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 == "":