help='The values that will be replaced.')
parser_update.add_argument('-t', nargs='+', action='store', dest='updates', required=True,
help='''The new value to assign to each selected row.''')
parser_update.set_defaults(func=updateDbFile)
return parser
if __name__ == '__main__':
"""
Parses command line arguments and calls main function
"""
# Parse arguments
parser = getArgParser()
args = parser.parse_args()
args_dict = parseCommonArgs(args)
# Convert case of fields
if 'id_field' in args_dict:
args_dict['id_field'] = args_dict['id_field'].upper()
if 'seq_field' in args_dict:
args_dict['seq_field'] = args_dict['seq_field'].upper()
if 'germ_field' in args_dict:
args_dict['germ_field'] = args_dict['germ_field'].upper()
if 'field' in args_dict:
args_dict['field'] = args_dict['field'].upper()
if 'cluster_field' in args_dict and args_dict['cluster_field'] is not None:
args_dict['cluster_field'] = args_dict['cluster_field'].upper()
if 'meta_fields' in args_dict and args_dict['meta_fields'] is not None:
args_dict['meta_fields'] = [f.upper() for f in args_dict['meta_fields']]
if 'fields' in args_dict:
args_dict['fields'] = [f.upper() for f in args_dict['fields']]
default=default_muscle_exec,
help='The location of the MUSCLE executable')
parser_block.set_defaults(group_func=groupRecords, align_func=alignBlocks)
return parser
if __name__ == '__main__':
"""
Parses command line arguments and calls main function
"""
# Parse arguments
parser = getArgParser()
checkArgs(parser)
args = parser.parse_args()
args_dict = parseCommonArgs(args)
# Check if a valid MUSCLE executable was specified for muscle mode
if not shutil.which(args.muscle_exec):
parser.error('%s does not exist or is not executable.' %
args.muscle_exec)
# Define align_args
args_dict['align_args'] = {'muscle_exec': args_dict['muscle_exec']}
del args_dict['muscle_exec']
# Define group_args
if args_dict['group_func'] is groupRecords:
args_dict['group_args'] = {
'fields': args_dict['group_fields'],
'calls': args_dict['calls'],
'mode': args_dict['mode'],
)
parser_split.set_defaults(func=splitDbFile)
return parser
if __name__ == '__main__':
"""
Parses command line arguments and calls main function
"""
# Parse arguments
parser = getArgParser()
checkArgs(parser)
args = parser.parse_args()
if args.command == 'merge':
args_dict = parseCommonArgs(args, in_list=True)
else:
args_dict = parseCommonArgs(args)
# Delete command declaration from argument dictionary
del args_dict['command']
del args_dict['func']
# Check argument pairs
if args.command == 'add' and len(args_dict['fields']) != len(
args_dict['values']):
parser.error('You must specify exactly one value (-u) per field (-f)')
elif args.command == 'rename' and len(args_dict['fields']) != len(
args_dict['names']):
parser.error(
'You must specify exactly one new name (-k) per field (-f)')
elif args.command == 'update' and len(args_dict['values']) != len(
help='''Specify if IMGT framework and CDR regions should be
included in the output. Adds the FWR1_IMGT, FWR2_IMGT,
FWR3_IMGT, FWR4_IMGT, CDR1_IMGT, CDR2_IMGT, and
CDR3_IMGT columns.''')
parser_imgt.set_defaults(func=parseIMGT)
return parser
if __name__ == "__main__":
"""
Parses command line arguments and calls main
"""
parser = getArgParser()
args = parser.parse_args()
args_dict = parseCommonArgs(args, in_arg='aligner_files')
# Set no ID parsing if sequence files are not provided
if 'seq_files' in args_dict and not args_dict['seq_files']:
args_dict['no_parse'] = True
# Delete
if 'seq_files' in args_dict: del args_dict['seq_files']
if 'aligner_files' in args_dict: del args_dict['aligner_files']
if 'command' in args_dict: del args_dict['command']
if 'func' in args_dict: del args_dict['func']
if args.command == 'imgt':
for i in range(len(args.__dict__['aligner_files'])):
args_dict['imgt_output'] = args.__dict__['aligner_files'][i]
args_dict['seq_file'] = args.__dict__['seq_files'][i] \
included in the output. Adds the FWR1_IMGT, FWR2_IMGT,
FWR3_IMGT, FWR4_IMGT, CDR1_IMGT, CDR2_IMGT, and
CDR3_IMGT columns.''')
parser_ihmm.set_defaults(func=parseIHMM)
return parser
if __name__ == "__main__":
"""
Parses command line arguments and calls main
"""
parser = getArgParser()
checkArgs(parser)
args = parser.parse_args()
args_dict = parseCommonArgs(args, in_arg='aligner_outputs')
# Set no ID parsing if sequence files are not provided
if 'seq_files' in args_dict and not args_dict['seq_files']:
args_dict['no_parse'] = True
# Delete
if 'seq_files' in args_dict: del args_dict['seq_files']
if 'aligner_outputs' in args_dict: del args_dict['aligner_outputs']
if 'command' in args_dict: del args_dict['command']
if 'func' in args_dict: del args_dict['func']
if args.command == 'imgt':
for i in range(len(args.__dict__['aligner_outputs'])):
args_dict['aligner_output'] = args.__dict__['aligner_outputs'][i]
args_dict['seq_file'] = args.__dict__['seq_files'][i] \
help='''Specify to include additional aligner specific fields in the output.
Adds the path score of the iHMMune-Align hidden Markov model as vdj_score;
adds fwr1, fwr2, fwr3, fwr4, cdr1, cdr2 and cdr3.''')
parser_ihmm.set_defaults(func=parseIHMM)
return parser
if __name__ == "__main__":
"""
Parses command line arguments and calls main
"""
parser = getArgParser()
checkArgs(parser)
args = parser.parse_args()
args_dict = parseCommonArgs(args, in_arg='aligner_files')
# Set no ID parsing if sequence files are not provided
if 'seq_files' in args_dict and not args_dict['seq_files']:
args_dict['asis_id'] = True
# Delete
if 'aligner_files' in args_dict: del args_dict['aligner_files']
if 'seq_files' in args_dict: del args_dict['seq_files']
if 'out_files' in args_dict: del args_dict['out_files']
if 'command' in args_dict: del args_dict['command']
if 'func' in args_dict: del args_dict['func']
# Call main
for i, f in enumerate(args.__dict__['aligner_files']):
args_dict['aligner_file'] = f