def parse_locus(locus, fh):
genome_id_str = '%s:%d-%d' % (locus.chrom, locus.start, locus.end)
logging.debug('LocusIndex: %s coords: %s transfrags: %d' %
(locus.name, genome_id_str, locus.num_lines))
# fast-forward to 'filepos'
fh.seek(locus.filepos)
# parse 'num_lines' from file into Transfrag objects
transfrags = []
for i in xrange(locus.num_lines):
transfrags.append(Transfrag.from_bed(fh.next()))
return transfrags
def parse_locus(locus, fh):
genome_id_str = '%s:%d-%d' % (locus.chrom, locus.start, locus.end)
logging.debug('LocusIndex: %s coords: %s transfrags: %d' %
(locus.name, genome_id_str, locus.num_lines))
# fast-forward to 'filepos'
fh.seek(locus.filepos)
# parse 'num_lines' from file into Transfrag objects
transfrags = []
for i in xrange(locus.num_lines):
transfrags.append(Transfrag.from_bed(fh.next()))
return transfrags
def main():
logging.basicConfig(level=logging.DEBUG)
parser = argparse.ArgumentParser()
parser.add_argument('genome_fasta_file')
parser.add_argument('bed_file')
args = parser.parse_args()
# check args
if not os.path.exists(args.genome_fasta_file):
parser.error('genome fasta file %s not found' % args.genome_fasta_file)
if not os.path.exists(args.bed_file):
parser.error('bed file %s not found' % args.bed_file)
logging.info('genome fasta file: %s' % args.genome_fasta_file)
logging.info('bed file: %s' % args.bed_file)
# process bed file to get junctions
logging.info('Reading Junctions')
splice_juncs = set()
fasta_fh = FastaFile(args.genome_fasta_file)
with open(args.bed_file) as bed_fh:
for line in bed_fh:
t = Transfrag.from_bed(line)
if t.chrom not in fasta_fh:
continue
for start, end in t.iterintrons():
splice_juncs.add((t.chrom, start, end, t.strand))
logging.info('Read %d Junctions' % (len(splice_juncs)))
logging.info('Profiling Splice Motifs')
motif_counter = Counter()
for chrom, start, end, strand in splice_juncs:
s = fasta_fh.fetch(chrom, start, start + 2)
s += fasta_fh.fetch(chrom, end - 2, end)
if strand == Strand.NEG:
s = dna_reverse_complement(s)
motif_counter[s] += 1
fasta_fh.close()
# report statistics
total = sum(motif_counter.values())
print '\t'.join(['motif', 'count', 'frac'])
for motif, count in motif_counter.most_common():
print '\t'.join([motif, str(count), str(float(count) / total)])
logging.info('Done')