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Parallel plot refactor #247

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merged 4 commits into from
Sep 14, 2022
Merged

Parallel plot refactor #247

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bf540de
Fix duplicate plotting in CRISPRessoBatch aggregate
Colelyman Sep 14, 2022
d0ef4e7
Refactor mulltiprocessing plots in CRISPRessoBatch
Colelyman Sep 14, 2022
e7f30d5
Refactor multiprocessing plots in CRISPRessoCORE
Colelyman Sep 14, 2022
5248f2b
Refactor multiprocessing plots for CRISPRessoAggregate
Colelyman Sep 14, 2022
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85 changes: 31 additions & 54 deletions CRISPResso2/CRISPRessoAggregateCORE.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -9,6 +9,7 @@
import glob
from copy import deepcopy
from concurrent.futures import ProcessPoolExecutor, wait
from functools import partial
import sys
import argparse
import numpy as np
Expand All @@ -18,7 +19,7 @@
from CRISPResso2 import CRISPRessoShared
from CRISPResso2 import CRISPRessoPlot
from CRISPResso2 import CRISPRessoReport
from CRISPResso2.CRISPRessoMultiProcessing import get_max_processes
from CRISPResso2.CRISPRessoMultiProcessing import get_max_processes, run_plot


import logging
Expand Down Expand Up @@ -108,6 +109,13 @@ def main():
process_pool = ProcessPoolExecutor(n_processes)
process_results = []

plot = partial(
run_plot,
num_processes=n_processes,
process_pool=process_pool,
process_results=process_results,
)

#glob returns paths including the original prefix
all_files = []
for prefix in args.prefix:
Expand Down Expand Up @@ -491,13 +499,10 @@ def main():
'quantification_window_idxs': include_idxs,
'group_column': 'Folder',
}
if n_processes > 1:
process_results.append(process_pool.submit(
CRISPRessoPlot.plot_nucleotide_quilt,
**nucleotide_quilt_input,
))
else:
CRISPRessoPlot.plot_nucleotide_quilt(**nucleotide_quilt_input)
plot(
CRISPRessoPlot.plot_nucleotide_quilt,
nucleotide_quilt_input,
)

plot_name = os.path.basename(this_window_nuc_pct_quilt_plot_name)
window_nuc_pct_quilt_plot_names.append(plot_name)
Expand Down Expand Up @@ -529,13 +534,10 @@ def main():
'quantification_window_idxs': include_idxs,
'group_column': 'Folder',
}
if n_processes > 1:
process_results.append(process_pool.submit(
CRISPRessoPlot.plot_nucleotide_quilt,
**nucleotide_quilt_input,
))
else:
CRISPRessoPlot.plot_nucleotide_quilt(**nucleotide_quilt_input)
plot(
CRISPRessoPlot.plot_nucleotide_quilt,
nucleotide_quilt_input,
)

plot_name = os.path.basename(this_nuc_pct_quilt_plot_name)
nuc_pct_quilt_plot_names.append(plot_name)
Expand Down Expand Up @@ -571,13 +573,10 @@ def main():
'quantification_window_idxs': consensus_include_idxs,
'group_column': 'Folder',
}
if n_processes > 1:
process_results.append(process_pool.submit(
CRISPRessoPlot.plot_nucleotide_quilt,
**nucleotide_quilt_input,
))
else:
CRISPRessoPlot.plot_nucleotide_quilt(**nucleotide_quilt_input)
plot(
CRISPRessoPlot.plot_nucleotide_quilt,
nucleotide_quilt_input,
)

plot_name = os.path.basename(this_nuc_pct_quilt_plot_name)
nuc_pct_quilt_plot_names.append(plot_name)
Expand Down Expand Up @@ -633,15 +632,10 @@ def main():
'plot_path': plot_path,
'title': modification_type,
}
if n_processes > 1:
process_results.append(process_pool.submit(
CRISPRessoPlot.plot_allele_modification_heatmap,
**allele_modification_heatmap_input,
))
else:
CRISPRessoPlot.plot_allele_modification_heatmap(
**allele_modification_heatmap_input,
)
plot(
CRISPRessoPlot.plot_allele_modification_heatmap,
allele_modification_heatmap_input,
)

crispresso2_info['results']['general_plots']['allele_modification_heatmap_plot_names'].append(plot_name)
crispresso2_info['results']['general_plots']['allele_modification_heatmap_plot_paths'][plot_name] = plot_path
Expand All @@ -668,15 +662,10 @@ def main():
'plot_path': plot_path,
'title': modification_type,
}
if n_processes > 1:
process_results.append(process_pool.submit(
CRISPRessoPlot.plot_allele_modification_line,
**allele_modification_line_input,
))
else:
CRISPRessoPlot.plot_allele_modification_line(
**allele_modification_line_input
)
plot(
CRISPRessoPlot.plot_allele_modification_line,
allele_modification_line_input,
)
crispresso2_info['results']['general_plots']['allele_modification_line_plot_names'].append(plot_name)
crispresso2_info['results']['general_plots']['allele_modification_line_plot_paths'][plot_name] = plot_path
crispresso2_info['results']['general_plots']['allele_modification_line_plot_titles'][plot_name] = 'CRISPRessoAggregate {0} Across Samples for {1}'.format(
Expand Down Expand Up @@ -778,13 +767,7 @@ def main():
'save_png': save_png,
'cutoff': args.min_reads_for_inclusion,
}
if n_processes > 1:
process_results.append(process_pool.submit(
CRISPRessoPlot.plot_reads_total,
**reads_total_input,
))
else:
CRISPRessoPlot.plot_reads_total(**reads_total_input)
plot(CRISPRessoPlot.plot_reads_total, reads_total_input)

plot_name = os.path.basename(plot_root)
crispresso2_info['results']['general_plots']['summary_plot_root'] = plot_name
Expand All @@ -801,13 +784,7 @@ def main():
'save_png': save_png,
'cutoff': args.min_reads_for_inclusion,
}
if n_processes > 1:
process_results.append(process_pool.submit(
CRISPRessoPlot.plot_unmod_mod_pcts,
**unmod_mod_pcts_input,
))
else:
CRISPRessoPlot.plot_unmod_mod_pcts(**unmod_mod_pcts_input)
plot(CRISPRessoPlot.plot_unmod_mod_pcts, unmod_mod_pcts_input)

plot_name = os.path.basename(plot_root)
crispresso2_info['results']['general_plots']['summary_plot_root'] = plot_name
Expand Down
109 changes: 39 additions & 70 deletions CRISPResso2/CRISPRessoBatchCORE.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -8,6 +8,7 @@
import os
from copy import deepcopy
from concurrent.futures import ProcessPoolExecutor, wait
from functools import partial
import sys
import traceback
from datetime import datetime
Expand Down Expand Up @@ -337,6 +338,13 @@ def main():
process_results = []
process_pool = ProcessPoolExecutor(n_processes_for_batch)

plot = partial(
CRISPRessoMultiProcessing.run_plot,
num_processes=n_processes_for_batch,
process_results=process_results,
process_pool=process_pool,
)

window_nuc_pct_quilt_plot_names = []
nuc_pct_quilt_plot_names = []
window_nuc_conv_plot_names = []
Expand Down Expand Up @@ -559,15 +567,10 @@ def main():
'sgRNA_intervals': sub_sgRNA_intervals,
'quantification_window_idxs': include_idxs,
}
if n_processes_for_batch > 1:
process_results.append(process_pool.submit(
CRISPRessoPlot.plot_nucleotide_quilt,
**nucleotide_quilt_input,
))
else:
CRISPRessoPlot.plot_nucleotide_quilt(
**nucleotide_quilt_input,
)
plot(
CRISPRessoPlot.plot_nucleotide_quilt,
nucleotide_quilt_input,
)
plot_name = os.path.basename(this_window_nuc_pct_quilt_plot_name)
window_nuc_pct_quilt_plot_names.append(plot_name)
crispresso2_info['results']['general_plots']['summary_plot_titles'][plot_name] = 'sgRNA: ' + sgRNA + ' Amplicon: ' + amplicon_name
Expand All @@ -587,15 +590,10 @@ def main():
'sgRNA_intervals': sub_sgRNA_intervals,
'quantification_window_idxs': include_idxs,
}
if n_processes_for_batch > 1:
process_results.append(process_pool.submit(
CRISPRessoPlot.plot_conversion_map,
**conversion_map_input,
))
else:
CRISPRessoPlot.plot_conversion_map(
**conversion_map_input,
)
plot(
CRISPRessoPlot.plot_conversion_map,
conversion_map_input,
)
plot_name = os.path.basename(this_window_nuc_conv_plot_name)
window_nuc_conv_plot_names.append(plot_name)
crispresso2_info['results']['general_plots']['summary_plot_titles'][plot_name] = 'sgRNA: ' + sgRNA + ' Amplicon: ' + amplicon_name
Expand All @@ -617,15 +615,10 @@ def main():
'sgRNA_intervals': consensus_sgRNA_intervals,
'quantification_window_idxs': include_idxs,
}
if n_processes_for_batch > 1:
process_results.append(process_pool.submit(
CRISPRessoPlot.plot_nucleotide_quilt,
**nucleotide_plot_input,
))
else:
CRISPRessoPlot.plot_nucleotide_quilt(
**nucleotide_plot_input,
)
plot(
CRISPRessoPlot.plot_nucleotide_quilt,
nucleotide_quilt_input,
)
plot_name = os.path.basename(this_nuc_pct_quilt_plot_name)
nuc_pct_quilt_plot_names.append(plot_name)
crispresso2_info['results']['general_plots']['summary_plot_titles'][plot_name] = 'Amplicon: ' + amplicon_name
Expand All @@ -644,15 +637,10 @@ def main():
'sgRNA_intervals': consensus_sgRNA_intervals,
'quantification_window_idxs': include_idxs,
}
if n_processes_for_batch > 1:
process_results.append(process_pool.submit(
CRISPRessoPlot.plot_conversion_map,
**conversion_map_input,
))
else:
CRISPRessoPlot.plot_conversion_map(
**conversion_map_input,
)
plot(
CRISPRessoPlot.plot_conversion_map,
conversion_map_input,
)
plot_name = os.path.basename(this_nuc_conv_plot_name)
nuc_conv_plot_names.append(plot_name)
crispresso2_info['results']['general_plots']['summary_plot_titles'][plot_name] = 'Amplicon: ' + amplicon_name
Expand All @@ -671,15 +659,10 @@ def main():
'fig_filename_root': this_nuc_pct_quilt_plot_name,
'save_also_png': save_png,
}
if n_processes_for_batch > 1:
process_results.append(process_pool.submit(
CRISPRessoPlot.plot_nucleotide_quilt,
**nucleotide_quilt_input,
))
else:
CRISPRessoPlot.plot_nucleotide_quilt(
**nucleotide_quilt_input,
)
plot(
CRISPRessoPlot.plot_nucleotide_quilt,
nucleotide_quilt_input,
)
plot_name = os.path.basename(this_nuc_pct_quilt_plot_name)
nuc_pct_quilt_plot_names.append(plot_name)
crispresso2_info['results']['general_plots']['summary_plot_labels'][plot_name] = 'Composition of each base for the amplicon ' + amplicon_name
Expand All @@ -693,15 +676,10 @@ def main():
'conversion_nuc_to': args.conversion_nuc_to,
'save_also_png': save_png,
}
if n_processes_for_batch > 1:
process_results.append(process_pool.submit(
CRISPRessoPlot.plot_conversion_map,
**conversion_map_input,
))
else:
CRISPRessoPlot.plot_conversion_map(
**conversion_map_input,
)
plot(
CRISPRessoPlot.plot_conversion_map,
conversion_map_input,
)
plot_name = os.path.basename(this_nuc_conv_plot_name)
nuc_conv_plot_names.append(plot_name)
crispresso2_info['results']['general_plots']['summary_plot_labels'][plot_name] = args.conversion_nuc_from + '->' + args.conversion_nuc_to +' conversion rates for the amplicon ' + amplicon_name
Expand Down Expand Up @@ -756,15 +734,10 @@ def main():
'plot_path': plot_path,
'title': modification_type,
}
if n_processes_for_batch > 1:
process_results.append(process_pool.submit(
CRISPRessoPlot.plot_allele_modification_heatmap,
**allele_modification_heatmap_input,
))
else:
CRISPRessoPlot.plot_allele_modification_heatmap(
**allele_modification_heatmap_input,
)
plot(
CRISPRessoPlot.plot_allele_modification_heatmap,
allele_modification_heatmap_input,
)

crispresso2_info['results']['general_plots']['allele_modification_heatmap_plot_names'].append(plot_name)
crispresso2_info['results']['general_plots']['allele_modification_heatmap_plot_paths'][plot_name] = plot_path
Expand All @@ -791,13 +764,9 @@ def main():
'plot_path': plot_path,
'title': modification_type,
}
if n_processes_for_batch > 1:
process_results.append(process_pool.submit(
CRISPRessoPlot.plot_allele_modification_line,
**allele_modification_line_input,
))
CRISPRessoPlot.plot_allele_modification_line(
**allele_modification_line_input,
plot(
CRISPRessoPlot.plot_allele_modification_line,
allele_modification_line_input,
)

crispresso2_info['results']['general_plots']['allele_modification_line_plot_names'].append(plot_name)
Expand Down