def main(**kwargs): kwargs = parse_cl(sys.argv[1:]) initialize_logger(kwargs['args'].out, kwargs['args'].debug, kwargs['args'].print_debug) logger = mylog.getLogger(__name__) start = time.time() if "gff" in kwargs: logger.info("Run annotation") reader(kwargs["args"]) elif "stats" in kwargs: logger.info("Run stats.") stats(kwargs["args"]) elif "compare" in kwargs: logger.info("Run compare.") compare(kwargs["args"]) elif "simulator" in kwargs: logger.info("Run simulation") simulate(kwargs["args"]) elif "counts" in kwargs: logger.info("Run convert of GFF to TSV containing expression") convert_gff_counts(kwargs["args"]) elif "export" in kwargs: logger.info("Run export of GFF into other format.") isomirs.convert(kwargs["args"]) elif "validator" in kwargs: logger.info("Run validator.") validator.check_multiple(kwargs["args"]) elif "query" in kwargs["args"]: logger.info("Not yet ready: This will allow queries to GFF files.") logger.info('It took %.3f minutes' % ((time.time()-start)/60))
def main(**kwargs): kwargs = parse_cl(sys.argv[1:]) initialize_logger(kwargs['args'].out, kwargs['args'].debug, kwargs['args'].print_debug) logger = mylog.getLogger(__name__) start = time.time() if "gff" in kwargs: logger.info("Run annotation") reader(kwargs["args"]) elif "stats" in kwargs: logger.info("Run stats.") stats(kwargs["args"]) elif "compare" in kwargs: logger.info("Run compare.") compare(kwargs["args"]) elif "simulator" in kwargs: logger.info("Run simulation") simulate(kwargs["args"]) elif "counts" in kwargs: logger.info("Run convert of GFF to TSV containing expression") convert_gff_counts(kwargs["args"]) elif "export" in kwargs: logger.info("Run export of GFF into other format.") isomirs.convert(kwargs["args"]) elif "validator" in kwargs: logger.info("Run validator.") validator.check_multiple(kwargs["args"]) elif "query" in kwargs["args"]: logger.info("Not yet ready: This will allow queries to GFF files.") logger.info('It took %.3f minutes' % ((time.time() - start) / 60))
def test_counts(self): """testing convert_gff_counts in convert.py function""" from mirtop.libs import logger from mirtop.gff.convert import convert_gff_counts import argparse logger.initialize_logger("test counts", True, True) logger = logger.getLogger(__name__) args = argparse.Namespace() args.hairpin = "data/examples/annotate/hairpin.fa" args.sps = "hsa" args.gtf = "data/examples/annotate/hsa.gff3" args.gff = 'data/examples/synthetic/let7a-5p.gtf' args.out = 'data/examples/synthetic' args.add_extra = True convert_gff_counts(args) os.remove(os.path.join(args.out, "expression_counts.tsv")) return True