# --------------------------------------------------------------------------- #
# This is the Wrapper script that runs the core code found in #
# hisatgenotype_modules/hisatgenotype_typing_core #
# --------------------------------------------------------------------------- #
if __name__ == '__main__':
parser = ArgumentParser(
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
from argparse import ArgumentParser, FileType
from hisatgenotype_typing_process import extract_reads
import hisatgenotype_args as arguments
# --------------------------------------------------------------------------- #
# This is the Wrapper script that runs the processing code found in #
# hisatgenotype_modules/hisatgenotype_typing_process #
# --------------------------------------------------------------------------- #
if __name__ == '__main__':
parser = ArgumentParser(description='Extract reads')
# Add Arguments
arguments.args_databases(parser, True,
True) # Add option to change genotype_genome name
arguments.args_input_output(parser)
arguments.args_aligner_inputs(parser)
arguments.args_set_aligner(parser, False) # No missmatch option
arguments.args_single_end(parser)
arguments.args_extract_reads(parser)
arguments.args_common(parser)
args = parser.parse_args()
if args.locus_list:
print(
"--locus-list option not implemented in this script yet, skipping")
if not args.graph_index:
print("--linear-index not implemented yet, skipping")
if not args.genotype_genome:
args.genotype_genome = 'genotype_genome'
