def main(): gtf_file = None try: opts, _ = getopt.getopt(sys.argv[1:], '', ['gtf=']) except getopt.GetoptError as err: print >> sys.stderr, str(err) sys.exit(1) for opt, arg in opts: if opt == '--gtf': gtf_file = arg if not gtf_file: print >> sys.stderr, "misisng" sys.exit(1) tr_exs = get_transcripts_exons(gtf_file) gene_loci = build_gene_loci(tr_exs) for chr_name, chr_gl in gene_loci.iteritems(): for gl in chr_gl: for exs in gl.t_exs.itervalues(): ld = 0 ex = gl.ex2chain[exs[0]] while ex.left: ld += 1 ex = choice(list(ex.left)) rd = 0 ex = gl.ex2chain[exs[-1]] while ex.right: rd += 1 ex = choice(list(ex.right)) print len(exs[0].left_exons), ld, len(exs[-1].right_exons), rd, len(gl.ex_chains)
def main(): gtf_file = None bam_file = None try: opts, _ = getopt.getopt(sys.argv[1:], '', ['gtf=', 'bam=']) except getopt.GetoptError as err: print >> sys.stderr, str(err) sys.exit(1) for opt, arg in opts: if opt == '--gtf': gtf_file = arg if opt == '--bam': bam_file = arg if (not gtf_file or not bam_file): print >> sys.stderr, "misisng" sys.exit(1) tr_exs = get_transcripts_exons(gtf_file) gene_loci = build_gene_loci(tr_exs)