def dostream(stream): reader = SamLocusStream(stream) while True: locus = reader.read_locus() if not locus: break print locus[0].chr + "\t" + str(locus[0].start - 1) + "\t" + str( locus[0].end)
def dopart(stream): reader = SamLocusStream(stream) v = [] while True: locus = reader.read_locus() if not locus: break v.append(locus[0].chr+"\t"+str(locus[0].start-1)+"\t"+str(locus[0].end)) return v
def dopart(stream): reader = SamLocusStream(stream) v = [] while True: locus = reader.read_locus() if not locus: break v.append(locus[0].chr + "\t" + str(locus[0].start - 1) + "\t" + str(locus[0].end)) return v
def main(): parser = argparse.ArgumentParser() parser.add_argument('--min_intron',type=int,default=68) parser.add_argument('--min_depth',type=int,default=1) parser.add_argument('-v','--verbose',action='store_true') parser.add_argument('input',help="BAM file or stream sam input with header with -") args = parser.parse_args() if args.input == '-': inf = sys.stdin else: cmd = "samtools view -h "+args.input p = Popen(cmd.split(),stdout=PIPE,bufsize=1) inf = p.stdout s = SamLocusStream(inf) #s.junctions_only = False while True: locus = s.read_locus() if not locus: break #print locus[0].get_range_string()+"\t"+str(len(locus[1])) process_locus(locus[1],args) if args.input != '-': p.communicate()
def dostream(stream): reader = SamLocusStream(stream) while True: locus = reader.read_locus() if not locus: break print locus[0].chr+"\t"+str(locus[0].start-1)+"\t"+str(locus[0].end)