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
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