sc_atac_bam2matrix.py

import argparse
import os
import subprocess

parser = argparse.ArgumentParser(description='A program to convert a deduplicated bam file to a matrix of sites by cells for scATAC-seq analysis.')
parser.add_argument('-B','--inbam', help='Deduplicated bam file',dest='inbam',required=True)
parser.add_argument('-I','--indextable', help='File listing acceptable barcodes',dest='indextable',required=True)
parser.add_argument('-O','--outdir', help='Output directory',dest='outdir',required=True)
parser.add_argument('-P','--prefix',help='Output file prefix',dest='prefix',required=True)
parser.add_argument('-C','--cutoff',help='Read depth cutoff for cells',dest='cutoff',required=False,default="auto")
parser.add_argument('-W','--windows',help='Bed file containing locations of windows reads should be counted in',dest='windows',required=True)
args = parser.parse_args()

def submitter(commander):
        """Submits commands directly to the command line and waits for the process to finish."""
        submiting = subprocess.Popen(commander,shell=True)
        submiting.wait()

if args.outdir[-1] != '/':
	args.outdir = args.outdir + '/'

try:
	os.makedirs(args.outdir)
except OSError:
	print 'Outdir already exists...'

print "Counting reads assigned to barcodes..."
scriptdir = os.path.dirname(os.path.abspath(__file__))
readcounter = 'python ' + scriptdir + '/sc_atac_barcode_read_counter.py ' + args.inbam + ' ' + args.indextable + ' ' + args.outdir + args.prefix + '.readcount.report.txt'
submitter(readcounter)

print "Determining read depth cutoff..."
cutoffer = 'Rscript ' + scriptdir + '/sc_atac_cell_cutoff.R ' + args.outdir + args.prefix + ' ' + args.cutoff
submitter(cutoffer)

print "Building cell matrix..."
builder = 'python ' + scriptdir + '/sc_atac_window_counter.py ' + args.inbam + ' ' + args.outdir + args.prefix + '.readdepth.cells.indextable.txt ' + args.windows + ' ' + args.outdir + args.prefix + '.cellmatrix.txt True'
submitter(builder)