global lock
lock = l
l = multiprocessing.Lock()
# --------------------------------------------------------------------------- #
# This is the Wrapper script that runs the processing code found in #
# hisatgenotype_modules/hisatgenotype_typing_process #
# --------------------------------------------------------------------------- #
if __name__ == '__main__':
parser = ArgumentParser(
description="Extract variants from multiple sequence alignments")
# Add Arguments
arguments.args_databases(parser, location=True)
arguments.args_var_gaps(parser)
arguments.args_extract_vars(parser)
arguments.args_no_partial(parser)
arguments.args_common(parser)
args = parser.parse_args()
if args.locus_list == "":
locus_list = []
else:
locus_list = args.locus_list.split(',')
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 typing_common.check_files(index_fnames):
print("Error: indexing failed! "\
"Perhaps, you may have forgotten to build %s executables?" \
% aligner,
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'
import re
import random
from argparse import ArgumentParser, FileType
from hisatgenotype_typing_core import genotyping_locus
import hisatgenotype_args as arguments
# --------------------------------------------------------------------------- #
# 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 == "":
