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))