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Create html report for CRISPRessoComparePooledWGS
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@kclem
kclem committed Jun 24, 2021
1 parent abe3054 commit 48d6c87
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Showing 2 changed files with 73 additions and 24 deletions.
4 changes: 2 additions & 2 deletions CRISPResso2/CRISPRessoCompareCORE.py
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Original file line number Diff line number Diff line change
Expand Up @@ -462,14 +462,14 @@ def get_plot_title_with_ref_name(plotTitle,refName):

if not args.suppress_report:
if (args.place_report_in_output_folder):
report_name = _jp("CRISPResso2Batch_report.html")
report_name = _jp("CRISPResso2Compare_report.html")
else:
report_name = OUTPUT_DIRECTORY+'.html'
CRISPRessoReport.make_compare_report_from_folder(report_name,crispresso2_info,OUTPUT_DIRECTORY,_ROOT)
crispresso2_info['report_location'] = report_name
crispresso2_info['report_filename'] = os.path.basename(report_name)

cp.dump(crispresso2_info, open(crispresso2Compare_info_file, 'wb' ) )
cp.dump(crispresso2_info, open(crispresso2Compare_info_file, 'wb'))

info('Analysis Complete!')
print(CRISPRessoShared.get_crispresso_footer())
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93 changes: 71 additions & 22 deletions CRISPResso2/CRISPRessoPooledWGSCompareCORE.py
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Original file line number Diff line number Diff line change
Expand Up @@ -5,16 +5,15 @@
(c) 2018 The General Hospital Corporation. All Rights Reserved.
'''

import argparse
from copy import deepcopy
import os
import errno
import sys
import subprocess as sb
import glob
import argparse
import re
from CRISPResso2 import CRISPRessoShared
from CRISPResso2 import CRISPRessoMultiProcessing
from CRISPResso2 import CRISPRessoReport
import traceback
import cPickle as cp


import logging
Expand Down Expand Up @@ -89,13 +88,19 @@ def main():
parser.add_argument('-n2','--sample_2_name', help='Sample 2 name', default='Sample_2')
parser.add_argument('-o','--output_folder', help='', default='')
parser.add_argument('-p','--n_processes',type=int, help='Number of processes to use for CRISPResso comparison',default=1)
parser.add_argument('--save_also_png',help='Save also .png images additionally to .pdf files',action='store_true')
parser.add_argument('--min_frequency_alleles_around_cut_to_plot', type=float, help='Minimum %% reads required to report an allele in the alleles table plot.', default=0.2)
parser.add_argument('--max_rows_alleles_around_cut_to_plot', type=int, help='Maximum number of rows to report in the alleles table plot. ', default=50)
parser.add_argument('--place_report_in_output_folder', help='If true, report will be written inside the CRISPResso output folder. By default, the report will be written one directory up from the report output.', action='store_true')
parser.add_argument('--suppress_report', help='Suppress output report', action='store_true')
parser.add_argument('--debug', help='Show debug messages', action='store_true')

args = parser.parse_args()
debug_flag = args.debug

crispresso_compare_options=['save_also_png',]
crispresso_compare_options=['min_frequency_alleles_around_cut_to_plot','max_rows_alleles_around_cut_to_plot','place_report_in_output_folder','suppress_report','debug']

sample_1_name = CRISPRessoShared.slugify(args.sample_1_name)
sample_2_name = CRISPRessoShared.slugify(args.sample_2_name)

#check that the CRISPRessoPooled output is present
quantification_summary_file_1=check_PooledWGS_output_folder(args.crispresso_pooled_wgs_output_folder_1)
Expand All @@ -107,7 +112,7 @@ def main():
if not args.name:
database_id='%s_VS_%s' % (get_name_from_folder(args.crispresso_pooled_wgs_output_folder_1),get_name_from_folder(args.crispresso_pooled_wgs_output_folder_2))
else:
database_id=args.name
database_id=CRISPRessoShared.slugify(args.name)


OUTPUT_DIRECTORY='CRISPRessoPooledWGSCompare_on_%s' % database_id
Expand All @@ -132,45 +137,89 @@ def main():
with open(log_filename,'w+') as outfile:
outfile.write('[Command used]:\nCRISPRessoPooledWGSCompare %s\n\n[Execution log]:\n' % ' '.join(sys.argv))

crispresso2Compare_info_file = os.path.join(OUTPUT_DIRECTORY,'CRISPResso2PooledWGSCompare_info.pickle')
crispresso2_info = {} #keep track of all information for this run to be pickled and saved at the end of the run
crispresso2_info['version'] = CRISPRessoShared.__version__
crispresso2_info['args'] = deepcopy(args)

crispresso2_info['log_filename'] = os.path.basename(log_filename)

crispresso2_info['summary_plot_names'] = []
crispresso2_info['summary_plot_titles'] = {}
crispresso2_info['summary_plot_labels'] = {}
crispresso2_info['summary_plot_datas'] = {}

save_png = True
if args.suppress_report:
save_png = False


#load data and calculate the difference
df_quant_1=pd.read_table(quantification_summary_file_1)
df_quant_2=pd.read_table(quantification_summary_file_2)
df_quant_1=pd.read_csv(quantification_summary_file_1,sep="\t")
df_quant_2=pd.read_csv(quantification_summary_file_2,sep="\t")
# df_comp=df_quant_1.set_index(['Name','Amplicon']).join(df_quant_2.set_index(['Name','Amplicon']),lsuffix='_%s' % args.sample_1_name,rsuffix='_%s' % args.sample_2_name)
df_comp=df_quant_1.set_index('Name').join(df_quant_2.set_index('Name'),lsuffix='_%s' % args.sample_1_name,rsuffix='_%s' % args.sample_2_name)
df_comp=df_quant_1.set_index('Name').join(df_quant_2.set_index('Name'),lsuffix='_%s' % sample_1_name,rsuffix='_%s' % sample_2_name)

df_comp['(%s-%s)_Unmodified%%' % (args.sample_1_name,args.sample_2_name)]=df_comp['Unmodified%%_%s' % args.sample_1_name]-df_comp['Unmodified%%_%s' % args.sample_2_name]
df_comp['(%s-%s)_Unmodified%%' % (sample_1_name,args.sample_2_name)]=df_comp['Unmodified%%_%s' % sample_1_name]-df_comp['Unmodified%%_%s' % args.sample_2_name]

df_comp.fillna('NA').to_csv(_jp('COMPARISON_SAMPLES_QUANTIFICATION_SUMMARIES.txt'),sep='\t')


#now run CRISPRessoCompare for the pairs for wich we have data in both folders
crispresso_cmds = []
processed_regions = set([])
processed_regions = []
processed_region_folder_names = {}
processed_region_html_files = {}
for idx,row in df_comp.iterrows():
if idx[0] in processed_regions:
if idx in processed_regions:
continue
if row.isnull().any():
warn('Skipping sample %s since it was not processed in one or both conditions' % idx[0])
warn('Skipping sample %s since it was not processed in one or both conditions' % idx)
else:
processed_regions.add(idx[0])
processed_regions.append(idx)
#crispresso_output_folder_1=os.path.join(args.crispresso_pooled_wgs_output_folder_1,'CRISPResso_on_%s' % idx)
#crispresso_output_folder_2=os.path.join(args.crispresso_pooled_wgs_output_folder_2,'CRISPResso_on_%s' % idx)
crispresso_output_folder_1=os.path.join(args.crispresso_pooled_wgs_output_folder_1,'CRISPResso_on_%s' % idx[0])
crispresso_output_folder_2=os.path.join(args.crispresso_pooled_wgs_output_folder_2,'CRISPResso_on_%s' % idx[0])
crispresso_compare_cmd=CRISPResso_compare_to_call +' "%s" "%s" -o "%s" -n1 "%s" -n2 "%s" ' % (crispresso_output_folder_1,
crispresso_output_folder_1=os.path.join(args.crispresso_pooled_wgs_output_folder_1,'CRISPResso_on_%s' % idx)
crispresso_output_folder_2=os.path.join(args.crispresso_pooled_wgs_output_folder_2,'CRISPResso_on_%s' % idx)
compare_output_name = "%s_%s_VS_%s"%(idx,sample_1_name,sample_2_name)
crispresso_compare_cmd=CRISPResso_compare_to_call +' "%s" "%s" -o "%s" -n %s -n1 "%s" -n2 "%s" ' % (crispresso_output_folder_1,
crispresso_output_folder_2,
OUTPUT_DIRECTORY,
args.sample_1_name+'_%s' % idx[0],
args.sample_2_name+'_%s' % idx[0],
compare_output_name,
sample_1_name+'_'+idx,
sample_2_name+'_'+idx
)

crispresso_compare_cmd=CRISPRessoShared.propagate_crispresso_options(crispresso_compare_cmd,crispresso_compare_options,args)
info('Running CRISPRessoCompare:%s' % crispresso_compare_cmd)
crispresso_cmds.append(crispresso_compare_cmd)
sub_folder = os.path.join(OUTPUT_DIRECTORY,"CRISPRessoCompare_on_"+compare_output_name)
this_sub_html_file = os.path.basename(sub_folder)+".html"
print(' 1 this_sub_html_file: ' + this_sub_html_file)
if args.place_report_in_output_folder:
this_sub_html_file = os.path.join(os.path.basename(sub_folder),"CRISPResso2Compare_report.html")
print('2 this_sub_html_file: ' + this_sub_html_file)
processed_region_html_files[idx] = this_sub_html_file
processed_region_folder_names[idx] = compare_output_name



print('debugGGG')
CRISPRessoMultiProcessing.run_crispresso_cmds(crispresso_cmds,args.n_processes,'Comparison')
crispresso2_info['processed_regions'] = processed_regions
crispresso2_info['processed_region_folder_names'] = processed_region_folder_names

if not args.suppress_report:
if args.place_report_in_output_folder:
report_name = _jp("CRISPResso2PooledWGSCompare_report.html")
else:
report_name = OUTPUT_DIRECTORY+'.html'
CRISPRessoReport.make_multi_report(processed_regions,processed_region_html_files,report_name,OUTPUT_DIRECTORY,_ROOT,'CRISPREssoPooledWGSCompare Report<br>'+sample_1_name+" vs" + sample_2_name)
crispresso2_info['report_location'] = report_name
crispresso2_info['report_filename'] = os.path.basename(report_name)

with open(crispresso2Compare_info_file,"wb") as info_file:
cp.dump(crispresso2_info, info_file)

info('All Done!')
print(CRISPRessoShared.get_crispresso_footer())
sys.exit(0)
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