def get_args(argv):
parser = argparse.ArgumentParser(
prog='multi_tusv.py',
description=
"runs tusv.py multiple times. Unmixes mixed copy numbers for breakpoints and segments and infers phylogenies with phylogenetic constraints across multiple patients"
)
parser.add_argument(
'-i',
'--input_directory',
required=True,
type=lambda x: fm.valid_master_dir_with_files_and_ext(
parser, x, [], '.vcf'),
help=
'directory containing multiple subdirectories each containing a .vcf for each sample from a single patient'
)
parser.add_argument(
'-o',
'--output_directory',
required=True,
type=lambda x: fm.valid_dir(parser, x),
help=
'empty directory where multiple subdirectories will be created. each will then contain output U.tsv, C.tsv, and T.dot files'
)
tusv.set_non_dir_args(parser)
return vars(parser.parse_args(argv))
def get_args(argv):
parser = argparse.ArgumentParser(
prog='tusv.py',
description=
"unmixes mixed copy numbers for breakpoints and segments and infers phylogeny with various phylogenetic constraints"
)
parser.add_argument(
'-i',
'--input_directory',
required=True,
type=lambda x: fm.valid_dir_ext(parser, x, '.vcf'),
help='directory containing a .vcf for each sample from a single patient'
)
parser.add_argument(
'-o',
'--output_directory',
required=True,
type=lambda x: fm.valid_dir(parser, x),
help='empty directory for output U.tsv, C.tsv, and T.dot files to go')
set_non_dir_args(parser)
return vars(parser.parse_args(argv))
def get_args(argv):
parser = argparse.ArgumentParser(
prog='experiment.py',
description=
"runs tusv.py on mulitple patients and validates the results")
parser.add_argument(
'-i',
'--input_directory',
required=True,
type=lambda x: fm.valid_master_dir_with_files_and_ext(
parser, x, FNAMES, EXTENSION),
help=
'directory one or multiple subdirectories. each subdirectory should contain T.dot, C.tsv, and U.tsv files that were generated by sim.py'
)
parser.add_argument(
'-o',
'--output_directory',
required=True,
type=lambda x: fm.valid_dir(parser, x),
help='directory where results from each experiment will go')
tusv.set_non_dir_args(parser)
return vars(parser.parse_args(argv))