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 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 "annotate" in kwargs: logger.info("Run annotation") mirna.miraligner(kwargs["args"]) elif "simulator" in kwargs: logger.info("Run simulation") simulate(kwargs["args"]) 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 "simulator" in kwargs: logger.info("Run simulation") simulate(kwargs["args"]) elif "check" in kwargs["args"]: logger.info("Not yet ready: This will check GFF files.") elif "query" in kwargs["args"]: logger.info("Not yet ready: This will allow queries to GFF files.") elif "convert" in kwargs["args"]: logger.info( "Not yet ready: This will output tabular format from GFF files.") logger.info('It took %.3f minutes' % ((time.time() - start) / 60))