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Failed batch runs #33

Merged
merged 8 commits into from
Jan 22, 2024
Merged

Failed batch runs #33

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3fb59cf
Reports, add reports to packages, colors, ordered pandas sort (#28)
Snicker7 Aug 14, 2023
97da958
changed tuple to list for matplotlib change (#31)
mbowcut2 Oct 9, 2023
937e9e2
Merge branch 'master' of github.com:edilytics/CRISPResso2
trevormartinj7 Oct 9, 2023
924ed95
Merge branch 'master' of github.com:edilytics/CRISPResso2
trevormartinj7 Nov 29, 2023
1259841
wgs and batch failed runs implementation
trevormartinj7 Dec 8, 2023
85e495b
Added failed run functionality including shared function, edits to Re…
trevormartinj7 Dec 20, 2023
e62873b
Merge CRISPRessoReports master into failed-batch-runs
Colelyman Jan 5, 2024
9d578e1
Cole's failed-batch-runs review and changes (#36)
Colelyman Jan 22, 2024
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2 changes: 1 addition & 1 deletion CRISPResso2/CRISPRessoAggregateCORE.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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


Expand Down
21 changes: 17 additions & 4 deletions CRISPResso2/CRISPRessoBatchCORE.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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

Expand Down Expand Up @@ -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.')
Expand Down Expand Up @@ -301,12 +302,16 @@ def main():
amplicon_names = {}
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')
if not os.path.isfile(run_data_file):
info("Skipping folder '%s'. Cannot find run data at '%s'."%(folder_name, run_data_file))
# 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

Expand All @@ -326,6 +331,8 @@ 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
Expand Down Expand Up @@ -596,6 +603,7 @@ 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(
Expand All @@ -620,6 +628,7 @@ 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(
Expand All @@ -646,6 +655,7 @@ 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(
Expand All @@ -669,6 +679,7 @@ 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(
Expand All @@ -692,6 +703,7 @@ 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(
Expand All @@ -710,6 +722,7 @@ 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(
Expand Down
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