elif not args.gtf_file:
if __name__ == '__main__':
p = Pool((args.ncores))
p.map(shuffle_bedtools_no_gtf, n_rand)
concatFiles(args.outfile + '.datamatrix/shuffled.entry.*.bed',
args.outfile + '.datamatrix/shuffled.bed')
list(
map(os.remove,
glob.glob(args.outfile + ".datamatrix/shuffled.entry.*.bed")))
cat_command = " ".join(['cat '+args.outfile+'.datamatrix/shuffled.bed '+\
args.outfile+'.datamatrix/input_list.bed > '+\
args.outfile+'.datamatrix/genomic_ranges.bed'])
p = Popen(cat_command, stdout=PIPE, shell=True)
p.communicate()
if args.n_rand == 0:
print()
print("Skipping randomized background step")
cat_command = " ".join([
'cat ' + args.outfile + '.datamatrix/input_list.bed > ' +
args.outfile + '.datamatrix/genomic_ranges.bed'
])
p = Popen(cat_command, stdout=PIPE, shell=True)
p.communicate()
bed = BedTool(args.outfile +
'.datamatrix/genomic_ranges.bed').to_dataframe().reset_index()
if strd == False:
