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"""
AIRR tools and utilities
"""
# Copyright (c) 2018 AIRR Community
#
# This file is part of the AIRR Community Standards.
#
# Author: Scott Christley <schristley@mac.com>
# Author: Jason Anthony Vander Heiden
# Date: March 29, 2018
#
# This library is free software; you can redistribute it and/or modify
# it under the terms of the Creative Commons Attribution 4.0 License.
#
# This library is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# Creative Commons Attribution 4.0 License for more details.
# System imports
import argparse
import sys
from warnings import warn
# Local imports
from airr import __version__
import airr.interface
# internal wrapper function before calling merge interface method
def merge_cmd(out_file, airr_files, drop=False, debug=False):
"""
Merge one or more AIRR rearrangements files
Arguments:
out_file (str): output file name.
airr_files (list): list of input files to merge.
drop (bool): drop flag. If True then drop fields that do not exist in all input
files, otherwise combine fields from all input files.
debug (bool): debug flag. If True print debugging information to standard error.
Returns:
bool: True if files were successfully merged, otherwise False.
"""
return airr.interface.merge_rearrangement(out_file, airr_files, drop=drop, debug=debug)
# internal wrapper function before calling validate interface method
def validate_rearrangement_cmd(airr_files, debug=True):
"""
Validates one or more AIRR rearrangements files
Arguments:
airr_files (list): list of input files to validate.
debug (bool): debug flag. If True print debugging information to standard error.
Returns:
boolean: True if all files passed validation, otherwise False
"""
valid = []
for f in airr_files:
try:
v = airr.interface.validate_rearrangement(f, debug=debug)
valid.append(v)
except Exception as e:
sys.stderr.write('%s\n' % e)
sys.stderr.write('Validation failed for file: %s\n\n' % f)
valid.append(False)
else:
if not v: sys.stderr.write('Validation failed for file: %s\n\n' % f)
return all(valid)
def validate_airr_cmd(airr_files, debug=True):
"""
Validates one or more AIRR Data Model files
Arguments:
airr_files (list): list of input files to validate.
debug (bool): debug flag. If True print debugging information to standard error.
Returns:
boolean: True if all files passed validation, otherwise False
"""
valid = []
for f in airr_files:
if debug: sys.stderr.write('Validating: %s\n' % f)
try:
data = airr.interface.read_airr(f, validate=False, debug=debug)
v = airr.interface.validate_airr(data, debug=debug)
valid.append(v)
except Exception as e:
sys.stderr.write('%s\n' % e)
sys.stderr.write('Validation failed for file: %s\n\n' % f)
valid.append(False)
return all(valid)
#### Deprecated ####
# internal wrapper function before calling validate interface method
def validate_repertoire_cmd(airr_files, debug=True):
"""
Validates one or more AIRR repertoire metadata files
Arguments:
airr_files (list): list of input files to validate.
debug (bool): debug flag. If True print debugging information to standard error.
Returns:
boolean: True if all files passed validation, otherwise False
"""
# Deprecation
warn('validate_repertoire_cmd is deprecated and will be removed in a future release.\nUse =validate_airr_cmd instead.\n',
DeprecationWarning, stacklevel=2)
valid = []
for f in airr_files:
try:
v = airr.interface.validate_repertoire(f, debug=debug)
valid.append(v)
except Exception as e:
sys.stderr.write('%s\n' % e)
sys.stderr.write('Validation failed for file: %s\n\n' % f)
valid.append(False)
return all(valid)
def define_args():
"""
Define commandline arguments
Returns:
argparse.ArgumentParser: argument parser.
"""
parser = argparse.ArgumentParser(add_help=False,
description='AIRR Community Standards utility commands.')
group_help = parser.add_argument_group('help')
group_help.add_argument('-h', '--help', action='help', help='show this help message and exit')
group_help.add_argument('--version', action='version',
version='%(prog)s:' + ' %s' % __version__)
# Setup subparsers
subparsers = parser.add_subparsers(title='subcommands', dest='command', metavar='',
help='Database operation')
# TODO: This is a temporary fix for Python issue 9253
subparsers.required = True
# Define arguments common to all subcommands
common_parser = argparse.ArgumentParser(add_help=False)
common_help = common_parser.add_argument_group('help')
common_help.add_argument('--version', action='version',
version='%(prog)s:' + ' %s' % __version__)
common_help.add_argument('-h', '--help', action='help', help='show this help message and exit')
# TODO: workflow provenance
# group_prov = common_parser.add_argument_group('provenance')
# group_prov.add_argument('-p', '--provenance', action='store', dest='prov_file', default=None,
# help='''File name for storing workflow provenance. If specified, airr-tools
# will record provenance for all activities performed.''')
# TODO: study metadata
# group_meta = common_parser.add_argument_group('study metadata')
# group_meta.add_argument('-m', '--metadata', action='store', dest='metadata_file', default=None,
# help='''File name containing study metadata.''')
# Subparser to merge files
parser_merge = subparsers.add_parser('merge', parents=[common_parser],
add_help=False,
help='Merge AIRR rearrangement files.',
description='Merge AIRR rearrangement files.')
group_merge = parser_merge.add_argument_group('merge arguments')
group_merge.add_argument('-o', action='store', dest='out_file', required=True,
help='''Output file name.''')
group_merge.add_argument('--drop', action='store_true', dest='drop',
help='''If specified, drop fields that do not exist in all input files.
Otherwise, include all columns in all files and fill missing data
with empty strings.''')
group_merge.add_argument('-a', nargs='+', action='store', dest='airr_files', required=True,
help='A list of AIRR rearrangement files.')
parser_merge.set_defaults(func=merge_cmd)
# Subparser to validate files
parser_validate = subparsers.add_parser('validate', parents=[common_parser],
add_help=False,
help='Validate files for AIRR Standards compliance.',
description='Validate files for AIRR Standards compliance.')
validate_subparser = parser_validate.add_subparsers(title='subcommands', metavar='',
help='Database operation')
# Subparser to validate rearrangement files
parser_validate = validate_subparser.add_parser('rearrangement', parents=[common_parser],
add_help=False,
help='Validate AIRR rearrangement files.',
description='Validate AIRR rearrangement files.')
group_validate = parser_validate.add_argument_group('validate arguments')
group_validate.add_argument('-a', nargs='+', action='store', dest='airr_files', required=True,
help='A list of AIRR rearrangement files.')
parser_validate.set_defaults(func=validate_rearrangement_cmd)
# Subparser to validate AIRR Data Model files
parser_validate = validate_subparser.add_parser('airr', parents=[common_parser],
add_help=False,
help='Validate AIRR Data Model files.',
description='Validate AIRR Data Model files.')
group_validate = parser_validate.add_argument_group('validate arguments')
group_validate.add_argument('-a', nargs='+', action='store', dest='airr_files', required=True,
help='A list of AIRR Data Model files.')
parser_validate.set_defaults(func=validate_airr_cmd)
# Subparser to validate repertoire files
parser_validate = validate_subparser.add_parser('repertoire', parents=[common_parser],
add_help=False,
help='Validate AIRR repertoire metadata files.',
description='Validate AIRR repertoire metadata files.')
group_validate = parser_validate.add_argument_group('validate arguments')
group_validate.add_argument('-a', nargs='+', action='store', dest='airr_files', required=True,
help='A list of AIRR repertoire metadata files.')
parser_validate.set_defaults(func=validate_repertoire_cmd)
return parser
def main():
"""
Utility commands for AIRR Community Standards files
"""
# Define argument parsers and print help if subcommand not specified
parser = define_args()
if len(sys.argv) == 1:
parser.print_help()
sys.exit(1)
# Parse arguments
args = parser.parse_args()
args_dict = args.__dict__.copy()
del args_dict['command']
del args_dict['func']
# Deprecation warnings
if args.func is validate_repertoire_cmd:
print('The "validate repertoire" subcommand is deprecated and will be removed in a future release.',
'\nUse the "validate airr" subcommand instead.\n')
# Call tool function
result = args.func(**args_dict)
# set return code to non-zero if error occurred
if args.__dict__['command'] == 'validate' or args.__dict__['command'] == 'merge':
if not result:
sys.exit(1)
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