cell_list = [x.split('_')[0] for x in fastq_list]
cell_list = list(set(cell_list))
cell_list.sort()
if not os.path.exists(options.s + '/work'):
subprocess.check_call('mkdir ' + options.s + '/work', shell=True)
#
parameters = []
for cell in cell_list:
work_dir = options.s + '/work/' + cell + '/'
if os.path.exists(work_dir):
subprocess.check_call('rm -rf ' + work_dir, shell=True)
subprocess.check_call('mkdir ' + work_dir, shell=True)
input1, input2 = options.s + '/data/' + cell + '_1.trim.fastq', options.s + '/data/' + cell + '_2.trim.fastq'
par = [work_dir, cell, options, input1, input2, chr_list]
parameters.append(par)
#### mapping(par)
#
pool = Pool(int(options.np))
pool.map(mapping, parameters)
pool.close()
pool.join()
#
#
for cell in cell_list:
work_dir = options.s + '/work/' + cell + '/'
marked_bam = work_dir + cell + '.marked.bam'
refSeqTSS = work_dir + cell + '.RefSeqTSS'
subroutines.draw_TSS_insert(options.tss, marked_bam, refSeqTSS)
#
#
os.popen('samtools merge -f ' + temp_bam + ' ' + marked)
os.popen('samtools index ' + temp_bam)
all_temp = ' '.join(temps)
os.popen('samtools merge -f ' + merged_bam + ' ' + all_temp)
#
os.popen('samtools index ' + merged_bam)
print '!!!!!! merge done !!!!!!'
print
#
hist_log = peak_folder + 'mergeAll.hist.log'
hist_pdf = peak_folder + 'mergeAll.hist.pdf'
os.popen('java -XX:+UseSerialGC -Xmx1g -jar '+options.picard+' CollectInsertSizeMetrics VALIDATION_STRINGENCY=SILENT I='
+ merged_bam + ' O=' + hist_log + ' H=' + hist_pdf + ' W=1000')
#
refSeqTSS = peak_folder + 'mergeAll.RefSeqTSS'
subroutines.draw_TSS_insert(tssFile, merged_bam, refSeqTSS)
#
print '!!!!!! call peak by macs2 !!!!!!'
peak_file = peak_folder + 'peaks'
os.popen('macs2 callpeak --nomodel -t ' + merged_bam + ' -n '
+ peak_file + ' --nolambda --keep-dup all --call-summits')
print '!!!!!! call peak done !!!!!!'
print
#
summit = peak_folder + 'peaks_summits.bed'
filtered_peak = peak_folder + 'filtered_peaks.bed'
if options.blist:
print '!!!!!! filter peaks !!!!!!'
os.popen('bedtools intersect -v -a ' + summit + ' -b ' + options.blist
+ " | sort -k5 -nr > " + filtered_peak)
print '!!!!!! filter peaks done !!!!!!'