crispresso_report_file + ' crispresso_folder : ' + crispresso_folder + ' root: ' + _ROOT) - - def add_fig_if_exists(fig_name, fig_root, fig_title, fig_caption, fig_data, - amplicon_fig_names, amplicon_fig_locs, amplicon_fig_titles, amplicon_fig_captions, amplicon_fig_datas): - """ - 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') - fullpath=os.path.join(crispresso_folder, fig_root+'.png') -# print('adding file ' + fig_root + ' at ' + fullpath) - if os.path.exists(fullpath): - amplicon_fig_names.append(fig_name) - #amplicon_fig_locs[fig_name]=os.path.basename(fig_root+'.png') - amplicon_fig_locs[fig_name]=os.path.basename(fig_root) - amplicon_fig_titles[fig_name] = fig_title - amplicon_fig_captions[fig_name] = fig_caption - amplicon_fig_datas[fig_name] = [] - for (data_caption, data_file) in fig_data: - if os.path.exists(os.path.join(crispresso_folder, data_file)): - amplicon_fig_datas[fig_name].append((data_caption, data_file)) - - global_fig_names= [] +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, encoding="utf-8") as html: + html_string = "
" + html_string += html.read() + html_string += "
" + amplicon_figures['htmls'][fig_name] = html_string + + +def assemble_figs(run_data, crispresso_folder): + """ + Helper function create the data structre for the figures + """ + 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 + 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, fig_locs, fig_titles, fig_captions, fig_datas) - + 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_fig_names = [] - amplicon_fig_locs = {} - amplicon_fig_titles = {} - amplicon_fig_captions = {} - amplicon_fig_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']: - fig_name = 'plot_'+ fig + 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'], - amplicon_fig_names, amplicon_fig_locs, amplicon_fig_titles, amplicon_fig_captions, amplicon_fig_datas) + 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 + # 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_fig_locs, amplicon_fig_titles, amplicon_fig_captions, amplicon_fig_datas) + 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 - fig_names[amplicon_name] = amplicon_fig_names - sgRNA_based_fig_names[amplicon_name] = this_sgRNA_based_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 - fig_locs[amplicon_name] = amplicon_fig_locs - fig_titles[amplicon_name] = amplicon_fig_titles - fig_captions[amplicon_name] = amplicon_fig_captions - fig_datas[amplicon_name] = amplicon_fig_datas + +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) + 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) + # 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 += "/"; + crispresso_data_path += "/" report_data = { - 'amplicons': amplicons, - 'fig_names': fig_names, - 'sgRNA_based_fig_names': sgRNA_based_fig_names, - 'fig_locs': fig_locs, - 'fig_titles': fig_titles, - 'fig_captions': fig_captions, - 'fig_datas': fig_datas, + '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, 'templates'))) - template = j2_env.get_template('report.html') + 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) -# 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', encoding="utf-8") as outfile: + outfile.write(render_template( + 'report.html', j2_env, report_data=report_data, + )) - 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'] @@ -206,12 +247,12 @@ def make_batch_report_from_folder(crispressoBatch_report_file, crispresso2_info, 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: + with open(heatmap_plot_path, encoding="utf-8") 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: + with open(line_plot_path, encoding="utf-8") 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) @@ -219,8 +260,7 @@ def make_batch_report_from_folder(crispressoBatch_report_file, crispresso2_info, if crispresso_data_path == ".": crispresso_data_path = "" else: - crispresso_data_path += "/"; - + crispresso_data_path += "/" sub_html_files = {} run_names = [] @@ -230,9 +270,9 @@ def make_batch_report_from_folder(crispressoBatch_report_file, crispresso2_info, 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) + raise Exception(f'CRISPResso run {sub_folder} has no report. Cannot add to batch report.') - this_sub_html_file = sub_folder+".html" + 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 @@ -241,7 +281,7 @@ def make_batch_report_from_folder(crispressoBatch_report_file, crispresso2_info, output_title = 'CRISPResso Batch Output' if crispresso2_info['running_info']['args'].name != '': - output_title += '
{0}'.format(crispresso2_info['running_info']['args'].name) + output_title += f"
{crispresso2_info['running_info']['args'].name}" make_multi_report( run_names, @@ -250,6 +290,7 @@ 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, @@ -269,33 +310,38 @@ def make_pooled_report_from_folder(crispresso_report_file, crispresso2_info, fol 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) + output_title += f"
{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) + output_title += "
{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, display_names=input_names) + output_title += "
{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'] - display_names = crispresso2_info['results']['good_region_display_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, display_names) + output_title += "
{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,display_names=None): +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 @@ -306,10 +352,11 @@ def make_multi_report_from_folder(crispresso2_info,names_arr,report_name,crispre 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) + 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 + Nothing """ summary_plot_names = [] @@ -335,15 +382,15 @@ def make_multi_report_from_folder(crispresso2_info,names_arr,report_name,crispre if display_names is not None: display_name = display_names[name] - folder_name = 'CRISPResso_on_%s' % name + folder_name = f'CRISPResso_on_{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) + raise Exception(f'CRISPResso run {sub_folder} has no report. Cannot add to report.') run_names.append(display_name) - this_sub_html_file = os.path.basename(folder_name)+".html" + 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 @@ -352,9 +399,9 @@ def make_multi_report_from_folder(crispresso2_info,names_arr,report_name,crispre 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" + 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_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 @@ -367,6 +414,7 @@ def make_multi_report_from_folder(crispresso2_info,names_arr,report_name,crispre folder, _ROOT, report_name, + crispresso_tool, summary_plots={ 'names': summary_plot_names, 'titles': summary_plot_titles, @@ -383,19 +431,15 @@ def make_multi_report( 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={}, + crispresso_tool, + window_nuc_pct_quilts=None, + nuc_pct_quilts=None, + window_nuc_conv_plots=None, + nuc_conv_plots=None, + summary_plots=None, + compact_plots_to_show=None, + allele_modification_heatmap_plot=None, + allele_modification_line_plot=None, ): """ Makes an HTML report for a run containing multiple crispresso runs @@ -407,7 +451,6 @@ 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 - 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 @@ -430,10 +473,17 @@ 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 - template = j2_env.get_template('multiReport.html') + 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), @@ -443,6 +493,10 @@ def fill_default(dictionary, key, default_type=list): else: crispresso_data_path += "/" + if allele_modification_heatmap_plot is None: + allele_modification_heatmap_plot = {} + if allele_modification_line_plot is None: + allele_modification_line_plot = {} dictionaries = [ allele_modification_heatmap_plot, allele_modification_line_plot, ] @@ -460,22 +514,37 @@ def fill_default(dictionary, key, default_type=list): 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, + if summary_plots is None: + summary_plots={ + 'names': [], + 'titles': [], + 'labels': [], + 'datas': [], + } + + for html in sub_html_files: + sub_html_files[html] = crispresso_data_path + sub_html_files[html] + with open(crispresso_multi_report_file, 'w', encoding="utf-8") as outfile: + outfile.write(render_template( + template, + j2_env, + window_nuc_pct_quilts=[] if window_nuc_pct_quilts is None else window_nuc_pct_quilts, + nuc_pct_quilts=[] if nuc_pct_quilts is None else nuc_pct_quilts, + window_nuc_conv_plots=[] if window_nuc_conv_plots is None else window_nuc_conv_plots, + nuc_conv_plots=[] if nuc_conv_plots is None else 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'], + '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, + compact_plots_to_show=[] if compact_plots_to_show is None else 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'], @@ -497,7 +566,7 @@ def make_aggregate_report( _ROOT, folder_arr, crispresso_html_reports, - compact_plots_to_show={}, + compact_plots_to_show=None, display_names=None, ): """ @@ -512,10 +581,11 @@ def make_aggregate_report( 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) + 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 + Nothing """ summary_plots = {} if 'summary_plot_names' in crispresso2_info['results']['general_plots']: @@ -589,7 +659,7 @@ def make_aggregate_report( run_names = [] sub_html_files = {} - for idx, folder in enumerate(folder_arr): + for folder in folder_arr: display_name = folder if display_names is not None: display_name = display_names[folder] @@ -597,7 +667,8 @@ def make_aggregate_report( 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 - + if compact_plots_to_show is None: + compact_plots_to_show = {} 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) @@ -606,12 +677,12 @@ def make_aggregate_report( 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: + with open(heatmap_plot_path, encoding="utf-8") 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: + with open(line_plot_path, encoding="utf-8") as fh: allele_modification_line_plot['htmls'][line_plot_name] = fh.read() make_multi_report( diff --git a/CRISPResso2/CRISPRessoReports/README.md b/CRISPResso2/CRISPRessoReports/README.md new file mode 100644 index 00000000..23b7b4a3 --- /dev/null +++ b/CRISPResso2/CRISPRessoReports/README.md @@ -0,0 +1,50 @@ +# CRISPRessoReports +Git Subtree Standard Operating Procedure (SOP) + +Created: February 3, 2023 + +Introduction +In a few of our repositories we use git subtrees to share common files shared across multiple repositories. The goal of using subtrees is to reduce duplicated code. + +Process +If you have a repository where you would like to add a subtree, run the following command from the parent repo (wherein you would like the external child repo to be stored). + +git subtree add --prefix {path to where subtree will be stored} --squash {url of child repo} {branch of child repo} + +Some notes about the above command: +- You can’t add a subtree to an empty repo. +- If you don’t specify the --squash parameter then all of the commits from the child repo will be brought into the parent repo history. +- When you do specify the --squash parameter then there will be two commits in the parent repo history. +- If you have the url of the child repo added as a remote, you can use that instead. +- You should now see the files in the child repo at the path you specified in the parent repo. + +If you edit the files in the child repo (from within the parent repo), you can push the changes you have made up to the child repo with this command. + +git subtree push --prefix {path to where subtree is stored} --rejoin {url of child repo} {branch of child repo} + +Some notes about the above command: +- You should separate your commits such that there are not files staged in both child and parent. +- If there are commits in the child repo that you need in the parent repo, you can use this command. + +git subtree pull --prefix {path to where subtree is stored} --squash {url of child repo} {branch of child repo} + +Some notes about the above command: +- A merge conflict can happen here, so be warned! + +If you are doing this regularly, the commands above can be cumbersome. You can create an alias in git to make these commands easier! Edit the .git/config file in your repo and add the following lines to it. + +[alias] + +The acronym stands for "CrispressoReports Add" + +cra = "!f() { git subtree add --prefix CRISPRessoWEB/CRISPRessoReports https://github.com/edilytics/CRISPRessoReports.git $1 --squash; }; f" + +The acronym stands for "CrispressoReports Update" + +cru = "!f() { git subtree pull --prefix CRISPRessoWEB/CRISPRessoReports https://github.com/edilytics/CRISPRessoReports.git $1 --squash; }; f" + +The acronym stands for "CrispressoReports Push" + +crp = "!f() { git subtree push --prefix CRISPRessoWEB/CRISPRessoReports https://github.com/edilytics/CRISPRessoReports.git $1; }; f" + + diff --git a/CRISPResso2/CRISPRessoReports/__init__.py b/CRISPResso2/CRISPRessoReports/__init__.py new file mode 100644 index 00000000..e69de29b diff --git a/CRISPResso2/templates/CRISPResso_justcup.png b/CRISPResso2/CRISPRessoReports/templates/CRISPResso_justcup.png similarity index 100% rename from CRISPResso2/templates/CRISPResso_justcup.png rename to CRISPResso2/CRISPRessoReports/templates/CRISPResso_justcup.png diff --git a/CRISPResso2/CRISPRessoReports/templates/batchReport.html b/CRISPResso2/CRISPRessoReports/templates/batchReport.html new file mode 100644 index 00000000..58a41e97 --- /dev/null +++ b/CRISPResso2/CRISPRessoReports/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/CRISPResso2/templates/favicon.ico b/CRISPResso2/CRISPRessoReports/templates/favicon.ico similarity index 100% rename from CRISPResso2/templates/favicon.ico rename to CRISPResso2/CRISPRessoReports/templates/favicon.ico diff --git a/CRISPResso2/CRISPRessoReports/templates/layout.html b/CRISPResso2/CRISPRessoReports/templates/layout.html new file mode 100644 index 00000000..209d6bcb --- /dev/null +++ b/CRISPResso2/CRISPRessoReports/templates/layout.html @@ -0,0 +1,238 @@ + + + + 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/CRISPResso2/templates/multiReport.html b/CRISPResso2/CRISPRessoReports/templates/multiReport.html similarity index 75% rename from CRISPResso2/templates/multiReport.html rename to CRISPResso2/CRISPRessoReports/templates/multiReport.html index 4f346efe..8e8d83ca 100644 --- a/CRISPResso2/templates/multiReport.html +++ b/CRISPResso2/CRISPRessoReports/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_partial('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_partial('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_partial('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_partial('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_partial('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/CRISPResso2/CRISPRessoReports/templates/pooledReport.html b/CRISPResso2/CRISPRessoReports/templates/pooledReport.html new file mode 100644 index 00000000..f4550e82 --- /dev/null +++ b/CRISPResso2/CRISPRessoReports/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/CRISPResso2/CRISPRessoReports/templates/report.html b/CRISPResso2/CRISPRessoReports/templates/report.html new file mode 100644 index 00000000..775aa0d1 --- /dev/null +++ b/CRISPResso2/CRISPRessoReports/templates/report.html @@ -0,0 +1,720 @@ +{% 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=fig_name, 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, 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/CRISPResso2/CRISPRessoReports/templates/shared/partials/fig_reports.html b/CRISPResso2/CRISPRessoReports/templates/shared/partials/fig_reports.html new file mode 100644 index 00000000..e503c54f --- /dev/null +++ b/CRISPResso2/CRISPRessoReports/templates/shared/partials/fig_reports.html @@ -0,0 +1,35 @@ +
+ {% 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'] %} + + {% elif fig_name in ['plot_10b', 'plot_10c'] %} + + {% 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'] %} + + {% elif fig_name in ['plot_10b', 'plot_10c'] %} + + {% 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/CRISPResso2/CRISPRessoReports/templates/shared/partials/fig_summaries.html b/CRISPResso2/CRISPRessoReports/templates/shared/partials/fig_summaries.html new file mode 100644 index 00000000..63d40dea --- /dev/null +++ b/CRISPResso2/CRISPRessoReports/templates/shared/partials/fig_summaries.html @@ -0,0 +1,15 @@ +
+ {% if report_data['htmls'] and report_data['htmls'][plot_name]%} + {{report_data['htmls'][plot_name]|safe}} + {% else %} + {% if plot_name in ['Nucleotide_conversion_map', 'Nucleotide_percentage_quilt'] %} + + {% else %} + + {% endif %} + {% endif %} + + {% for (data_label,data_path) in report_data['datas'][plot_name] %} +

Data: {{data_label}}

+ {% endfor %} +
diff --git a/CRISPResso2/CRISPRessoReports/templates/shared/partials/log_params.html b/CRISPResso2/CRISPRessoReports/templates/shared/partials/log_params.html new file mode 100644 index 00000000..43a0cc5f --- /dev/null +++ b/CRISPResso2/CRISPRessoReports/templates/shared/partials/log_params.html @@ -0,0 +1,23 @@ +
+

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

+
+ +
+

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/CRISPResso2/CRISPRessoReports/templates/wgsReport.html b/CRISPResso2/CRISPRessoReports/templates/wgsReport.html new file mode 100644 index 00000000..0a5a1277 --- /dev/null +++ b/CRISPResso2/CRISPRessoReports/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 %} diff --git a/CRISPResso2/CRISPRessoShared.py b/CRISPResso2/CRISPRessoShared.py index 3225540a..62c8088d 100644 --- a/CRISPResso2/CRISPRessoShared.py +++ b/CRISPResso2/CRISPRessoShared.py @@ -9,6 +9,9 @@ import errno import gzip import json +import sys +import importlib.util + import numpy as np import os import pandas as pd @@ -19,6 +22,7 @@ import subprocess as sb import unicodedata import logging +from inspect import getmodule, stack from CRISPResso2 import CRISPResso2Align from CRISPResso2 import CRISPRessoCOREResources @@ -30,39 +34,51 @@ class FlashException(Exception): pass + class TrimmomaticException(Exception): pass + class NoReadsAlignedException(Exception): pass + class AlignmentException(Exception): pass + class SgRNASequenceException(Exception): pass + class NTException(Exception): pass + class ExonSequenceException(Exception): pass + class DuplicateSequenceIdException(Exception): pass + class NoReadsAfterQualityFilteringException(Exception): pass + class BadParameterException(Exception): pass + class AutoException(Exception): pass + class OutputFolderIncompleteException(Exception): pass + class InstallationException(Exception): pass @@ -301,6 +317,7 @@ def getCRISPRessoArgParser(parser_title="CRISPResso Parameters", required_params parser.add_argument('--suppress_plots', help='Suppress output plots', action='store_true') parser.add_argument('--write_cleaned_report', action='store_true', help=argparse.SUPPRESS) # trims working directories from output in report (for web access) + parser.add_argument('--config_file', help='File path to JSON file with config elements', type=str) # base editor parameters parser.add_argument('--base_editor_output', @@ -523,7 +540,7 @@ def clean_filename(filename): validFilenameChars = "+-_.()%s%s" % (string.ascii_letters, string.digits) filename = slugify(str(filename).replace(' ', '_')) cleanedFilename = unicodedata.normalize('NFKD', filename) - return(''.join(c for c in cleanedFilename if c in validFilenameChars)) + return (''.join(c for c in cleanedFilename if c in validFilenameChars)) def check_file(filename): try: @@ -1810,3 +1827,73 @@ def zip_results(results_folder): ) sb.call(cmd_to_zip, shell=True) return + + +def is_C2Pro_installed(): + try: + spec = importlib.util.find_spec("crispressoPro") + if spec is None: + return False + else: + return True + except: + return False + + +def check_custom_config(args): + """Check if the config_file argument was provided. If so load the configurations from the file, otherwise load default configurations. + + Parameters: + ------------- + args : dict + All arguments passed into the crispresso run. + + Returns: + ------------- + style : dict + A dict with a 'colors' key that contains hex color values for different report items. + + -OR- + + custom_style : dict + A dict with a 'colors' key that contains hex color values for different report items loaded from a user provided json file. + + """ + config = { + "colors": { + 'Substitution': '#0000FF', + 'Insertion': '#008000', + 'Deletion': '#FF0000', + 'A': '#7FC97F', + 'T': '#BEAED4', + 'C': '#FDC086', + 'G': '#FFFF99', + 'N': '#C8C8C8', + '-': '#C1C1C1' + } + } + + logger = logging.getLogger(getmodule(stack()[1][0]).__name__) + + #Check if crispresso.pro is installed + if not is_C2Pro_installed(): + return config + if args.config_file: + try: + with open(args.config_file, "r") as json_file: + custom_config = json.load(json_file) + + if 'colors' not in custom_config.keys(): + logger.warn("Json file does not contain the colors key. Defaulting all values.") + return config + + for key in config['colors']: + if key not in custom_config['colors']: + logger.warn(f"Value for {key} not provided, defaulting") + custom_config['colors'][key] = config['colors'][key] + + return custom_config + except Exception as e: + logger.warn("Cannot read json file '%s', defaulting style parameters." % args.config_file) + print(e) + return config diff --git a/CRISPResso2/CRISPRessoWGSCORE.py b/CRISPResso2/CRISPRessoWGSCORE.py index 29fc2f72..ff651337 100644 --- a/CRISPResso2/CRISPRessoWGSCORE.py +++ b/CRISPResso2/CRISPRessoWGSCORE.py @@ -18,7 +18,7 @@ import unicodedata from CRISPResso2 import CRISPRessoShared from CRISPResso2 import CRISPRessoMultiProcessing -from CRISPResso2 import CRISPRessoReport +from CRISPResso2.CRISPRessoReports import CRISPRessoReport from CRISPResso2 import CRISPRessoPlot diff --git a/CRISPResso2/default_style.json b/CRISPResso2/default_style.json new file mode 100644 index 00000000..9876b670 --- /dev/null +++ b/CRISPResso2/default_style.json @@ -0,0 +1,13 @@ +{ + "colors": { + "Substitution": "#0000FF", + "Insertion": "#008000", + "Deletion": "#FF0000", + "A": "#7FC97F", + "T": "#BEAED4", + "C": "#FDC086", + "G": "#FFFF99", + "N": "#C8C8C8", + "-": "#C1C1C1" + } +} \ No newline at end of file diff --git a/CRISPResso2/templates/layout.html b/CRISPResso2/templates/layout.html deleted file mode 100644 index 5eba4687..00000000 --- a/CRISPResso2/templates/layout.html +++ /dev/null @@ -1,104 +0,0 @@ - - - - CRISPResso2 Report - - - - - - - - - - - - - - - - - - - {% block head %}{% endblock %} - - - - -
- -
-
-
-
-
-

CRISPResso2

-

Analysis of genome editing outcomes from deep sequencing data

-
-
- -
-
- -
- {% block content %}{% endblock %} - -
- -
- - -
- -
- - - - - - - - - {% block foot %}{% endblock %} - - - diff --git a/CRISPResso2/templates/report.html b/CRISPResso2/templates/report.html deleted file mode 100644 index 37cc4bae..00000000 --- a/CRISPResso2/templates/report.html +++ /dev/null @@ -1,854 +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
-
    -
  • - -
    • -
  • - -
    • -
-
-
-
-
- - - {% for (data_label,data_path) in report_data['fig_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['fig_locs']['plot_1d'] %} -
  • - -
    • - {% endif %} -
-
-
-
-
- - - {% for (data_label,data_path) in report_data['fig_datas']['plot_1b'] %} -

Data: {{data_label}}

- {% endfor %} -
-
- - - {% for (data_label,data_path) in report_data['fig_datas']['plot_1c'] %} -

Data: {{data_label}}

- {% endfor %} -
- {% if report_data['fig_locs']['plot_1d'] %} -
- - - {% for (data_label,data_path) in report_data['fig_datas']['plot_1d'] %} -

Data: {{data_label}}

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

Data: {{data_label}}

- {% endfor %} -
-
- {% endif %} - - {% if report_data['fig_locs']['plot_6a'] %} -
-
-
Global frameshift mutagenesis profiles
-
-
- - - {% for (data_label,data_path) in report_data['fig_datas']['plot_6a'] %} -

Data: {{data_label}}

- {% endfor %} -
-
- {% endif %} - - {% if report_data['fig_locs']['plot_8a'] %} -
-
-
Global splicing analysis
-
-
- - - {% for (data_label,data_path) in report_data['fig_datas']['plot_8a'] %} -

Data: {{data_label}}

- {% endfor %} -
-
- {% endif %} - {# end of global coding sequence analysis #} - - {# start hdr summary #} - {% if report_data['fig_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['fig_datas'][report_data.amplicons[0]]['plot_4g'] %} -

Data: {{data_label}}

- {% endfor %} -
-
- {% endif %} - {# end HDR summary #} - - {# start prime editing report #} - {% if report_data['fig_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['fig_datas'][report_data.amplicons[0]]['plot_11a'] %} -

Data: {{data_label}}

- {% endfor %} -
-
- {% endif %} - - {% if report_data['sgRNA_based_fig_names'][report_data.amplicons[0]] and report_data['sgRNA_based_fig_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['sgRNA_based_fig_names'][report_data.amplicons[0]]['11b'] %} -
- - - {% for (data_label,data_path) in report_data['fig_datas'][report_data.amplicons[0]][fig_name] %} -

Data: {{data_label}}

- {% endfor %} -
- {% endfor %} -
-
- {% endif %} {# end plot 11b for prime editing #} - - {% if report_data['fig_locs']['plot_11c'] %} -
-
-
Scaffold insertions
-
-
- - - {% for (data_label,data_path) in report_data['fig_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['fig_locs'][amplicon_name]['plot_2a'] %} -
-
-
- -
-
- - - - {% for (data_label,data_path) in report_data['fig_datas'][amplicon_name]['plot_2a'] %} -

Data: {{data_label}}

- {% endfor %} - {% endif %} - - {% if report_data['sgRNA_based_fig_names'][amplicon_name] and report_data['sgRNA_based_fig_names'][amplicon_name]['2b']%} -
- {% for fig_name in report_data['sgRNA_based_fig_names'][amplicon_name]['2b'] %} - - - {% for (data_label,data_path) in report_data['fig_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['fig_locs'][amplicon_name]['plot_3a'] %} -
  • - -
    • - {% endif %} - {% if report_data['fig_locs'][amplicon_name]['plot_3b'] %} -
  • - -
    • - {% endif %} -
-
-
-
- {% if report_data['fig_locs'][amplicon_name]['plot_3a'] %} -
- - - {% for (data_label,data_path) in report_data['fig_datas'][amplicon_name]['plot_3a'] %} -

Data: {{data_label}}

- {% endfor %} -
- {% endif %} - - {% if report_data['fig_locs'][amplicon_name]['plot_3b'] %} -
- - - {% for (data_label,data_path) in report_data['fig_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['fig_locs'][amplicon_name]['plot_4a'] %} -
  • - -
    • - {% endif %} - {% if report_data['fig_locs'][amplicon_name]['plot_4b'] %} -
  • - -
    • - {% endif %} - {% if report_data['fig_locs'][amplicon_name]['plot_4c'] %} -
  • - -
    • - {% endif %} - {% if report_data['fig_locs'][amplicon_name]['plot_4d'] %} -
  • - -
    • - {% endif %} - {% if report_data['fig_locs'][amplicon_name]['plot_4e'] %} -
  • - -
    • - {% endif %} - {% if report_data['fig_locs'][amplicon_name]['plot_4f'] %} -
  • - -
    • - {% endif %} -
-
{# end card head #} -
-
- {% if report_data['fig_locs'][amplicon_name]['plot_4a'] %} -
- - - {% for (data_label,data_path) in report_data['fig_datas'][amplicon_name]['plot_4a'] %} -

Data: {{data_label}}

- {% endfor %} -
- {% endif %} - {% if report_data['fig_locs'][amplicon_name]['plot_4b'] %} -
- - - {% for (data_label,data_path) in report_data['fig_datas'][amplicon_name]['plot_4b'] %} -

Data: {{data_label}}

- {% endfor %} -
- {% endif %} - {% if report_data['fig_locs'][amplicon_name]['plot_4c'] %} -
- - - - {% for (data_label,data_path) in report_data['fig_datas'][amplicon_name]['plot_4c'] %} -

Data: {{data_label}}

- {% endfor %} -
- {% endif %} - - {% if report_data['fig_locs'][amplicon_name]['plot_4d'] %} -
- - - {% for (data_label,data_path) in report_data['fig_datas'][amplicon_name]['plot_4d'] %} -

Data: {{data_label}}

- {% endfor %} -
- {% endif %} - - {% if report_data['fig_locs'][amplicon_name]['plot_4e'] %} -
- - - {% for (data_label,data_path) in report_data['fig_datas'][amplicon_name]['plot_4e'] %} -

Data: {{data_label}}

- {% endfor %} -
- {% endif %} - - {% if report_data['fig_locs'][amplicon_name]['plot_4f'] %} -
- - - {% for (data_label,data_path) in report_data['fig_datas'][amplicon_name]['plot_4f'] %} -

Data: {{data_label}}

- {% endfor %} -
- {% endif %} -
-
{# end card body #} -
{# end card #} - - - {% if report_data['fig_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['fig_datas'][amplicon_name]['plot_5'] %} -

Data: {{data_label}}

- {% endfor %} -
-
- {% endif %} - - {% if report_data['fig_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['fig_datas'][amplicon_name]['plot_6'] %} -

Data: {{data_label}}

- {% endfor %} -
-
- {% endif %} - - {% if report_data['fig_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['fig_datas'][amplicon_name]['plot_7'] %} -

Data: {{data_label}}

- {% endfor %} -
-
- {% endif %} - - {% if report_data['fig_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['fig_datas'][amplicon_name]['plot_8'] %} -

Data: {{data_label}}

- {% endfor %} -
-
- {% endif %} - - - {% if report_data['sgRNA_based_fig_names'][amplicon_name] and report_data['sgRNA_based_fig_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['sgRNA_based_fig_names'][amplicon_name]['9'] %} -
- - - {% for (data_label,data_path) in report_data['fig_datas'][amplicon_name][fig_name] %} -

Data: {{data_label}}

- {% endfor %} -
- {% endfor %} -
-
- {% endif %} - - {% if report_data['fig_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['fig_locs'][amplicon_name]['plot_10a'] %} -
  • - -
    • - {% endif %} - {% if report_data['sgRNA_based_fig_names'][amplicon_name] and report_data['sgRNA_based_fig_names'][amplicon_name]['10d']%} -
  • - -
    • - {% endif %} - {% if report_data['sgRNA_based_fig_names'][amplicon_name] and report_data['sgRNA_based_fig_names'][amplicon_name]['10e']%} -
  • - -
    • - {% endif %} - {% if report_data['sgRNA_based_fig_names'][amplicon_name] and report_data['sgRNA_based_fig_names'][amplicon_name]['10f']%} -
  • - -
    • - {% endif %} -
-
-
-
- {% if report_data['fig_locs'][amplicon_name]['plot_10c'] %} -
-
- - - {% for (data_label,data_path) in report_data['fig_datas'][amplicon_name]['plot_10a'] %} -

Data: {{data_label}}

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

Data: {{data_label}}

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

Data: {{data_label}}

- {% endfor %} -
-
- {% else %} -
-
- - - {% for (data_label,data_path) in report_data['fig_datas'][amplicon_name]['plot_10a'] %} -

Data: {{data_label}}

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

Data: {{data_label}}

- {% endfor %} -
-
- {% endif %} - {% if report_data['sgRNA_based_fig_names'][amplicon_name] and report_data['sgRNA_based_fig_names'][amplicon_name]['10d']%} -
- {% for fig_name in report_data['sgRNA_based_fig_names'][amplicon_name]['10d'] %} -
- - - {% for (data_label,data_path) in report_data['fig_datas'][amplicon_name][fig_name] %} -

Data: {{data_label}}

- {% endfor %} -
- {% endfor %} -
- {% endif %} - {% if report_data['sgRNA_based_fig_names'][amplicon_name] and report_data['sgRNA_based_fig_names'][amplicon_name]['10e']%} -
- {% for fig_name in report_data['sgRNA_based_fig_names'][amplicon_name]['10e'] %} -
- - - {% for (data_label,data_path) in report_data['fig_datas'][amplicon_name][fig_name] %} -

Data: {{data_label}}

- {% endfor %} -
- {% endfor %} -
- {% endif %} - - {% if report_data['sgRNA_based_fig_names'][amplicon_name] and report_data['sgRNA_based_fig_names'][amplicon_name]['10f']%} -
- {% for fig_name in report_data['sgRNA_based_fig_names'][amplicon_name]['10f'] %} -
- - - {% for (data_label,data_path) in report_data['fig_datas'][amplicon_name][fig_name] %} -

Data: {{data_label}}

- {% endfor %} -
- {% endfor %} - - {% for fig_name in report_data['sgRNA_based_fig_names'][amplicon_name]['10g'] %} -
- - - {% for (data_label,data_path) in report_data['fig_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 %} diff --git a/MANIFEST.in b/MANIFEST.in index 59f8ed4c..cc437970 100644 --- a/MANIFEST.in +++ b/MANIFEST.in @@ -1,2 +1,2 @@ include CRISPResso2/EDNAFULL -include CRISPResso2/templates/* +include CRISPResso2/CRISPRessoReports/templates/* diff --git a/setup.py b/setup.py index cba9ac76..20cc3598 100644 --- a/setup.py +++ b/setup.py @@ -70,7 +70,7 @@ def main(): url='http://github.com/pinellolab/CRISPResso2', package_dir={'CRISPResso2' : 'CRISPResso2'}, include_package_data = True, - packages=['CRISPResso2'], + packages=['CRISPResso2', 'CRISPResso2.CRISPRessoReports'], entry_points=entry_points, description="Software pipeline for the analysis of genome editing outcomes from deep sequencing data", classifiers=[ @@ -89,6 +89,7 @@ def main(): 'matplotlib', # '>=1.3.1,<=2.2.3', 'seaborn', # '>0.7.1,<0.10', 'jinja2', + 'jinja_partials', 'scipy', 'numpy', 'plotly', From 97da958bd2b5057e93c75a3d967977a9fed0b00b Mon Sep 17 00:00:00 2001 From: mbowcut2 <55161542+mbowcut2@users.noreply.github.com> Date: Mon, 9 Oct 2023 13:54:05 -0600 Subject: [PATCH 2/6] changed tuple to list for matplotlib change (#31) --- CRISPResso2/CRISPRessoPlot.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CRISPResso2/CRISPRessoPlot.py b/CRISPResso2/CRISPRessoPlot.py index 6ac35e86..16cf2a9c 100644 --- a/CRISPResso2/CRISPRessoPlot.py +++ b/CRISPResso2/CRISPRessoPlot.py @@ -1831,7 +1831,7 @@ def plot_scaffold_indel_lengths( plot_root, save_also_png=False, ): - colors = 'b', 'g' + colors = ['b', 'g'] fig, ax = plt.subplots(figsize=(12, 6)) ax.hist( [ From 1259841bc2b896ec5bbe76db4ea12ca063823746 Mon Sep 17 00:00:00 2001 From: Trevor Martin Date: Fri, 8 Dec 2023 09:24:41 -0700 Subject: [PATCH 3/6] wgs and batch failed runs implementation --- CRISPResso2/CRISPRessoBatchCORE.py | 28 +++++++++++++-- CRISPResso2/CRISPRessoPooledCORE.py | 34 ++++++++++++++++++- .../CRISPRessoReports/CRISPRessoReport.py | 10 +++++- .../templates/batchReport.html | 19 +++++++++++ .../templates/pooledReport.html | 16 +++++++++ .../templates/wgsReport.html | 15 ++++++++ 6 files changed, 117 insertions(+), 5 deletions(-) diff --git a/CRISPResso2/CRISPRessoBatchCORE.py b/CRISPResso2/CRISPRessoBatchCORE.py index 6e673051..de7b1ec3 100644 --- a/CRISPResso2/CRISPRessoBatchCORE.py +++ b/CRISPResso2/CRISPRessoBatchCORE.py @@ -208,6 +208,7 @@ def main(): has_input = False if 'fastq_r1' in row and row.fastq_r1 != '': CRISPRessoShared.check_file(row.fastq_r1) + print(row.fastq_r1) has_input = True if 'fastq_r2' in row and row.fastq_r2 != '': @@ -293,23 +294,43 @@ def main(): crispresso2_info['results']['batch_names_arr'] = batch_names_arr crispresso2_info['results']['batch_input_names'] = batch_input_names - + CRISPRessoMultiProcessing.run_crispresso_cmds(crispresso_cmds, n_processes_for_batch, 'batch', args.skip_failed, start_end_percent=[10, 90]) - run_datas = [] # crispresso2 info from each row all_amplicons = set() amplicon_names = {} amplicon_counts = {} completed_batch_arr = [] + failed_batch_arr = [] for idx, row in batch_params.iterrows(): batch_name = CRISPRessoShared.slugify(row["name"]) folder_name = os.path.join(OUTPUT_DIRECTORY, 'CRISPResso_on_%s' % batch_name) run_data_file = os.path.join(folder_name, 'CRISPResso2_info.json') - if not os.path.isfile(run_data_file): + status_info = os.path.join(folder_name, 'CRISPResso_status.txt') + # breakpoint() + if not os.path.isfile(run_data_file) or not os.path.isfile(status_info): info("Skipping folder '%s'. Cannot find run data at '%s'."%(folder_name, run_data_file)) run_datas.append(None) + failed_batch_arr.append(batch_name) continue + else: + with open(status_info) as fh: + try: + percent_complete, status = re.search(r'(\d+\.\d+)% (.+)', fh.read()).groups() + # breakpoint() + if percent_complete != '100.00': + info("Skipping folder '%s'. Run is not complete (%s)."%(folder_name, status)) + run_datas.append(None) + failed_batch_arr.append(batch_name) + continue + except: + info("Skipping folder '%s'. Cannot parse status file '%s'."%(folder_name, status_info)) + run_datas.append(None) + failed_batch_arr.append(batch_name) + continue + + run_data = CRISPRessoShared.load_crispresso_info(folder_name) run_datas.append(run_data) @@ -327,6 +348,7 @@ def main(): completed_batch_arr.append(batch_name) + crispresso2_info['results']['failed_batch_arr'] = failed_batch_arr crispresso2_info['results']['completed_batch_arr'] = completed_batch_arr # make sure amplicon names aren't super long diff --git a/CRISPResso2/CRISPRessoPooledCORE.py b/CRISPResso2/CRISPRessoPooledCORE.py index 56031988..6a7acacf 100644 --- a/CRISPResso2/CRISPRessoPooledCORE.py +++ b/CRISPResso2/CRISPRessoPooledCORE.py @@ -880,8 +880,40 @@ def main(): else: warn('Skipping amplicon [%s] because no reads align to it\n'% idx) - + print(1111111111) + print(1111111111) + print(1111111111) + print(1111111111) + print(1111111111) + print(1111111111) + print(1111111111) + print("hey") + CRISPRessoMultiProcessing.run_crispresso_cmds(crispresso_cmds, n_processes_for_pooled, 'amplicon', args.skip_failed, start_end_percent=(16, 80)) + # Initialize array to track failed runs + failed_batch_arr = [] + # Iterate over each command to check if the run was successful + # print(crispresso_cmds) + for cmd in crispresso_cmds: + + # Extract the folder name from the CRISPResso command + folder_name_regex = re.search(r'-o\s+\S+\s+--name\s+(\S+)', cmd) + if folder_name_regex: + folder_name = os.path.join(OUTPUT_DIRECTORY, 'CRISPResso_on_%s' % folder_name_regex.group(1)) + status_file = os.path.join(folder_name, 'CRISPResso_status.txt') + + # Check if the status file exists and contains '100.00' + try: + with open(status_file, 'r') as f: + status_content = f.read() + if '100.00' not in status_content: + failed_batch_arr.append(folder_name_regex.group(1)) + except IOError: + # Status file doesn't exist, mark as failed + failed_batch_arr.append(folder_name_regex.group(1)) + + # Store the failed runs in crispresso2_info for later use + crispresso2_info['results']['failed_batch_arr'] = failed_batch_arr df_template['n_reads']=n_reads_aligned_amplicons df_template['n_reads_aligned_%']=df_template['n_reads']/float(N_READS_ALIGNED)*100 diff --git a/CRISPResso2/CRISPRessoReports/CRISPRessoReport.py b/CRISPResso2/CRISPRessoReports/CRISPRessoReport.py index e6616ae1..d511192a 100644 --- a/CRISPResso2/CRISPRessoReports/CRISPRessoReport.py +++ b/CRISPResso2/CRISPRessoReports/CRISPRessoReport.py @@ -180,6 +180,7 @@ def make_report(run_data, crispresso_report_file, crispresso_folder, _ROOT): def make_batch_report_from_folder(crispressoBatch_report_file, crispresso2_info, batch_folder, _ROOT): batch_names = crispresso2_info['results']['completed_batch_arr'] + failed_runs = crispresso2_info['results']['failed_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'] @@ -285,6 +286,7 @@ def make_batch_report_from_folder(crispressoBatch_report_file, crispresso2_info, make_multi_report( run_names, + failed_runs, sub_html_files, crispressoBatch_report_file, batch_folder, @@ -307,6 +309,7 @@ def make_batch_report_from_folder(crispressoBatch_report_file, crispresso2_info, def make_pooled_report_from_folder(crispresso_report_file, crispresso2_info, folder, _ROOT): + print(crispresso2_info['results']['failed_batch_arr']) names_arr = crispresso2_info['results']['good_region_names'] output_title = 'CRISPResso Pooled Output' if crispresso2_info['running_info']['args'].name != '': @@ -373,6 +376,9 @@ def make_multi_report_from_folder(crispresso2_info, names_arr, report_name, cris summary_plot_datas = crispresso2_info['results']['general_plots']['summary_plot_datas'] run_names = [] + failed_runs = crispresso2_info['results']['failed_batch_arr'] + print("Failed runs:") + print(failed_runs) sub_html_files = {} sub_2a_labels = {} sub_2a_pdfs = {} @@ -406,9 +412,9 @@ def make_multi_report_from_folder(crispresso2_info, names_arr, report_name, cris sub_2a_labels[display_name] = this_sub_2a_labels sub_2a_pdfs[display_name] = this_sub_2a_pdfs - make_multi_report( run_names, + failed_runs, sub_html_files, crispresso_report_file, folder, @@ -426,6 +432,7 @@ def make_multi_report_from_folder(crispresso2_info, names_arr, report_name, cris def make_multi_report( run_names, + failed_runs, sub_html_files, crispresso_multi_report_file, crispresso_folder, @@ -542,6 +549,7 @@ def fill_default(dictionary, key, default_type=list): 'crispresso_data_path': crispresso_data_path, }, run_names=run_names, + failed_runs=failed_runs, sub_html_files=sub_html_files, report_name=report_name, compact_plots_to_show=[] if compact_plots_to_show is None else compact_plots_to_show, diff --git a/CRISPResso2/CRISPRessoReports/templates/batchReport.html b/CRISPResso2/CRISPRessoReports/templates/batchReport.html index 58a41e97..7ee48dc9 100644 --- a/CRISPResso2/CRISPRessoReports/templates/batchReport.html +++ b/CRISPResso2/CRISPRessoReports/templates/batchReport.html @@ -66,6 +66,23 @@
{{report_name}}
{% endif %} + {% if failed_runs|length > 0 %} +
+
+
Failed Runs
+
+
+
+ {% for failed_run in failed_runs %} +
{{failed_run}}
+ + {% endfor %} +
+
+
+ {% endif %} + + {% if window_nuc_pct_quilts|length > 0 %}
@@ -155,6 +172,8 @@
{{report_data['titles'][plot_name]}}
{# column #} +

Hey Trevor! Your edit worked.

+
{% endblock %} diff --git a/CRISPResso2/CRISPRessoReports/templates/pooledReport.html b/CRISPResso2/CRISPRessoReports/templates/pooledReport.html index f4550e82..5a8452ac 100644 --- a/CRISPResso2/CRISPRessoReports/templates/pooledReport.html +++ b/CRISPResso2/CRISPRessoReports/templates/pooledReport.html @@ -65,6 +65,21 @@
{{report_name}}
{% endif %} + {% if failed_runs|length > 0 %} +
+
+
Failed Regions
+
+
+
+ {% for failed_run in failed_runs %} +
{{failed_run}}
+ + {% endfor %} +
+
+
+ {% endif %} {% if report_data['names']|length > 0 %} {% for plot_name in report_data['names'] %} @@ -78,6 +93,7 @@
{{report_data['titles'][plot_name]}}
{% endfor %} {% endif %} +
Download report diff --git a/CRISPResso2/CRISPRessoReports/templates/wgsReport.html b/CRISPResso2/CRISPRessoReports/templates/wgsReport.html index 0a5a1277..8b20bb77 100644 --- a/CRISPResso2/CRISPRessoReports/templates/wgsReport.html +++ b/CRISPResso2/CRISPRessoReports/templates/wgsReport.html @@ -63,6 +63,21 @@
{{report_name}}
+ {% if failed_runs|length > 0 %} +
+
+
Failed Regions
+
+
+
+ {% for failed_run in failed_runs %} +
{{failed_run}}
+ + {% endfor %} +
+
+
+ {% endif %} {% if report_data['names']|length > 0 %} {% for plot_name in report_data['names'] %} From 85e495b252abbac948b6fada00b22c67ef1ed04a Mon Sep 17 00:00:00 2001 From: Trevor Martin Date: Wed, 20 Dec 2023 15:59:16 -0700 Subject: [PATCH 4/6] Added failed run functionality including shared function, edits to Report, and displaying with HTML and Javascript --- CRISPResso2/CRISPRessoBatchCORE.py | 34 +++----- CRISPResso2/CRISPRessoPooledCORE.py | 27 ++----- CRISPResso2/CRISPRessoPooledWGSCompareCORE.py | 4 + .../CRISPRessoReports/CRISPRessoReport.py | 16 +++- .../templates/batchReport.html | 66 ++++++++++++++-- .../templates/multiReport.html | 67 ++++++++++++++++ .../templates/pooledReport.html | 61 ++++++++++++-- .../templates/wgsReport.html | 79 ++++++++++++++++--- CRISPResso2/CRISPRessoShared.py | 44 +++++++++++ CRISPResso2/CRISPRessoWGSCORE.py | 10 ++- 10 files changed, 332 insertions(+), 76 deletions(-) diff --git a/CRISPResso2/CRISPRessoBatchCORE.py b/CRISPResso2/CRISPRessoBatchCORE.py index de7b1ec3..92e6625e 100644 --- a/CRISPResso2/CRISPRessoBatchCORE.py +++ b/CRISPResso2/CRISPRessoBatchCORE.py @@ -208,7 +208,6 @@ def main(): has_input = False if 'fastq_r1' in row and row.fastq_r1 != '': CRISPRessoShared.check_file(row.fastq_r1) - print(row.fastq_r1) has_input = True if 'fastq_r2' in row and row.fastq_r2 != '': @@ -294,8 +293,9 @@ def main(): crispresso2_info['results']['batch_names_arr'] = batch_names_arr crispresso2_info['results']['batch_input_names'] = batch_input_names - + CRISPRessoMultiProcessing.run_crispresso_cmds(crispresso_cmds, n_processes_for_batch, 'batch', args.skip_failed, start_end_percent=[10, 90]) + run_datas = [] # crispresso2 info from each row all_amplicons = set() @@ -303,34 +303,17 @@ def main(): amplicon_counts = {} completed_batch_arr = [] failed_batch_arr = [] + failed_batch_arr_desc = [] for idx, row in batch_params.iterrows(): batch_name = CRISPRessoShared.slugify(row["name"]) folder_name = os.path.join(OUTPUT_DIRECTORY, 'CRISPResso_on_%s' % batch_name) - run_data_file = os.path.join(folder_name, 'CRISPResso2_info.json') - status_info = os.path.join(folder_name, 'CRISPResso_status.txt') - # breakpoint() - if not os.path.isfile(run_data_file) or not os.path.isfile(status_info): - info("Skipping folder '%s'. Cannot find run data at '%s'."%(folder_name, run_data_file)) - run_datas.append(None) + # check if run failed + failed_run_bool, failed_status_string = CRISPRessoShared.check_if_failed_run(folder_name, info) + if failed_run_bool: failed_batch_arr.append(batch_name) + failed_batch_arr_desc.append(failed_status_string) + run_datas.append(None) continue - else: - with open(status_info) as fh: - try: - percent_complete, status = re.search(r'(\d+\.\d+)% (.+)', fh.read()).groups() - # breakpoint() - if percent_complete != '100.00': - info("Skipping folder '%s'. Run is not complete (%s)."%(folder_name, status)) - run_datas.append(None) - failed_batch_arr.append(batch_name) - continue - except: - info("Skipping folder '%s'. Cannot parse status file '%s'."%(folder_name, status_info)) - run_datas.append(None) - failed_batch_arr.append(batch_name) - continue - - run_data = CRISPRessoShared.load_crispresso_info(folder_name) run_datas.append(run_data) @@ -349,6 +332,7 @@ def main(): completed_batch_arr.append(batch_name) crispresso2_info['results']['failed_batch_arr'] = failed_batch_arr + crispresso2_info['results']['failed_batch_arr_desc'] = failed_batch_arr_desc crispresso2_info['results']['completed_batch_arr'] = completed_batch_arr # make sure amplicon names aren't super long diff --git a/CRISPResso2/CRISPRessoPooledCORE.py b/CRISPResso2/CRISPRessoPooledCORE.py index 6a7acacf..09cb7eae 100644 --- a/CRISPResso2/CRISPRessoPooledCORE.py +++ b/CRISPResso2/CRISPRessoPooledCORE.py @@ -880,40 +880,25 @@ def main(): else: warn('Skipping amplicon [%s] because no reads align to it\n'% idx) - print(1111111111) - print(1111111111) - print(1111111111) - print(1111111111) - print(1111111111) - print(1111111111) - print(1111111111) - print("hey") - + CRISPRessoMultiProcessing.run_crispresso_cmds(crispresso_cmds, n_processes_for_pooled, 'amplicon', args.skip_failed, start_end_percent=(16, 80)) # Initialize array to track failed runs failed_batch_arr = [] - # Iterate over each command to check if the run was successful - # print(crispresso_cmds) + failed_batch_arr_desc = [] for cmd in crispresso_cmds: # Extract the folder name from the CRISPResso command folder_name_regex = re.search(r'-o\s+\S+\s+--name\s+(\S+)', cmd) if folder_name_regex: folder_name = os.path.join(OUTPUT_DIRECTORY, 'CRISPResso_on_%s' % folder_name_regex.group(1)) - status_file = os.path.join(folder_name, 'CRISPResso_status.txt') - - # Check if the status file exists and contains '100.00' - try: - with open(status_file, 'r') as f: - status_content = f.read() - if '100.00' not in status_content: - failed_batch_arr.append(folder_name_regex.group(1)) - except IOError: - # Status file doesn't exist, mark as failed + failed_run_bool, failed_status_string = CRISPRessoShared.check_if_failed_run(folder_name, info) + if failed_run_bool: failed_batch_arr.append(folder_name_regex.group(1)) + failed_batch_arr_desc.append(failed_status_string) # Store the failed runs in crispresso2_info for later use crispresso2_info['results']['failed_batch_arr'] = failed_batch_arr + crispresso2_info['results']['failed_batch_arr_desc'] = failed_batch_arr_desc df_template['n_reads']=n_reads_aligned_amplicons df_template['n_reads_aligned_%']=df_template['n_reads']/float(N_READS_ALIGNED)*100 diff --git a/CRISPResso2/CRISPRessoPooledWGSCompareCORE.py b/CRISPResso2/CRISPRessoPooledWGSCompareCORE.py index bfddca5c..abac3cea 100644 --- a/CRISPResso2/CRISPRessoPooledWGSCompareCORE.py +++ b/CRISPResso2/CRISPRessoPooledWGSCompareCORE.py @@ -354,8 +354,12 @@ def main(): report_name = _jp("CRISPResso2PooledWGSCompare_report.html") else: report_name = OUTPUT_DIRECTORY+'.html' + empty_failed_runs_arr = [] + empty_failed_runs_arr_desc = [] CRISPRessoReport.make_multi_report( processed_regions, + empty_failed_runs_arr, + empty_failed_runs_arr_desc, processed_region_html_files, report_name, OUTPUT_DIRECTORY, diff --git a/CRISPResso2/CRISPRessoReports/CRISPRessoReport.py b/CRISPResso2/CRISPRessoReports/CRISPRessoReport.py index d511192a..fa9a781a 100644 --- a/CRISPResso2/CRISPRessoReports/CRISPRessoReport.py +++ b/CRISPResso2/CRISPRessoReports/CRISPRessoReport.py @@ -181,6 +181,7 @@ def make_report(run_data, crispresso_report_file, crispresso_folder, _ROOT): def make_batch_report_from_folder(crispressoBatch_report_file, crispresso2_info, batch_folder, _ROOT): batch_names = crispresso2_info['results']['completed_batch_arr'] failed_runs = crispresso2_info['results']['failed_batch_arr'] + failed_runs_desc = crispresso2_info['results']['failed_batch_arr_desc'] display_names = crispresso2_info['results']['batch_input_names'] window_nuc_pct_quilts = crispresso2_info['results']['general_plots']['window_nuc_pct_quilt_plot_names'] @@ -287,6 +288,7 @@ def make_batch_report_from_folder(crispressoBatch_report_file, crispresso2_info, make_multi_report( run_names, failed_runs, + failed_runs_desc, sub_html_files, crispressoBatch_report_file, batch_folder, @@ -309,7 +311,6 @@ def make_batch_report_from_folder(crispressoBatch_report_file, crispresso2_info, def make_pooled_report_from_folder(crispresso_report_file, crispresso2_info, folder, _ROOT): - print(crispresso2_info['results']['failed_batch_arr']) names_arr = crispresso2_info['results']['good_region_names'] output_title = 'CRISPResso Pooled Output' if crispresso2_info['running_info']['args'].name != '': @@ -377,8 +378,7 @@ def make_multi_report_from_folder(crispresso2_info, names_arr, report_name, cris run_names = [] failed_runs = crispresso2_info['results']['failed_batch_arr'] - print("Failed runs:") - print(failed_runs) + failed_runs_desc = crispresso2_info['results']['failed_batch_arr_desc'] sub_html_files = {} sub_2a_labels = {} sub_2a_pdfs = {} @@ -412,9 +412,11 @@ def make_multi_report_from_folder(crispresso2_info, names_arr, report_name, cris sub_2a_labels[display_name] = this_sub_2a_labels sub_2a_pdfs[display_name] = this_sub_2a_pdfs + make_multi_report( run_names, failed_runs, + failed_runs_desc, sub_html_files, crispresso_report_file, folder, @@ -433,6 +435,7 @@ def make_multi_report_from_folder(crispresso2_info, names_arr, report_name, cris def make_multi_report( run_names, failed_runs, + failed_runs_desc, sub_html_files, crispresso_multi_report_file, crispresso_folder, @@ -550,6 +553,7 @@ def fill_default(dictionary, key, default_type=list): }, run_names=run_names, failed_runs=failed_runs, + failed_runs_desc=failed_runs_desc, sub_html_files=sub_html_files, report_name=report_name, compact_plots_to_show=[] if compact_plots_to_show is None else compact_plots_to_show, @@ -692,9 +696,15 @@ def make_aggregate_report( for line_plot_name, line_plot_path in allele_modification_line_plot['paths'].items(): with open(line_plot_path, encoding="utf-8") as fh: allele_modification_line_plot['htmls'][line_plot_name] = fh.read() + + # make_multi_report expects two arrays here for other calls of this function + empty_failed_runs = [] + empty_failed_runs_desc = [] make_multi_report( run_names, + empty_failed_runs, + empty_failed_runs_desc, sub_html_files, crispresso_report_file, crispresso_report_folder, diff --git a/CRISPResso2/CRISPRessoReports/templates/batchReport.html b/CRISPResso2/CRISPRessoReports/templates/batchReport.html index 7ee48dc9..37580c5f 100644 --- a/CRISPResso2/CRISPRessoReports/templates/batchReport.html +++ b/CRISPResso2/CRISPRessoReports/templates/batchReport.html @@ -44,6 +44,46 @@ {% endblock %} {% block content %} + + + +
@@ -65,17 +105,30 @@
{{report_name}}
{% endif %} + + {% if failed_runs|length > 0 %} -
-
-
Failed Runs
+
+
+ +
Failed Runs
+
+
{% for failed_run in failed_runs %} -
{{failed_run}}
- + + + {{failed_run}} + + + {% endfor %}
@@ -83,6 +136,7 @@
Failed Runs
{% endif %} + {% if window_nuc_pct_quilts|length > 0 %}
@@ -172,8 +226,6 @@
{{report_data['titles'][plot_name]}}
{# column #} -

Hey Trevor! Your edit worked.

-
{% endblock %} diff --git a/CRISPResso2/CRISPRessoReports/templates/multiReport.html b/CRISPResso2/CRISPRessoReports/templates/multiReport.html index 8e8d83ca..a66b0f5c 100644 --- a/CRISPResso2/CRISPRessoReports/templates/multiReport.html +++ b/CRISPResso2/CRISPRessoReports/templates/multiReport.html @@ -44,6 +44,45 @@ {% endblock %} {% block content %} + + +
@@ -65,6 +104,34 @@
{{report_name}}
{% endif %} + {% if failed_runs|length > 0 %} +
+
+ +
Failed Runs
+ +
+ +
+
+ {% for failed_run in failed_runs %} + + + {{failed_run}} + + + + {% endfor %} +
+
+
+ {% endif %} + {% if window_nuc_pct_quilts|length > 0 %}
diff --git a/CRISPResso2/CRISPRessoReports/templates/pooledReport.html b/CRISPResso2/CRISPRessoReports/templates/pooledReport.html index 5a8452ac..30122c0d 100644 --- a/CRISPResso2/CRISPRessoReports/templates/pooledReport.html +++ b/CRISPResso2/CRISPRessoReports/templates/pooledReport.html @@ -44,6 +44,45 @@ {% endblock %} {% block content %} + + +
@@ -66,15 +105,27 @@
{{report_name}}
{% endif %} {% if failed_runs|length > 0 %} -
-
-
Failed Regions
+
+
+ +
Failed Runs
+
+
{% for failed_run in failed_runs %} -
{{failed_run}}
- + + + {{failed_run}} + + + {% endfor %}
diff --git a/CRISPResso2/CRISPRessoReports/templates/wgsReport.html b/CRISPResso2/CRISPRessoReports/templates/wgsReport.html index 8b20bb77..f199ce5f 100644 --- a/CRISPResso2/CRISPRessoReports/templates/wgsReport.html +++ b/CRISPResso2/CRISPRessoReports/templates/wgsReport.html @@ -44,6 +44,45 @@ {% endblock %} {% block content %} + + +
@@ -63,21 +102,35 @@
{{report_name}}
- {% if failed_runs|length > 0 %} -
-
-
Failed Regions
-
-
-
- {% for failed_run in failed_runs %} -
{{failed_run}}
- - {% endfor %} -
+ + {% if failed_runs|length > 0 %} +
+
+ +
Failed Runs
+ +
+ +
+
+ {% for failed_run in failed_runs %} + + + {{failed_run}} + + + + {% endfor %}
- {% endif %} +
+ {% endif %} + {% if report_data['names']|length > 0 %} {% for plot_name in report_data['names'] %} diff --git a/CRISPResso2/CRISPRessoShared.py b/CRISPResso2/CRISPRessoShared.py index 9ca987e5..7849a654 100644 --- a/CRISPResso2/CRISPRessoShared.py +++ b/CRISPResso2/CRISPRessoShared.py @@ -1024,6 +1024,50 @@ def default_sigpipe(): return seq_lines +def check_if_failed_run(folder_name, info): + """ + Check the output folder for a info.json file and a status.txt file to see if the run completed successfully or not + + input: + folder_name: path to output folder + info: logger + + + returns: + bool True if run completed successfully, False otherwise + string describing why it failed + """ + + run_data_file = os.path.join(folder_name, 'CRISPResso2_info.json') + status_info = os.path.join(folder_name, 'CRISPResso_status.txt') + if not os.path.isfile(run_data_file) or not os.path.isfile(status_info): + info("Skipping folder '%s'. Cannot find run data status file at '%s'."%(folder_name, run_data_file)) + if "CRISPRessoPooled" in folder_name: + unit = "amplicon" + elif "CRISPRessoWGS" in folder_name: + unit = "region" + else: + unit = "sample" + + return True, f"CRISPResso failed for this {unit}! Please check your input files and parameters." + else: + with open(status_info) as fh: + try: + file_contents = fh.read() + search_result = re.search(r'(\d+\.\d+)% (.+)', file_contents) + if search_result: + percent_complete, status = search_result.groups() + if percent_complete != '100.00': + info("Skipping folder '%s'. Run is not complete (%s)." % (folder_name, status)) + return True, status + else: + return True, file_contents + except Exception as e: + print(e) + info("Skipping folder '%s'. Cannot parse status file '%s'." % (folder_name, status_info)) + return True, "Cannot parse status file '%s'." % (status_info) + return False, "" + def guess_amplicons(fastq_r1,fastq_r2,number_of_reads_to_consider,flash_command,max_paired_end_reads_overlap,min_paired_end_reads_overlap,aln_matrix,needleman_wunsch_gap_open,needleman_wunsch_gap_extend,split_interleaved_input=False,min_freq_to_consider=0.2,amplicon_similarity_cutoff=0.95): """ diff --git a/CRISPResso2/CRISPRessoWGSCORE.py b/CRISPResso2/CRISPRessoWGSCORE.py index 2ac826d4..861b124d 100644 --- a/CRISPResso2/CRISPRessoWGSCORE.py +++ b/CRISPResso2/CRISPRessoWGSCORE.py @@ -650,15 +650,19 @@ def set_filenames(row): header_el_count = len(header_els) empty_line_els = [np.nan]*(header_el_count-1) n_reads_index = header_els.index('Reads_total') - 1 + failed_batch_arr = [] + failed_batch_arr_desc = [] for idx, row in df_regions.iterrows(): run_name = CRISPRessoShared.slugify(str(idx)) folder_name = 'CRISPResso_on_%s' % run_name + failed_run_bool, failed_run_desc = CRISPRessoShared.check_if_failed_run(_jp(folder_name), info) all_region_names.append(run_name) all_region_read_counts[run_name] = row.n_reads - run_file = os.path.join(_jp(folder_name), 'CRISPResso2_info.json') - if not os.path.exists(run_file): + if failed_run_bool: + failed_batch_arr.append(run_name) + failed_batch_arr_desc.append(failed_run_desc) warn('Skipping the folder %s: not enough reads, incomplete, or empty folder.'% folder_name) this_els = empty_line_els[:] this_els[n_reads_index] = row.n_reads @@ -710,6 +714,8 @@ def set_filenames(row): else: df_summary_quantification.fillna('NA').to_csv(samples_quantification_summary_filename, sep='\t', index=None) + crispresso2_info['results']['failed_batch_arr'] = failed_batch_arr + crispresso2_info['results']['failed_batch_arr_desc'] = failed_batch_arr_desc crispresso2_info['results']['alignment_stats']['samples_quantification_summary_filename'] = os.path.basename(samples_quantification_summary_filename) crispresso2_info['results']['regions'] = df_regions crispresso2_info['results']['all_region_names'] = all_region_names From e62873b8c1ff436a0ca4cd4e740cec5e31cfe75f Mon Sep 17 00:00:00 2001 From: Cole Lyman Date: Fri, 5 Jan 2024 11:42:49 -0700 Subject: [PATCH 5/6] Merge CRISPRessoReports master into failed-batch-runs --- .../CRISPRessoReports/CRISPRessoReport.py | 8 +- CRISPResso2/CRISPRessoReports/README.md | 199 +++++++++++++++--- .../templates/batchReport.html | 3 +- .../CRISPRessoReports/templates/layout.html | 36 ++-- .../templates/multiReport.html | 13 +- .../templates/pooledReport.html | 3 +- .../CRISPRessoReports/templates/report.html | 14 +- .../shared/partials/fig_reports.html | 10 +- .../templates/shared/partials/log_params.html | 41 ++-- .../templates/wgsReport.html | 3 +- 10 files changed, 240 insertions(+), 90 deletions(-) diff --git a/CRISPResso2/CRISPRessoReports/CRISPRessoReport.py b/CRISPResso2/CRISPRessoReports/CRISPRessoReport.py index fa9a781a..5030fe78 100644 --- a/CRISPResso2/CRISPRessoReports/CRISPRessoReport.py +++ b/CRISPResso2/CRISPRessoReports/CRISPRessoReport.py @@ -34,6 +34,8 @@ def custom_partial_render(partial_template_name, **partial_data): render_partial=generate_render_partial( custom_partial_render, ), + is_default_user=False, + is_web=False, ) return template.render(**partial_data) return render_partial( @@ -356,7 +358,7 @@ def make_multi_report_from_folder(crispresso2_info, names_arr, report_name, cris 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 + 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: @@ -593,7 +595,7 @@ def make_aggregate_report( 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 + 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: @@ -696,7 +698,7 @@ def make_aggregate_report( for line_plot_name, line_plot_path in allele_modification_line_plot['paths'].items(): with open(line_plot_path, encoding="utf-8") as fh: allele_modification_line_plot['htmls'][line_plot_name] = fh.read() - + # make_multi_report expects two arrays here for other calls of this function empty_failed_runs = [] empty_failed_runs_desc = [] diff --git a/CRISPResso2/CRISPRessoReports/README.md b/CRISPResso2/CRISPRessoReports/README.md index 23b7b4a3..b31cff80 100644 --- a/CRISPResso2/CRISPRessoReports/README.md +++ b/CRISPResso2/CRISPRessoReports/README.md @@ -1,50 +1,191 @@ # CRISPRessoReports -Git Subtree Standard Operating Procedure (SOP) -Created: February 3, 2023 +This repo holds the shared reports code and HTML templates that are used by the CLI and web projects. -Introduction -In a few of our repositories we use git subtrees to share common files shared across multiple repositories. The goal of using subtrees is to reduce duplicated code. +Take care when committing into these files as not to mix unrelated git histories. -Process -If you have a repository where you would like to add a subtree, run the following command from the parent repo (wherein you would like the external child repo to be stored). +## How do I work with this repo? -git subtree add --prefix {path to where subtree will be stored} --squash {url of child repo} {branch of child repo} +Step 1 only needs to be done once per cloned repo, the other steps will need to be dne more frequently. -Some notes about the above command: -- You can’t add a subtree to an empty repo. -- If you don’t specify the --squash parameter then all of the commits from the child repo will be brought into the parent repo history. -- When you do specify the --squash parameter then there will be two commits in the parent repo history. -- If you have the url of the child repo added as a remote, you can use that instead. -- You should now see the files in the child repo at the path you specified in the parent repo. +1. Add the remote to this repo to the "parent" repo (i.e. `CRISPResso2` or `C2Web`). **You should only have to do this once.** -If you edit the files in the child repo (from within the parent repo), you can push the changes you have made up to the child repo with this command. +``` shell +git remote add reports https://github.com/edilytics/CRISPRessoReports.git +``` -git subtree push --prefix {path to where subtree is stored} --rejoin {url of child repo} {branch of child repo} +*Note:* you can change the `reports` above to whatever you would like, just don't forget to replace `reports` with it in the other steps. -Some notes about the above command: -- You should separate your commits such that there are not files staged in both child and parent. -- If there are commits in the child repo that you need in the parent repo, you can use this command. +2. In the parent repo, fetch the latest changes from `CRISPRessoReports`. -git subtree pull --prefix {path to where subtree is stored} --squash {url of child repo} {branch of child repo} +``` shell +git fetch reports +``` -Some notes about the above command: -- A merge conflict can happen here, so be warned! +3. Checkout a `CRISPRessoReports` branch. -If you are doing this regularly, the commands above can be cumbersome. You can create an alias in git to make these commands easier! Edit the .git/config file in your repo and add the following lines to it. +``` shell +git checkout -b master-reports reports/master +``` -[alias] +*Note:* you can obviously change the names of these branches (or select a branch other than `master`). I would recommend naming all branches from `CRISPRessoReports` with the same prefix or suffix (i.e. `*-reports`) because it can get confusing to keep all of the branches straight... + +4. Read `CRISPRessoReports` into the parent repo as a subtree. This is when the code in `CRISPRessoReports` will finally be added to the parent repo. + +**Very important**, switch to the branch in the parent repo where you want the code to be added! For example: + +``` shell +git checkout +``` + +Then, you will read the commits into wherever `CRISPRessoReports` are stored for that repo. **Note:** you should only have to do this if `CRISPRessoReports` has not been added to the parent repo, if it is already there, do not repeat this step. + +``` shell +git read-tree --prefix=CRISPResso2/CRISPRessoReports -u master-reports +``` + +Run `git status` and you should see the files added! + +5. Stage and commit your files as you normally would. + +### How do I pull commits that are in `CRISPRessoReports` into the parent repo? + +1. In the parent repo, switch to the `-reports` branch. + +``` shell +git checkout -reports +``` + +2. Pull the changes from `CRISPRessoReports`. + +``` shell +git pull +``` + +You should see the updates that you are looking for. + +3. **Very important**, switch back to whichever branch you are working on in the parent repo. + +``` shell +git checkout +``` + +4. Merge the changes in and resolve any merge conflicts. + +``` shell +git merge --squash -Xsubtree="CRISPResso2/CRISPRessoReports" --no-commit --allow-unrelated-histories -reports +``` + +*Note:* You may need to change the value of the `-Xsubtree` parameter to match where `CRISPRessoReports` is located in the parent repo. + +5. Commit your changes and resolve merge conflicts. + +Also, note that the default commit message may have a summary of all commits, please shorten it to be descriptive of the most recent changes. + +### How do I push commits that are in my parent repo's `CRISPRessoReports` into the shared `CRISPRessoReports` repo? + +1. In the parent repo, switch to (or create) the branch on `CRISPRessoReports` that will have the changes you push. + +If you are creating a new branch based off of `CRISPRessoReports` master, run this: + +``` shell +git checkout -b -reports reports/master +``` + +Or if you would like to push to an existing branch on `CRISPRessoReports`, run this: + +``` shell +git checkout -reports +``` -The acronym stands for "CrispressoReports Add" +2. Merge the changes in and resove any merge conflicts. -cra = "!f() { git subtree add --prefix CRISPRessoWEB/CRISPRessoReports https://github.com/edilytics/CRISPRessoReports.git $1 --squash; }; f" +``` shell +git merge --squash -Xsubtree="CRISPResso2/CRISPRessoReports" --no-commit --allow-unrelated-histories +``` -The acronym stands for "CrispressoReports Update" +*Note:* `` is the branch of the parent repo that contains the changes inside the `CRISPRessoReports` sub-directory. -cru = "!f() { git subtree pull --prefix CRISPRessoWEB/CRISPRessoReports https://github.com/edilytics/CRISPRessoReports.git $1 --squash; }; f" +### I am working on a feature that requires changing `CRISPRessoReports`, what do I do? -The acronym stands for "CrispressoReports Push" +If a feature that you are working on requires changes to CRISPRessoReports, you will need to perform a few steps to get setup. + +1. Create a feature branch in the parent repo, based on the parent repo master. + +``` shell +git checkout -b origin/master +``` + +2. Create a feature branch on `CRISPRessoReports`. + +Checkout your local `CRISPRessoReports` master branch. + +``` shell +git checkout master-reports +``` + +Pull in the latest changes. + +``` shell +git pull +``` + +Create the `CRISPRessoReports` feature branch based on `reports/master`. + +``` shell +git checkout -b -reports reports/master +``` + +*Note:* if your branch is named `cool-feature` in the parent repo, then follow the convention of naming the corresponding `CRISPRessoReports` branch `cool-feature-reports`. + +If you run `git status` at this point you should see any directories in the parent repo as untracked files, this is normal and expected. + +3. Switch back to the feature-branch in the parent repo, and develop your changes. + +``` shell +git checkout +``` + +*Note:* you can mingle your changes in `CRISPRessoReports` and the parent repo in the same commits. + +4. Merge and push your changes up to `CRISPRessoReports`. + +Switch to the `-reports` branch. + +``` shell +git checkout -reports +``` + +Merge the changes from the parent repo into the `-reports` branch. + +``` shell +git merge --squash -Xsubtree="CRISPResso2/CRISPRessoReports" --no-commit --allow-unrelated-histories +``` + +# FAQ + +## There are lots of merge conflicts, how do I just accept all of the incoming changes? + +If you want to blindly accept all of the incoming changes, you can add the parameter `-Xtheirs` to the `git merge...` command and anything that was a merge conflict before, should now be overwritten by the incoming change. + +## I tired of typing `git merge --squash ...`, what can I do?! + +Typing out the `git merge...` command is long and is a big pain. Here are some shortcuts to add to your `.git/config` file in order to make this easier to type. + +``` git-config +[alias] + # merge in branch and resolve merge conflicts + m = "!f() { git merge --squash -Xsubtree='CRISPResso2/CRISPRessoReports' --no-commit --allow-unrelated-histories $1; }; f" + # merge in branch and accept all of the incoming changes + mt = "!f() { git merge --squash -Xtheirs -Xsubtree='CRISPResso2/CRISPRessoReports' --no-commit --allow-unrelated-histories $1; }; f" +``` -crp = "!f() { git subtree push --prefix CRISPRessoWEB/CRISPRessoReports https://github.com/edilytics/CRISPRessoReports.git $1; }; f" +Now you can just run `git m ` to merge `` into your current branch. Or run `git mt ` to accept all of the incoming changes. +# Sources and helpful links +- This method was heavily based off of what was described in [this blog post](http://johnatten.com/2013/03/16/git-subtree-merge-the-quick-version/) +- If you want to know more about git merging, the manual is [very helpful](https://git-scm.com/book/en/v2/Git-Tools-Advanced-Merging) +- If you messed up (merging the wrong branch), you can undo it using `git reset --hard `. **Beware:** this can cause you to lose work, so use with care. [Learn more here](https://stackoverflow.com/a/8888015/1947159). +- If you need to rewrite git history, try using [git-filter-repo](https://github.com/newren/git-filter-repo) +- After rewriting git history (from a mirror repo), if you can't push to GitHub, [try this](https://stackoverflow.com/a/34266401/1947159) diff --git a/CRISPResso2/CRISPRessoReports/templates/batchReport.html b/CRISPResso2/CRISPRessoReports/templates/batchReport.html index 37580c5f..cfd79e26 100644 --- a/CRISPResso2/CRISPRessoReports/templates/batchReport.html +++ b/CRISPResso2/CRISPRessoReports/templates/batchReport.html @@ -1,5 +1,6 @@ {% extends "layout.html" %} {% block head %} + --> + + #} + {% endif %}
-
- Download report - Link to report - -
+ + {{render_partial('shared/partials/report_footer_buttons.html', report_zip_filename=report_zip_filename, report_path=report_path)}} + {# data bit for web version: #} {#

Data: {{data_label}}

#} -
{# jumbotron_content #} -
{# jumbrotron #} - -
{# column #} - -
+
+
{% endblock %} diff --git a/CRISPResso2/CRISPRessoReports/templates/layout.html b/CRISPResso2/CRISPRessoReports/templates/layout.html index 60f2f4b7..a028254c 100644 --- a/CRISPResso2/CRISPRessoReports/templates/layout.html +++ b/CRISPResso2/CRISPRessoReports/templates/layout.html @@ -9,10 +9,7 @@ - - - --> - - {% endif %} - {% if compact_plots_to_show|length > 0 %}
@@ -310,20 +147,14 @@
Summary Plots
{% for compact_plot in compact_plots_to_show %} - - {% endfor %} -
+ + {% endfor %} +
- {% endif %} + {% endif %} -
- {% if report_zip_filename %} - Download report - {% endif %} - Link to report - -
+ {{render_partial('shared/partials/report_footer_buttons.html', report_zip_filename=report_zip_filename, report_path=report_path)}}
{# jumbotron_content #}
{# jumbrotron #} diff --git a/CRISPResso2/CRISPRessoReports/templates/pooledReport.html b/CRISPResso2/CRISPRessoReports/templates/pooledReport.html index 59fc054c..ba944d90 100644 --- a/CRISPResso2/CRISPRessoReports/templates/pooledReport.html +++ b/CRISPResso2/CRISPRessoReports/templates/pooledReport.html @@ -45,44 +45,6 @@ {% block content %} - -
@@ -98,39 +60,14 @@
{{report_name}}
{% for region_name in run_names %} - {{region_name}} - {% endfor %} + {{region_name}} + {% endfor %}
{% endif %} - {% if failed_runs|length > 0 %} -
-
- -
Failed Runs
- -
-
-
- {% for failed_run in failed_runs %} - - - {{failed_run}} - - - - {% endfor %} -
-
-
- {% endif %} + {{render_partial('shared/partials/failed_runs.html', failed_runs=failed_runs, failed_runs_desc=failed_runs_desc)}} {% if report_data['names']|length > 0 %} {% for plot_name in report_data['names'] %} @@ -139,17 +76,14 @@
Failed Runs
{{report_data['titles'][plot_name]}}
- {{ render_partial('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 %} - {% endif %} + {% endif %} + + {{render_partial('shared/partials/report_footer_buttons.html', report_zip_filename=report_zip_filename, report_path=report_path)}} -
- Download report - Link to report - -
{# data bit for web version: #} {#

Data: {{data_label}}

diff --git a/CRISPResso2/CRISPRessoReports/templates/report.html b/CRISPResso2/CRISPRessoReports/templates/report.html index dbee21c0..9214d168 100644 --- a/CRISPResso2/CRISPRessoReports/templates/report.html +++ b/CRISPResso2/CRISPRessoReports/templates/report.html @@ -79,7 +79,7 @@ {% block content %}
-
+
@@ -549,27 +549,20 @@
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_10b', amplicon_name=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_10c', amplicon_name=amplicon_name)}}
+ {% endif %}
- {% 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'] %} @@ -610,13 +603,8 @@
Base editing for {{amplicon_name}}
{% endfor %}
{# tab content #}
-
- {% if report_zip_filename %} - Download report - {% endif %} - Link to report - -
+ + {{render_partial('shared/partials/report_footer_buttons.html', report_zip_filename=report_zip_filename, report_path=report_path)}}
{# jumbotron_content #}
{# jumbrotron #}
{# column #} diff --git a/CRISPResso2/CRISPRessoReports/templates/shared/partials/failed_runs.html b/CRISPResso2/CRISPRessoReports/templates/shared/partials/failed_runs.html new file mode 100644 index 00000000..015dda0f --- /dev/null +++ b/CRISPResso2/CRISPRessoReports/templates/shared/partials/failed_runs.html @@ -0,0 +1,65 @@ +{% if failed_runs|length > 0 %} +
+
+ +
Failed Runs
+ +
+ +
+
+ {% for failed_run in failed_runs %} + {# Toggle the description visibility on click #} + + {{failed_run}} + + {# Initially hide the description and add a light background with dark text for readability #} + + {% endfor %} +
+
+
+ + +{% endif %} diff --git a/CRISPResso2/CRISPRessoReports/templates/shared/partials/fig_reports.html b/CRISPResso2/CRISPRessoReports/templates/shared/partials/fig_reports.html index 90adc37d..e21c6853 100644 --- a/CRISPResso2/CRISPRessoReports/templates/shared/partials/fig_reports.html +++ b/CRISPResso2/CRISPRessoReports/templates/shared/partials/fig_reports.html @@ -1,35 +1,34 @@ -
- {% if amplicon_name is defined %} - {% if 'htmls' in report_data['figures'] and fig_name in report_data['figures']['htmls'][amplicon_name] %} +
+ {# Set the width based on the plot #} + {%- if fig_name in ['plot_1a', 'plot_1b', 'plot_1c', 'plot_1d', 'plot_3a', 'plot_4a', 'plot_4b', 'plot_4c', 'plot_4e', 'plot_4f', 'plot_5a', 'plot_7', 'plot_8', 'plot_8a', 'plot_11c'] -%} + {% set width = '40%' %} + {%- elif fig_name in ['plot_10b', 'plot_10c'] -%} + {% set width = '35%' %} + {%- elif fig_name in ['plot_10a'] -%} + {% set width = '70%' %} + {%- else -%} + {% set width = '100%' %} + {%- endif -%} + + {%- 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'] %} - - {% elif fig_name in ['plot_10b', 'plot_10c'] %} - - {% else %} - - {% endif %} - {% endif %} + {%- else -%} + + {% endif -%} - {% for (data_label,data_path) in report_data['figures']['datas'][amplicon_name][fig_name] %} + {%- 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'] %} + {%- 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'] %} - - {% elif fig_name in ['plot_10b', 'plot_10c'] %} - - {% else %} - - {% endif %} - {% endif %} + {%- else -%} + + {% endif -%} - {% for (data_label,data_path) in report_data['figures']['datas'][fig_name] %} + {%- for (data_label,data_path) in report_data['figures']['datas'][fig_name] %}

Data: {{data_label}}

- {% endfor %} - {% endif %} + {%- endfor -%} + {%- endif %}
diff --git a/CRISPResso2/CRISPRessoReports/templates/shared/partials/report_footer_buttons.html b/CRISPResso2/CRISPRessoReports/templates/shared/partials/report_footer_buttons.html new file mode 100644 index 00000000..fa6ab71d --- /dev/null +++ b/CRISPResso2/CRISPRessoReports/templates/shared/partials/report_footer_buttons.html @@ -0,0 +1,9 @@ +
+ {% if is_web -%} + {%- if report_zip_filename -%} + Download report + {% endif %} + Link to report + {% endif %} + +
diff --git a/CRISPResso2/CRISPRessoReports/templates/wgsReport.html b/CRISPResso2/CRISPRessoReports/templates/wgsReport.html index 889656cf..5f2008a4 100644 --- a/CRISPResso2/CRISPRessoReports/templates/wgsReport.html +++ b/CRISPResso2/CRISPRessoReports/templates/wgsReport.html @@ -46,44 +46,6 @@ {% block content %} - -
@@ -93,47 +55,20 @@
-
{{report_name}}
+
{{report_name}}
{% for region_name in run_names %} - {{region_name}} - {% endfor %} + {{region_name}} + {% endfor %}
- {% if failed_runs|length > 0 %} -
-
- -
Failed Runs
- -
- -
-
- {% for failed_run in failed_runs %} - - - {{failed_run}} - - - - {% endfor %} -
-
-
- {% endif %} + {{render_partial('shared/partials/failed_runs.html', failed_runs=failed_runs, failed_runs_desc=failed_runs_desc)}} - - {% if report_data['names']|length > 0 %} + {% if report_data['names']|length > 0 %} {% for plot_name in report_data['names'] %}
@@ -146,11 +81,7 @@
{{report_data['titles'][plot_name]}}
{% endfor %} {% endif %} -
- Download report - Link to report - -
+ {{render_partial('shared/partials/report_footer_buttons.html', report_zip_filename=report_zip_filename, report_path=report_path)}} {# data bit for web version: #} {#

Data: {{data_label}}

diff --git a/CRISPResso2/CRISPRessoShared.py b/CRISPResso2/CRISPRessoShared.py index 7849a654..d6a0ed93 100644 --- a/CRISPResso2/CRISPRessoShared.py +++ b/CRISPResso2/CRISPRessoShared.py @@ -635,7 +635,7 @@ def assert_fastq_format(file_path, max_lines_to_check=100): params: file_path: path to fastq file max_lines_to_check: number of lines to check in the file - returns: + returns: True if the file is in the correct format """ @@ -1037,7 +1037,7 @@ def check_if_failed_run(folder_name, info): bool True if run completed successfully, False otherwise string describing why it failed """ - + run_data_file = os.path.join(folder_name, 'CRISPResso2_info.json') status_info = os.path.join(folder_name, 'CRISPResso_status.txt') if not os.path.isfile(run_data_file) or not os.path.isfile(status_info): @@ -1048,7 +1048,7 @@ def check_if_failed_run(folder_name, info): unit = "region" else: unit = "sample" - + return True, f"CRISPResso failed for this {unit}! Please check your input files and parameters." else: with open(status_info) as fh: @@ -1902,7 +1902,7 @@ def is_C2Pro_installed(): def check_custom_config(args): """Check if the config_file argument was provided. If so load the configurations from the file, otherwise load default configurations. - + Parameters: ------------- args : dict @@ -1912,9 +1912,9 @@ def check_custom_config(args): ------------- style : dict A dict with a 'colors' key that contains hex color values for different report items. - + -OR- - + custom_style : dict A dict with a 'colors' key that contains hex color values for different report items loaded from a user provided json file. @@ -1929,10 +1929,10 @@ def check_custom_config(args): 'C': '#FDC086', 'G': '#FFFF99', 'N': '#C8C8C8', - '-': '#C1C1C1' - } + '-': '#1E1E1E', + } } - + logger = logging.getLogger(getmodule(stack()[1][0]).__name__) #Check if crispresso.pro is installed @@ -1946,12 +1946,12 @@ def check_custom_config(args): if 'colors' not in custom_config.keys(): logger.warn("Json file does not contain the colors key. Defaulting all values.") return config - + for key in config['colors']: if key not in custom_config['colors']: logger.warn(f"Value for {key} not provided, defaulting") custom_config['colors'][key] = config['colors'][key] - + return custom_config except Exception as e: logger.warn("Cannot read json file '%s', defaulting style parameters." % args.config_file)