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Sam/try plots #71

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merged 11 commits into from
May 6, 2024
Merged

Sam/try plots #71

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f7b74ce
Fix batch mode pandas warning. (#70)
mbowcut2 Apr 26, 2024
f68b625
Functional
Snicker7 May 1, 2024
7e28ff6
Cole/fix status file name (#69)
Colelyman May 1, 2024
b7d319c
Try catch all futures
Snicker7 May 1, 2024
1d275e9
Merge remote-tracking branch 'origin/master' into sam/try-plots
Snicker7 May 1, 2024
324ff7e
Fix test fail plots
Snicker7 May 1, 2024
7a1a061
Point test to try-plots
Snicker7 May 2, 2024
20b2ec2
Fix d3 not showing and plotly mixing with matplotlib
Snicker7 May 2, 2024
a2a3e71
Merge branch 'sam/try-plots' of https://github.com/edilytics/CRISPRes…
Snicker7 May 2, 2024
45b6dc3
Use logger for warnings and debug statements
Snicker7 May 6, 2024
0b4b233
Point tests back at master
Snicker7 May 6, 2024
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11 changes: 8 additions & 3 deletions CRISPResso2/CRISPRessoAggregateCORE.py
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Original file line number Diff line number Diff line change
Expand Up @@ -71,7 +71,7 @@ def main():

parser.add_argument('--debug', help='Show debug messages', action='store_true')
parser.add_argument('-v', '--verbosity', type=int, help='Verbosity level of output to the console (1-4), 4 is the most verbose', default=3)

# CRISPRessoPro params
parser.add_argument('--use_matplotlib', action='store_true',
help='Use matplotlib for plotting instead of plotly/d3 when CRISPRessoPro is installed')
Expand All @@ -98,7 +98,7 @@ def main():

log_filename=_jp('CRISPRessoAggregate_RUNNING_LOG.txt')
logger.addHandler(logging.FileHandler(log_filename))
logger.addHandler(CRISPRessoShared.StatusHandler(_jp('CRISPRessoAggregate_status.json')))
logger.addHandler(CRISPRessoShared.StatusHandler(os.path.join(OUTPUT_DIRECTORY, 'CRISPRessoAggregate_status.json')))

with open(log_filename, 'w+') as outfile:
outfile.write('[Command used]:\n%s\n\n[Execution log]:\n' % ' '.join(sys.argv))
Expand Down Expand Up @@ -869,7 +869,12 @@ def main():
debug('Plot pool results:')
for future in process_futures:
debug('future: ' + str(future))
future_results = [f.result() for f in process_futures] #required to raise exceptions thrown from within future
for future in process_futures:
try:
future.result()
except Exception as e:
logger.warning('Error in plot pool: %s' % e)
logger.debug(traceback.format_exc())
process_pool.shutdown()

info('Analysis Complete!', {'percent_complete': 100})
Expand Down
28 changes: 18 additions & 10 deletions CRISPResso2/CRISPRessoBatchCORE.py
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Original file line number Diff line number Diff line change
Expand Up @@ -18,7 +18,7 @@
from CRISPResso2.CRISPRessoReports import CRISPRessoReport

if CRISPRessoShared.is_C2Pro_installed():
from CRISPRessoPro import __version__ as CRISPRessoProVersion
import CRISPRessoPro
C2PRO_INSTALLED = True
else:
C2PRO_INSTALLED = False
Expand Down Expand Up @@ -127,7 +127,7 @@ def main():

log_filename = _jp('CRISPRessoBatch_RUNNING_LOG.txt')
logger.addHandler(logging.FileHandler(log_filename))
status_handler = CRISPRessoShared.StatusHandler(_jp('CRISPRessoBatch_status.json'))
status_handler = CRISPRessoShared.StatusHandler(os.path.join(OUTPUT_DIRECTORY, 'CRISPRessoBatch_status.json'))
logger.addHandler(status_handler)

with open(log_filename, 'w+') as outfile:
Expand Down Expand Up @@ -178,7 +178,7 @@ def main():
'plot_window_size', 'max_rows_alleles_around_cut_to_plot']
for int_col in int_columns:
if int_col in batch_params.columns:
batch_params[int_col].fillna(getattr(args, int_col), inplace=True)
batch_params.fillna(value={int_col: getattr(args, int_col)}, inplace=True)
batch_params[int_col] = batch_params[int_col].astype(int)

# rename column "a" to "amplicon_seq", etc
Expand Down Expand Up @@ -398,7 +398,10 @@ def main():
large_plot_cutoff = 300

percent_complete_start, percent_complete_end = 90, 99
percent_complete_step = (percent_complete_end - percent_complete_start) / len(all_amplicons)
if all_amplicons:
percent_complete_step = (percent_complete_end - percent_complete_start) / len(all_amplicons)
else:
percent_complete_step = 0
# report for amplicons
for amplicon_index, amplicon_seq in enumerate(all_amplicons):
# only perform comparison if amplicon seen in more than one sample
Expand Down Expand Up @@ -604,7 +607,7 @@ def main():
# and add it to the list
sub_sgRNA_intervals.append((newstart, newend))

this_window_nuc_pct_quilt_plot_name = _jp(amplicon_plot_name + 'Nucleotide_percentage_quilt_around_sgRNA_'+sgRNA)
this_window_nuc_pct_quilt_plot_name = _jp(amplicon_plot_name.replace('.', '') + 'Nucleotide_percentage_quilt_around_sgRNA_'+sgRNA)
nucleotide_quilt_input = {
'nuc_pct_df': sub_nucleotide_percentage_summary_df,
'mod_pct_df': sub_modification_percentage_summary_df,
Expand All @@ -622,8 +625,6 @@ def main():
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
if len(consensus_guides) == 1:
crispresso2_info['results']['general_plots']['summary_plot_titles'][plot_name] = ''
crispresso2_info['results']['general_plots']['summary_plot_labels'][plot_name] = 'Composition of each base around the guide ' + sgRNA + ' for the amplicon ' + amplicon_name
crispresso2_info['results']['general_plots']['summary_plot_datas'][plot_name] = [('Nucleotide frequencies', os.path.basename(nucleotide_frequency_summary_filename)), ('Modification frequencies', os.path.basename(modification_frequency_summary_filename))]

Expand Down Expand Up @@ -656,7 +657,7 @@ def main():
# done with per-sgRNA plots

if not args.suppress_plots and not args.suppress_batch_summary_plots: # plot the whole region
this_nuc_pct_quilt_plot_name = _jp(amplicon_plot_name + 'Nucleotide_percentage_quilt')
this_nuc_pct_quilt_plot_name = _jp(amplicon_plot_name.replace('.', '') + 'Nucleotide_percentage_quilt')
nucleotide_quilt_input = {
'nuc_pct_df': nucleotide_percentage_summary_df,
'mod_pct_df': modification_percentage_summary_df,
Expand Down Expand Up @@ -706,7 +707,7 @@ def main():

else: # guides are not the same
if not args.suppress_plots and not args.suppress_batch_summary_plots:
this_nuc_pct_quilt_plot_name = _jp(amplicon_plot_name + 'Nucleotide_percentage_quilt')
this_nuc_pct_quilt_plot_name = _jp(amplicon_plot_name.replace('.', '') + 'Nucleotide_percentage_quilt')
nucleotide_quilt_input = {
'nuc_pct_df': nucleotide_percentage_summary_df,
'mod_pct_df': modification_percentage_summary_df,
Expand Down Expand Up @@ -775,6 +776,7 @@ def main():
'sample_sgRNA_intervals': sgRNA_intervals,
'plot_path': plot_path,
'title': modification_type,
'amplicon_name': amplicon_name,
}
debug('Plotting allele modification heatmap for {0}'.format(amplicon_name))
plot(
Expand Down Expand Up @@ -806,6 +808,7 @@ def main():
'sample_sgRNA_intervals': sgRNA_intervals,
'plot_path': plot_path,
'title': modification_type,
'amplicon_name': amplicon_name,
}
debug('Plotting allele modification line plot for {0}'.format(amplicon_name))
plot(
Expand Down Expand Up @@ -901,7 +904,12 @@ def main():
debug('CRISPResso batch results:')
for future in process_futures:
debug('future: ' + str(future))
future_results = [f.result() for f in process_futures] #required to raise exceptions thrown from within future
for future in process_futures:
try:
future.result()
except Exception as e:
logger.warning('Error in plot pool: %s' % e)
logger.debug(traceback.format_exc())
process_pool.shutdown()

if not args.suppress_report:
Expand Down
17 changes: 11 additions & 6 deletions CRISPResso2/CRISPRessoCORE.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1288,7 +1288,7 @@ def print_stacktrace_if_debug():
with open(log_filename, 'w+') as outfile:
outfile.write('CRISPResso version %s\n[Command used]:\n%s\n\n[Execution log]:\n' %(CRISPRessoShared.__version__, crispresso_cmd_to_write))

logger.addHandler(CRISPRessoShared.StatusHandler(_jp('CRISPResso_status.json')))
logger.addHandler(CRISPRessoShared.StatusHandler(os.path.join(OUTPUT_DIRECTORY, 'CRISPResso_status.json')))

aln_matrix_loc = os.path.join(_ROOT, "EDNAFULL")
CRISPRessoShared.check_file(aln_matrix_loc)
Expand Down Expand Up @@ -3776,11 +3776,11 @@ def count_alternate_alleles(sub_base_vectors, ref_name, ref_sequence, ref_total_
mod_df_for_plot.insert(0, 'Batch', ref_name)

plot_root = _jp('2a.'+ ref_plot_name + 'Nucleotide_percentage_quilt')
pro_output_name = f'plot_{os.path.basename(plot_root)}.json'
pro_output_name = os.path.join(OUTPUT_DIRECTORY, f'plot_{os.path.basename(plot_root)}.json')
plot_2a_input = {
'nuc_pct_df': nuc_df_for_plot,
'mod_pct_df': mod_df_for_plot,
'fig_filename_root': f'{_jp(pro_output_name)}' if not args.use_matplotlib and C2PRO_INSTALLED else plot_root,
'fig_filename_root': pro_output_name if not args.use_matplotlib and C2PRO_INSTALLED else plot_root,
'save_also_png': save_png,
'sgRNA_intervals': sgRNA_intervals,
'sgRNA_names': sgRNA_names,
Expand Down Expand Up @@ -3824,11 +3824,11 @@ def count_alternate_alleles(sub_base_vectors, ref_name, ref_sequence, ref_total_
for x in include_idxs_list:
new_include_idx += [x - new_sel_cols_start]
plot_root = _jp('2b.'+ ref_plot_name + 'Nucleotide_percentage_quilt_around_' + sgRNA_label)
pro_output_name = f'plot_{os.path.basename(plot_root)}.json'
pro_output_name = os.path.join(OUTPUT_DIRECTORY, f'plot_{os.path.basename(plot_root)}.json')
plot_2b_input = {
'nuc_pct_df': nuc_df_for_plot.iloc[:, sel_cols],
'mod_pct_df': mod_df_for_plot.iloc[:, sel_cols],
'fig_filename_root': f'{_jp(pro_output_name)}' if not args.use_matplotlib and C2PRO_INSTALLED else plot_root,
'fig_filename_root': pro_output_name if not args.use_matplotlib and C2PRO_INSTALLED else plot_root,
'save_also_png': save_png,
'sgRNA_intervals': new_sgRNA_intervals,
'sgRNA_names': sgRNA_names,
Expand Down Expand Up @@ -4893,7 +4893,12 @@ def get_scaffold_len(row, scaffold_start_loc, scaffold_seq):
debug('Plot pool results:')
for future in process_futures:
debug('future: ' + str(future))
future_results = [f.result() for f in process_futures] #required to raise exceptions thrown from within future
for future in process_futures:
try:
future.result()
except Exception as e:
logger.warning('Error in plot pool: %s' % e)
logger.debug(traceback.format_exc())
process_pool.shutdown()

info('Done!')
Expand Down
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