def build_one_list_args(parser, default_background_strategy='regulatory'):
parser.add_argument(
'-o',
'--output_prefix',
required=False,
type=is_valid_prefix,
help='Output file prefix. If left empty, will write results to stdout.'
)
parser.add_argument(
'--background_strategy',
choices=public_config.get('lisa_params',
'background_strategies').split(','),
default=default_background_strategy,
help=
"""Background genes selection strategy. LISA samples background genes to compare to user\'s genes-of-interest from a diverse
regulatory background (regulatory - recommended), randomly from all genes (random), or uses a user-provided list (provided).
""")
background_genes_group = parser.add_mutually_exclusive_group()
background_genes_group.add_argument(
'--background_list',
type=argparse.FileType('r', encoding='utf-8'),
required=False,
help=
'user-supplied list of backgroung genes. Used when --background_strategy flag is set to "provided"'
)
background_genes_group.add_argument(
'-b',
'--num_background_genes',
type=int,
default=public_config.get('lisa_params', 'background_genes'),
help=
'Number of sampled background genes to compare to user-supplied genes')
parser.add_argument('-v', '--verbose', type=int, default=4)
def build_multiple_lists_args(parser):
parser.add_argument(
'query_lists',
type=argparse.FileType('r', encoding='utf-8'),
nargs="+",
help=
'user-supplied gene lists. One gene per line in either symbol or refseqID format'
)
parser.add_argument('-o',
'--output_prefix',
required=True,
type=is_valid_prefix,
help='Output file prefix.')
parser.add_argument('-v', '--verbose', type=int, default=2)
parser.add_argument(
'-b',
'--num_background_genes',
type=int,
default=public_config.get('lisa_params', 'background_genes'),
help=
'Number of sampled background genes to compare to user-supplied genes. These genes are selection from other gene lists.'
)
parser.add_argument(
'--random_background',
action='store_const',
const='random',
default='regulatory',
dest='background_strategy',
help=
'Use random background selection rather than "regulatory" selection.')
def build_from_genes_args(parser, add_assays=True):
#parser.add_argument('-c','--cores', required = True, type = int)
if add_assays:
parser.add_argument(
'-a',
'--assays',
nargs='+',
default=['Direct', 'H3K27ac', 'DNase'],
choices=['Direct', 'H3K27ac', 'DNase'],
help='Which set of insilico-deletion assays to run.')
parser.add_argument(
'--rp_map_style',
dest='rp_map',
choices=public_config.get('lisa_params', 'rp_map_styles').split(','),
default=public_config.get('lisa_params',
'rp_map_styles').split(',')[0],
help=
'Which style of rp_map to assess influence of regions on genes. "basic" is stricly distance-based, while "enhanced" masks the exon and promoter regions of nearby genes.'
)