Failed batch runs (#33)

* 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 * changed tuple to list for matplotlib change (#31) * wgs and batch failed runs implementation * Added failed run functionality including shared function, edits to Report, and displaying with HTML and Javascript * Merge CRISPRessoReports master into failed-batch-runs * Cole's failed-batch-runs review and changes (#36) * Fix showing link to report in CLI (only show in web) * Remove styling of jumbotron The p-5 added some weird space at the top of the container, the rounded-3 did not make a difference (because there is no background), and the h-100 also did not make a difference. * Remove extra spaces at end of the line * Remove color legend from figure caption in plot 4f * Refactor fig_reports.html partial to reduce duplication * Add opacity to custom colors on allele quilt plot * Remove extra spaces * Change default color of deletion It looked too similar to `N` and was difficult to tell apart. * Refactor plot 10c, refactor displaying of figures This commit adds flexbox to the plots, this was mainly for plots 10b and 10c because their alignment was off. * Add more plots to get the correct percentages for width * Remove setting the height of the plots * Check for failed batch info before retrieving it in `make_multi_report_from_folder` * Fix extraneous whitespace in `fig_reports` partial * Only load certain resources when on web mode * Move jQuery import to bottom of the page to improve performance * Extract out report footer buttons to partial * Fix too many closing divs in batchReport.html * Refactor failed runs to be a partial * Move the failed run JS to the partial This has the benefit of keeping the relevant code close, and also prevents the error that we were running into before where `chevronIcon` wasn't found when there were no failed runs (because the element wasn't there). * Remove `report_name` id because it probably has spaces * Move existing Plotly plots to batchReport from multiReport * Fix typo in fig 11c and resize it to 40% --------- Co-authored-by: Samuel Nichols <[email protected]> Co-authored-by: mbowcut2 <[email protected]> Co-authored-by: Cole Lyman <[email protected]>
edilytics · Nov 8, 2024 · 2bd6590 · 2bd6590
1 parent 18efdea
commit 2bd6590
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Showing 21 changed files with 425 additions and 694 deletions.
diff --git a/CRISPResso2/CRISPRessoAggregateCORE.py b/CRISPResso2/CRISPRessoAggregateCORE.py
@@ -17,6 +17,7 @@
 import traceback
 from datetime import datetime
 from CRISPResso2 import CRISPRessoShared
+from CRISPResso2 import CRISPRessoPlot
 from CRISPResso2.CRISPRessoReports import CRISPRessoReport
 from CRISPResso2.CRISPRessoMultiProcessing import get_max_processes, run_plot
 

diff --git a/CRISPResso2/CRISPRessoBatchCORE.py b/CRISPResso2/CRISPRessoBatchCORE.py
@@ -17,12 +17,6 @@
 from CRISPResso2 import CRISPRessoMultiProcessing
 from CRISPResso2.CRISPRessoReports import CRISPRessoReport
 
-if CRISPRessoShared.is_C2Pro_installed():
-    import CRISPRessoPro
-    C2PRO_INSTALLED = True
-else:
-    C2PRO_INSTALLED = False
-
 import logging
 
 logger = logging.getLogger(__name__)
@@ -115,7 +109,7 @@ def main():
         crispresso_options_for_batch = list(crispresso_options-options_to_ignore)
 
         CRISPRessoShared.check_file(args.batch_settings)
-        custom_config = CRISPRessoShared.check_custom_config(args)
+        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.')
@@ -643,7 +637,7 @@ def main():
                                 'sgRNA_intervals': sub_sgRNA_intervals,
                                 'sgRNA_sequences': consensus_guides,
                                 'quantification_window_idxs': include_idxs,
-                                'custom_colors': custom_config['colors'],
+                                'custom_colors': config['colors'],
                             }
                             debug('Plotting nucleotide percentage quilt for amplicon {0}, sgRNA {1}'.format(amplicon_name, sgRNA))
                             plot(
@@ -666,7 +660,7 @@ def main():
                                     'save_also_png': save_png,
                                     'sgRNA_intervals': sub_sgRNA_intervals,
                                     'quantification_window_idxs': include_idxs,
-                                    'custom_colors': custom_config['colors']
+                                    'custom_colors': config['colors']
                                 }
                                 debug('Plotting nucleotide conversion map for amplicon {0}, sgRNA {1}'.format(amplicon_name, sgRNA))
                                 plot(
@@ -694,7 +688,7 @@ def main():
                             'sgRNA_intervals': consensus_sgRNA_intervals,
                             'sgRNA_sequences': consensus_guides,
                             'quantification_window_idxs': include_idxs,
-                            'custom_colors': custom_config['colors'],
+                            'custom_colors': config['colors'],
                         }
                         debug('Plotting nucleotide quilt for {0}'.format(amplicon_name))
                         plot(
@@ -718,7 +712,7 @@ def main():
                                 'save_also_png': save_png,
                                 'sgRNA_intervals': consensus_sgRNA_intervals,
                                 'quantification_window_idxs': include_idxs,
-                                'custom_colors': custom_config['colors']
+                                'custom_colors': config['colors']
                             }
                             debug('Plotting nucleotide conversion map for {0}'.format(amplicon_name))
                             plot(
@@ -742,7 +736,7 @@ def main():
                             'mod_pct_df': modification_percentage_summary_df,
                             'fig_filename_root': f'{this_nuc_pct_quilt_plot_name}.json' if not args.use_matplotlib and C2PRO_INSTALLED else this_nuc_pct_quilt_plot_name,
                             'save_also_png': save_png,
-                            'custom_colors': custom_config['colors'],
+                            'custom_colors': config['colors'],
                         }
                         debug('Plotting nucleotide quilt for {0}'.format(amplicon_name))
                         plot(
@@ -761,7 +755,7 @@ def main():
                                 'conversion_nuc_from': args.conversion_nuc_from,
                                 'conversion_nuc_to': args.conversion_nuc_to,
                                 'save_also_png': save_png,
-                                'custom_colors': custom_config['colors']
+                                '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
@@ -3553,7 +3553,7 @@ def save_count_vectors_to_file(vectors, vectorNames, refSeq, filename):
             info('Making Plots...')
         ###############################################################################################################################################
         save_png = True
-        custom_config = CRISPRessoShared.check_custom_config(args)
+        config = CRISPRessoShared.check_custom_config(args)
         if args.suppress_report:
             save_png = False
 
@@ -3787,7 +3787,7 @@ def count_alternate_alleles(sub_base_vectors, ref_name, ref_sequence, ref_total_
                         'sgRNA_mismatches': sgRNA_mismatches,
                         'sgRNA_sequences': sgRNA_sequences,
                         'quantification_window_idxs': include_idxs_list,
-                        'custom_colors': custom_config["colors"],
+                        'custom_colors': config["colors"],
                     }
                     debug('Plotting nucleotide quilt across amplicon')
                     plot(CRISPRessoPlot.plot_nucleotide_quilt, plot_2a_input)
@@ -3836,7 +3836,7 @@ def count_alternate_alleles(sub_base_vectors, ref_name, ref_sequence, ref_total_
                             'sgRNA_mismatches': sgRNA_mismatches,
                             'sgRNA_sequences': sgRNA_sequences,
                             'quantification_window_idxs': new_include_idx,
-                            'custom_colors': custom_config["colors"],
+                            '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)
@@ -4017,7 +4017,7 @@ def count_alternate_alleles(sub_base_vectors, ref_name, ref_sequence, ref_total_
                         ),
                     },
                     'plot_root': plot_root,
-                    'custom_colors': custom_config["colors"],
+                    'custom_colors': config["colors"],
                     'save_also_png': save_png,
                 }
                 debug('Plotting amplication modifications for {0}'.format(ref_name))
@@ -4047,7 +4047,7 @@ def count_alternate_alleles(sub_base_vectors, ref_name, ref_sequence, ref_total_
                         'Mutation position distribution', ref_name,
                     ),
                     'plot_root': plot_root,
-                    'custom_colors': custom_config["colors"],
+                    'custom_colors': config["colors"],
                     'save_also_png': save_png,
                 }
                 debug('Plotting modification frequency for {0}'.format(ref_name))
@@ -4076,7 +4076,7 @@ def count_alternate_alleles(sub_base_vectors, ref_name, ref_sequence, ref_total_
                     ),
                     'ref_name': ref_name,
                     'plot_root': plot_root,
-                    'custom_colors': custom_config["colors"],
+                    'custom_colors': config["colors"],
                     'save_also_png': save_png,
                 }
                 debug('Plotting quantification window locations for {0}'.format(ref_name))
@@ -4134,7 +4134,7 @@ 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': custom_config["colors"],
+                        'custom_colors': config["colors"],
                         'save_also_png': save_png,
                     }
                     if ref_name == ref_names[0]:
@@ -4207,8 +4207,7 @@ 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,
-                        'sgRNA_sequences': sgRNA_sequences,
-                        'custom_colors': custom_config["colors"],
+                        'custom_colors': config["colors"],
                     }
                     debug('Plotting HDR nucleotide quilt')
                     plot(CRISPRessoPlot.plot_nucleotide_quilt, plot_4g_input)
@@ -4311,7 +4310,7 @@ def count_alternate_alleles(sub_base_vectors, ref_name, ref_sequence, ref_total_
                             ref_name,
                         ),
                         'plot_root': plot_root,
-                        'custom_colors': custom_config["colors"],
+                        'custom_colors': config["colors"],
                         'save_also_png': save_png,
                         'ref_name': ref_name,
                     }
@@ -4354,8 +4353,7 @@ 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': custom_config['colors'],
-                        'ref_name': ref_name,
+                        'custom_colors': config['colors']
                     }
                     debug('Plotting substitutions across reference for {0}'.format(ref_name))
                     plot(CRISPRessoPlot.plot_subs_across_ref, plot_10a_input)
@@ -4374,7 +4372,7 @@ def count_alternate_alleles(sub_base_vectors, ref_name, ref_sequence, ref_total_
                         ),
                         'fig_filename_root': fig_filename_root,
                         'save_also_png': save_png,
-                        'custom_colors': custom_config['colors']
+                        'custom_colors': config['colors']
                     }
                     debug('Plotting substitution frequency barplot for {0}'.format(ref_name))
                     plot(CRISPRessoPlot.plot_sub_freqs, plot_10b_input)
@@ -4389,7 +4387,7 @@ def count_alternate_alleles(sub_base_vectors, ref_name, ref_sequence, ref_total_
                         '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,
-                        'custom_colors': custom_config['colors']
+                        '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)
@@ -4481,6 +4479,7 @@ 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)
@@ -4567,7 +4566,7 @@ 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': custom_config['colors'],
+                            '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(
@@ -4587,7 +4586,7 @@ 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': custom_config['colors']
+                            '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(
@@ -4610,7 +4609,7 @@ 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': custom_config['colors']
+                            '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(
@@ -4808,7 +4807,7 @@ def get_scaffold_len(row, scaffold_start_loc, scaffold_seq):
                     'sgRNA_mismatches': sgRNA_mismatches,
                     'sgRNA_sequences': sgRNA_sequences,
                     'quantification_window_idxs': include_idxs_list,
-                    'custom_colors': custom_config['colors']
+                    'custom_colors': config['colors']
                 }
                 info('Plotting prime editing nucleotide percentage quilt', {'percent_complete': 96})
                 plot(CRISPRessoPlot.plot_nucleotide_quilt, plot_11a_input)
@@ -4869,7 +4868,7 @@ def get_scaffold_len(row, scaffold_start_loc, scaffold_seq):
                         'sgRNA_mismatches': sgRNA_mismatches,
                         'sgRNA_sequences': sgRNA_sequences,
                         'quantification_window_idxs': new_include_idx,
-                        'custom_colors': custom_config['colors']
+                        '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
@@ -9,6 +9,7 @@
 import sys
 import traceback
 from CRISPResso2 import CRISPRessoShared
+from CRISPResso2 import CRISPRessoPlot
 from CRISPResso2.CRISPRessoReports import CRISPRessoReport
 
 import logging