description='hisatgenotype_locus')
# Add Arguments
arguments.args_databases(parser,
True) # Add option to rename genotype_genome
arguments.args_bamfile(parser)
arguments.args_input_output(parser,
indir=False) # Remove --read-dir option
arguments.args_aligner_inputs(parser,
True) # Add option to keep alignments
arguments.args_set_aligner(parser,
False) # No option to set missmatch
arguments.args_locus(parser)
arguments.args_no_partial(parser)
arguments.args_assembly(parser)
arguments.args_common(parser,
debug = True) # Add option for debug
args = parser.parse_args()
if args.locus_list == "":
locus_list = []
else:
locus_list = args.locus_list.split(',')
if args.base_fname == "genome":
assert ':' in args.locus_list
for i in range(len(locus_list)):
assert ':' in locus_list[i] and '-' in locus_list[i]
chr, coord = locus_list[i].split(':')
left, right = coord.split('-')
locus_list[i] = [chr, int(left), int(right)]
if args.only_locus_list == "":
file=sys.stderr)
sys.exit(1)
# --------------------------------------------------------------------------- #
# Main function to build index and run script #
# --------------------------------------------------------------------------- #
if __name__ == '__main__':
parser = ArgumentParser(description="Build genotype genome")
# Add Arguments
arguments.args_databases(parser)
arguments.args_var_gaps(parser)
arguments.args_set_aligner(parser, False) # no missmatch option
arguments.args_build_genome(parser)
arguments.args_common(parser)
args = parser.parse_args()
if args.inter_gap > args.intra_gap:
print("Error: --inter-gap (%d) must be smaller than --intra-gap (%d)" \
% (args.inter_gap, args.intra_gap),
file=sys.stderr)
sys.exit(1)
if not args.base_fname:
args.base_fname = 'genotype_genome'
if not args.locus_list:
database_list = []
typing_common.clone_hisatgenotype_database()
for database in os.listdir("hisatgenotype_db"):
file=codis_data_file)
codis_data_file.close()
# --------------------------------------------------------------------------- #
# Main Function #
# --------------------------------------------------------------------------- #
if __name__ == '__main__':
parser = ArgumentParser(
description="Extract multiple sequence alignments for DNA "\
"Fingerprinting loci")
# Add Arguments
arguments.args_databases(parser)
arguments.args_common(parser,
threads = False) # No threading option
args = parser.parse_args()
if not args.base_fname:
base_fname = 'codis'
base_dname = ''
elif args.base_fname.find('/') != -1:
elems = args.base_fname.split('/')
base_fname = elems[-1]
base_dname = '/'.join(elems[:-1])
else:
base_fname = args.base_fname
base_dname = ""
if args.locus_list != "":
locus_list = args.locus_list.split(',')
else: