def filter_strand_conflicts(bedfile):
trees = collections.defaultdict(lambda: IntervalTree())
genes = []
for g in BedGene.parse(open(bedfile)):
for start, end in g.exons:
trees[g.chrom].insert_interval(Interval(start, end, strand=g.strand, chrom=g.chrom))
genes.append(g)
exon_count = 0
new_exon_count = 0
for g in genes:
new_exons = []
for start, end in g.exons:
exon_count += 1
ambig = False
for hit in trees[g.chrom].find(start,end):
if hit.strand != g.strand:
ambig = True
logging.debug("Filtering ambiguous exon %s:%d-%d" % (g.chrom, start, end))
break
if not ambig:
new_exon_count += 1
new_exons.append((start,end))
g.exons = new_exons
logging.info("%d exons" % (exon_count))
logging.info("%d unambiguous exons" % (new_exon_count))
return genes
def main():
logging.basicConfig(level=logging.DEBUG,
format="%(asctime)s - %(levelname)s - %(message)s")
parser = argparse.ArgumentParser()
parser.add_argument("--stranded", dest="stranded", action="store_true", default=False)
parser.add_argument("--ambiguous", dest="ambiguous", action="store_true", default=False)
parser.add_argument("--aliases", dest="alias_file", default=None)
parser.add_argument("bed")
parser.add_argument("track_files", nargs="+")
options = parser.parse_args()
alias_dict = {}
alias_header = []
if options.alias_file is not None:
for line in open(options.alias_file):
if line.startswith("#"):
alias_header = line.strip()[1:].split('\t')
continue
fields = line.strip().split('\t')
alias_dict[fields[0]] = fields[1:]
header_fields = alias_header + ["gene_name", "gene_interval", "gene_length"]
tracks = []
for track_path in options.track_files:
name, path = track_path.split("@")
file_path, h5_path = path.split(":")
tf = TrackFactory(file_path, "r")
t = tf.get_track(h5_path)
tracks.append((name, tf, t, set(t.get_rnames())))
if options.stranded:
header_fields.append("%s_sense" % name)
header_fields.append("%s_antisense" % name)
else:
header_fields.append(name)
# output header
print '\t'.join(map(str, header_fields))
# read genes
if options.ambiguous:
genes = list(BedGene.parse(open(options.bed)))
else:
genes = filter_strand_conflicts(options.bed)
# get counts
for g in genes:
alias_fields = alias_dict.get(g.name, ["None"] * len(alias_header))
fields = ([g.name] + alias_fields +
["%s[%s]:%d-%d" % (g.chrom, g.strand, g.tx_start, g.tx_end),
sum((end-start) for start,end in g.exons)])
sense_strand = NEG_STRAND if g.strand == "+" else POS_STRAND
antisense_strand = int(not sense_strand)
rname_found = False
for name, tf, t, rnames in tracks:
if g.chrom not in rnames:
continue
rname_found = True
if options.stranded:
sense_count = 0
antisense_count = 0
for start, end in g.exons:
sense_count += t.count((g.chrom, start, end, sense_strand))
antisense_count += t.count((g.chrom, start, end, antisense_strand))
fields.append(sense_count)
fields.append(antisense_count)
else:
count = 0
for start, end in g.exons:
count += t.count((g.chrom, start, end))
fields.append(count)
if rname_found:
print '\t'.join(map(str, fields))
for name,tf,t,rnames in tracks:
tf.close()