def do_seq(seq,args,fname): cmd = 'samtools view '+args.input+' '+seq p = Popen(cmd.split(),stdout=PIPE) cmd = 'bedtools genomecov -i - -bg -g '+fname po2 = Popen(cmd.split(),stdin=PIPE,stdout=PIPE) cmd = 'sort -k 1,1 -k2,2n -k3,3n -S1G --parallel='+str(args.threads) if args.tempdir: cmd += ' -T '+args.tempdir po1 = Popen(cmd.split(),stdin=PIPE,stdout=po2.stdin) for line in p.stdout: sam = SAM(line) if not sam.is_aligned(): continue for ex in sam.get_target_transcript(min_intron=68).exons: bed = "\t".join([str(x) for x in ex.get_range().get_bed_array()]) po1.stdin.write(bed+"\n") po1.communicate() res = po2.communicate()[0] return res
def do_seq(seq, args, fname): cmd = 'samtools view ' + args.input + ' ' + seq p = Popen(cmd.split(), stdout=PIPE) cmd = 'bedtools genomecov -i - -bg -g ' + fname po2 = Popen(cmd.split(), stdin=PIPE, stdout=PIPE) cmd = 'sort -k 1,1 -k2,2n -k3,3n -S1G --parallel=' + str(args.threads) if args.tempdir: cmd += ' -T ' + args.tempdir po1 = Popen(cmd.split(), stdin=PIPE, stdout=po2.stdin) for line in p.stdout: sam = SAM(line) if not sam.is_aligned(): continue for ex in sam.get_target_transcript(min_intron=68).exons: bed = "\t".join([str(x) for x in ex.get_range().get_bed_array()]) po1.stdin.write(bed + "\n") po1.communicate() res = po2.communicate()[0] return res