def main():
args = parseArgs()
# debug mode
if args.debug: args.verbose = "debug"
sys.stderr = Unbuffered(sys.stderr)
if args.window:
windows = [args.window]
elif args.regions:
windows = [bed_to_coord(x) for x in args.regions]
else:
if args.verbose:
print("converting the whole genome", file=sys.stderr)
windows = get_windows_from_bam(args.bam, 100000)
if args.verbose:
print("{} regions to parse".format(len(windows)), file=sys.stderr)
# read in fasta
if args.fasta:
fasta = pysam.FastaFile(args.fasta)
# initialize mp
manager = mp.Manager()
q = manager.Queue()
pool = mp.Pool(processes=args.threads)
if args.verbose:
print("using {} parallel processes".format(args.threads),
file=sys.stderr)
# watcher for output
watcher = pool.apply_async(listener, (q, args.bam, args.out, args.verbose))
# which convert function
if args.gpc is None: converter = convert_cpg
else: converter = convert_nome
# start processing
if args.fasta:
jobs = list()
for win in windows:
chrom, start, end = coord_to_bed(win)
seq = fasta.fetch(reference=chrom).upper()
jobs.append(
pool.apply_async(convertBam,
args=(args.bam, seq, converter, args.cpg,
args.gpc, win, args.remove_poor,
args.verbose, q)))
else:
jobs = [
pool.apply_async(convertBam,
args=(args.bam, 0, converter, args.cpg, args.gpc,
win, args.remove_poor, args.verbose, q))
for win in windows
]
output = [p.get() for p in jobs]
# done
q.put('kill')
q.join()
pool.close()
if args.verbose:
print("time elapsed : {} seconds".format(time.time() - start_time),
file=sys.stderr)
def __init__(self, regline):
self.regline = regline
self.regfields = regline.strip().split("\t")
self.coord = bed_to_coord(regline)
self.chrom, self.start, self.end = coord_to_bed(self.coord)
if len(self.regfields) > 6:
self.title = "{} {} ({})".format(self.regfields[6], self.coord,
self.regfields[5])
elif len(self.regfields) > 4:
self.title = "{} {} ({})".format(self.regfields[3], self.coord,
self.regfields[5])
elif len(self.regfields) > 3:
self.title = "{} ({})".format(self.coord, self.regfields[5])
else:
self.title = self.coord
self.center = self.start + np.floor((self.end - self.start) / 2)
self.metharrays = []
self.totreads = 0
def main():
args = parseArgs()
if args.window:
windows = [args.window]
elif args.regions:
windows = [bed_to_coord(x) for x in args.regions]
else:
if args.verbose:
print("extracting all reads in the bam file", file=sys.stderr)
windows = get_windows_from_bam(args.bam, 100000)
if args.verbose:
print("{} regions to parse".format(len(windows)), file=sys.stderr)
if args.random:
print("separating reads randomly", file=sys.stderr)
# initialize mp
manager = mp.Manager()
q = manager.Queue()
pool = mp.Pool(processes=args.threads)
if args.verbose:
print("using {} parallel processes".format(args.threads),
file=sys.stderr)
# watcher for output
watcher = pool.apply_async(listener, (q, args.pre, args.verbose))
# start processing
jobs = [
pool.apply_async(split_bed_haplotypes,
args=(args.bam, args.bed, win, args.random,
args.verbose, q)) for win in windows
]
output = [p.get() for p in jobs]
# done
q.put('kill')
q.join()
pool.close()
if args.verbose:
print("time elapsed : {} seconds".format(time.time() - start_time),
file=sys.stderr)