def view_track(parser, options):
tf = TrackFactory(options.file, "r")
if not tf.has_track(options.name):
tf.close()
parser.error("trackfactory '%s' does not contain track '%s'" %
(options.file, options.name))
region = parse_interval(options.region)
t = tf.get_track(options.name)
track_type = t.get_type()
logging.debug("opened track '%s' type '%s'" % (options.name, track_type))
if track_type == SequenceTrack.__name__:
print t[region]
if track_type == ArrayTrack.__name__:
if options.file_type == "bedgraph":
t.tobedgraph(region, sys.stdout)
else:
print t[region]
elif track_type == VectorTrack.__name__:
if options.file_type == "bedgraph":
readnum = options.readnum
allele = options.allele
t.tobedgraph(region, sys.stdout, norm=True,
read=readnum, allele=allele)
else:
print t[region]
elif track_type == RnaseqTrack.__name__:
cov_track = t.get_coverage_track()
print cov_track.density(region)
junc_track = t.get_junction_track()
print junc_track[region]
logging.debug("done")
tf.close()
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()
