"""Tool for wrangling a Matrix."""
import argparse
import json
from lmpy import Matrix
from lmpy.data_wrangling.factory import WranglerFactory
from lmpy.tools._config_parser import _process_arguments
DESCRIPTION = '''\
Perform various wrangle operations on a matrix such as subsetting and reordering.'''
# .....................................................................................
[docs]def wrangle_matrix(mtx, wranglers):
"""Wrangle the Matrix as configured.
Args:
mtx (Matrix): A Matrix to wrangle.
wranglers (list): A list of tree data wranglers.
Returns:
Matrix: The modified Matrix object.
list: A list of report dictionaries.
"""
report = []
for wrangler in wranglers:
mtx = wrangler.wrangle_matrix(mtx)
report.append(wrangler.get_report())
return mtx, report
# .....................................................................................
[docs]def cli():
"""Provice a command-line interface to the wrangle matrix tool."""
parser = argparse.ArgumentParser(description=DESCRIPTION)
parser.add_argument('--config_file', type=str, help='Path to configuration file.')
parser.add_argument(
'-r',
'--report_filename',
type=str,
help='File location to write the wrangler report.'
)
parser.add_argument(
'in_matrix_filename', type=str, help='Path to the input Matrix.'
)
parser.add_argument(
'wrangler_configuration_file',
type=str,
help='Path to Matrix wrangler configuration.',
)
parser.add_argument(
'out_matrix_filename', type=str, help='Path to the outut Matrix.'
)
args = _process_arguments(parser, config_arg='config_file')
in_mtx = Matrix.load(args.in_matrix_filename)
with open(args.wrangler_configuration_file, mode='rt') as in_json:
wrangler_factory = WranglerFactory()
wranglers = wrangler_factory.get_wranglers(json.load(in_json))
wrangled_mtx, report = wrangle_matrix(in_mtx, wranglers)
wrangled_mtx.write(args.out_matrix_filename)
if args.report_filename is not None:
with open(args.report_filename, mode='wt') as report_out:
json.dump(report, report_out)
# .....................................................................................
__all__ = ['cli', 'wrangle_matrix']
# .....................................................................................
if __name__ == '__main__': # pragma: no cover
cli()