def make_annotation(args): """ Make GFF annotation. Takes GFF tables directory and an output directory. """ tables_dir = utils.pathify(args.tables_dir) output_dir = utils.pathify(args.output_dir) print "Making GFF alternative events annotation..." print " - UCSC tables read from: %s" % (tables_dir) print " - Output dir: %s" % (output_dir) t1 = time.time() table_fnames = def_events.load_ucsc_tables(tables_dir) num_tables = len(table_fnames) if num_tables == 0: raise Exception, "No UCSC tables found in %s." % (tables_dir) print "Loaded %d UCSC tables." % (num_tables) def_events.defineAllSplicing(tables_dir, output_dir, flanking=args.flanking_rule, multi_iso=args.multi_iso, genome_label=args.genome_label, sanitize=args.sanitize) t2 = time.time() print "Took %.2f minutes to make the annotation." \ %((t2 - t1)/60.)
def make_miso_annotation(tables_dir, output_dir, org_build): """ Make GFF annotation. Takes GFF tables directory and an output directory. Adapted from https://github.com/yarden/rnaseqlib/ """ tables_dir = utils.pathify(tables_dir) output_dir = utils.pathify(output_dir) print "Making GFF alternative events annotation..." print " - UCSC tables read from: %s" % (tables_dir) print " - Output dir: %s" % (output_dir) t1 = time.time() table_fnames = def_events.load_ucsc_tables(tables_dir) num_tables = len(table_fnames) if num_tables == 0: raise Exception("No UCSC tables found in %s." % (tables_dir)) print "Loaded %d UCSC tables." % (num_tables) def_events.defineAllSplicing(tables_dir, output_dir, flanking="commonshortest", multi_iso=False, sanitize=False, genome_label=org_build) t2 = time.time() print "Took %.2f minutes to make the annotation." \ % ((t2 - t1)/60.)
def make_annotation(args): """ Make GFF annotation. Takes GFF tables directory and an output directory. """ tables_dir = utils.pathify(args.tables_dir) output_dir = utils.pathify(args.output_dir) print "Making GFF alternative events annotation..." print " - UCSC tables read from: %s" %(tables_dir) print " - Output dir: %s" %(output_dir) t1 = time.time() table_fnames = def_events.load_ucsc_tables(tables_dir) num_tables = len(table_fnames) if num_tables == 0: raise Exception, "No UCSC tables found in %s." %(tables_dir) print "Loaded %d UCSC tables." %(num_tables) def_events.defineAllSplicing(tables_dir, output_dir, flanking=args.flanking_rule, multi_iso=args.multi_iso, genome_label=args.genome_label, sanitize=args.sanitize) t2 = time.time() print "Took %.2f minutes to make the annotation." \ %((t2 - t1)/60.)