if __name__ == '__main__':
description = 'Generates input files and infers a coalescent-based species tree' # TODO: Get Description
parser, optional, required = help_formatter.initialize_argparse(
name='astral_runner.py',
desc=description,
usage='astral_runner.py '
'[OPTIONS] -i /path/to/input/')
# Optional Arguments
# optional.add_argument('--in_format', metavar='<format>', type=str, default='fasta',
# help=textwrap.dedent("""\
# Desired format of the output steps.
# Options: fasta, nexus, phylip (names truncated at 10 characters),
# or phylip-relaxed (names are not truncated)
# Default: phylip-relaxed
# """))
in_help = 'Path to directory containing single gene trees and their corresponding bootstrap value files.'
args = help_formatter.get_args(parser, optional, required, in_help=in_help)
args.output = os.path.abspath(args.output)
args.input = os.path.abspath(args.input)
if os.path.isdir(args.output):
shutil.rmtree(args.output)
os.mkdir(args.output)
make_astral_inputs()
run_astral()
'--get_lower',
default=None,
help=textwrap.dedent("""\
Return table with orthologs, paralogs for organisms from a given Lower Taxonomy.
"""))
optional.add_argument('-o',
'--get_org',
default=None,
help=textwrap.dedent("""\
Return information about a given organism using its short name.
"""))
args = help_formatter.get_args(parser,
optional,
required,
pre_suf=False,
out_dir=False,
inp_dir=False)
config = configparser.ConfigParser()
config.read('config.ini')
if args.database:
dfo = str(Path(args.database).resolve())
else:
dfo = str(Path(config['PATHS']['database_folder']).resolve())
ortholog_folder = str(Path(dfo, f'orthologs'))
paralog_folder = str(Path(dfo, f'paralogs'))
metadata = str(os.path.join(dfo, 'metadata.tsv'))
metadata_handle = Metadata(metadata, ortholog_folder, paralog_folder)
Desired format of the RTC binned alignments.
Options: fasta, nexus, phylip (names truncated at 10 characters),
or phylip-relaxed (names are not truncated)
Default: fasta
"""))
optional.add_argument('-s', '--suffix', metavar='<suffix>', type=str, default='NONE',
help=textwrap.dedent("""\
Suffix of RAxML output files
Example: RAxML_bipartitions.GENE.<SUFFIX>, RAxML_bootstrap.GENE.<SUFFIX>
Default: NONE
"""))
in_help = ('Path to directory containing single gene trees built from only orthologs, \n'
'corresponding bootstrap value files, and corresponding alignments.')
args = help_formatter.get_args(parser, optional, required, in_help=in_help, pre_suf=False)
args.output = os.path.abspath(args.output)
args.input = os.path.abspath(args.input)
out_dict = {'fasta': 'fas',
'phylip': 'phy',
'phylip-relaxed': 'phy',
'nexus': 'nex'}
if args.suffix and args.suffix[0] != '.':
args.suffix = f'.{args.suffix}'
if os.path.isdir(args.output):
shutil.rmtree(args.output)
os.mkdir(args.output)