def process_buffer(mpa):
mpa.populate_query()
#separate entires by Locus
loci = RangeBasics.Loci()
loci.set_use_direction(True)
minimum_locus_distance = 400000
for entry in mpa.entries:
rng = RangeBasics.Bed(entry.value('tName'),
entry.value('tStart') - minimum_locus_distance,
entry.value('tEnd') + minimum_locus_distance,
entry.value('strand'))
rng.set_payload(entry)
locus = RangeBasics.Locus()
locus.set_use_direction(True)
locus.add_member(rng)
loci.add_locus(locus)
loci.update_loci()
outputs = []
for locus in loci.loci:
mpsl = PSLBasics.MultiplePSLAlignments()
mpsl.set_minimum_coverage(20)
for member in locus.members:
mpsl.add_entry(member.get_payload())
mpsl.populate_query()
bac = mpsl.best_query()
#if len(bac.segments) > 2:
segtrimmed = bac.get_trimmed_entries()
stitched = PSLBasics.stitch_query_trimmed_psl_entries(segtrimmed)
#bac.print_report()
#for segpsl in bac.segment_trimmed_entries:
# print str(segpsl.value('qStart'))+"\t"+str(segpsl.value('qEnd'))+"\t"+str(segpsl.value('tStart'))+"\t"+str(segpsl.value('tEnd'))
##print stitched.get_line()
if not stitched.validate():
sys.exit()
outputs.append(stitched.get_line())
return outputs
def main():
parser = argparse.ArgumentParser(description="Analyze ORDERED psl alignments of long reads.")
parser.add_argument('psl_file',help="Alignment file. Must be ordered by query name. use - for stdin")
parser.add_argument('--output',help="Write to output file, default is STDIN")
parser.add_argument('--noheader',action='store_true')
#parser.add_argument('--best',action='store_true')
#parser.add_argument('--split',action='store_true')
parser.add_argument('--minimum_coverage',type=int,help="Only consider alignments with at least this many bp aligned")
parser.add_argument('--threads',type=int,default=multiprocessing.cpu_count(),help="INT default cpu_count")
parser.add_argument('--tempbuffer',help="DIRECTORY store the results in a temporary file until they are ready to output. suggest using /tmp if you don't know what to use")
args = parser.parse_args()
seen_names = set()
last_name = ''
buffer = PSLBasics.MultiplePSLAlignments()
inf = sys.stdin
if args.psl_file != '-':
inf = open(args.psl_file)
global of
tname = None
if args.tempbuffer:
if not args.output:
sys.stderr.write("ERROR if you want to buffer outputs in a temp file you need to specify a final output file.\n")
sys.exit()
rnum = random.randint(1,1000000000);
tname = args.tempbuffer.rstrip('/')+'/weirathe.'+str(rnum)+'.meta'
of = open(tname,'w')
if args.output and not args.tempbuffer:
of = open(args.output,'w')
global lock
if not args.noheader:
lock.acquire()
of.write("QueryName\tSegmentCount\tLocusCount\tHasOverlapped\tHasMultiplyMapped\n")
lock.release()
pool = multiprocessing.Pool(args.threads)
for line in inf:
e = PSLBasics.line_to_entry(line.rstrip())
if e['qName'] != last_name: # we have a new name
if e['qName'] in seen_names:
sys.stderr.write("ERROR psl entries are not ordered by query name.\n")
sys.exit()
seen_names.add(e['qName'])
if buffer.get_alignment_count() > 0:
#process_buffer(buffer)
pool.apply_async(process_buffer,[buffer],callback=print_result)
buffer = PSLBasics.MultiplePSLAlignments()
if args.minimum_coverage > 1:
buffer.set_minimum_coverage(args.minimum_coverage)
last_name = e['qName']
buffer.add_entry(e)
inf.close()
if buffer.get_alignment_count() > 0:
#process_buffer(buffer) # if we still have something left to do
pool.apply_async(process_buffer,[buffer],callback=print_result) # if we still have something left to do
pool.close()
pool.join()
of.close()
if args.tempbuffer:
of = open(args.output,'w')
with open(tname) as inf:
for line in inf:
of.write(line)
of.close()
os.remove(tname)
