# Subparser for conversion of SRA headers
parser_sra = subparsers.add_parser('sra', parents=[parser_parent],
formatter_class=CommonHelpFormatter,
help='''Converts NCBI SRA sequence headers.''')
parser_sra.set_defaults(convert_func=convertSRAHeader)
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)
# Create convert_args
convert_keys = ['simple']
args_dict['convert_args'] = dict((k, args_dict[k]) for k in args_dict \
if k in convert_keys)
for k in args_dict['convert_args']: del args_dict[k]
# Calls header conversion function
del args_dict['seq_files']
for f in args.__dict__['seq_files']:
args_dict['seq_file'] = f
convertHeaders(**args_dict)
default=default_usearch_exec,
help='''The path to the usearch executable file.''')
parser_ref.set_defaults(assemble_func=referenceAssembly)
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, in_arg='ref_file')
# Convert case of fields
if args_dict['head_fields']: args_dict['head_fields'] = list(map(str.upper, args_dict['head_fields']))
if args_dict['tail_fields']: args_dict['tail_fields'] = list(map(str.upper, args_dict['tail_fields']))
# Define assemble_args dictionary to pass to maskPrimers
if args_dict['assemble_func'] is alignAssembly:
args_dict['assemble_args'] = {'alpha': args_dict['alpha'],
'max_error': args_dict['max_error'],
'min_len': args_dict['min_len'],
'max_len': args_dict['max_len'],
'scan_reverse': args_dict['scan_reverse'],
'assembly_stats': AssemblyStats(args_dict['max_len'] + 1)}
del args_dict['alpha']
del args_dict['max_error']
failed=False, log=False)],
formatter_class=CommonHelpFormatter)
parser.add_argument('--version', action='version',
version='%(prog)s:' + ' %s-%s' %(__version__, __date__))
parser.add_argument('-l', nargs='+', action='store', dest='record_files', required=True,
help='List of log files to parse.')
parser.add_argument('-f', nargs='+', action='store', dest='fields', required=True,
help='''List of fields to collect. The sequence identifier may
be specified using the hidden field name "ID".''')
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, in_arg='record_files')
# Convert case of fields
if args_dict['fields']: args_dict['fields'] = list(map(str.upper, args_dict['fields']))
# Call parseLog for each log file
del args_dict['record_files']
for f in args.__dict__['record_files']:
args_dict['record_file'] = f
tableLog(**args_dict)
'Assemble pairs by first attempting de novo assembly, then reference guided assembly.'
)
parser_two.set_defaults(assemble_func=sequentialAssembly)
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, in_arg='ref_file')
# Convert case of fields
if args_dict['head_fields']:
args_dict['head_fields'] = list(
map(str.upper, args_dict['head_fields']))
if args_dict['tail_fields']:
args_dict['tail_fields'] = list(
map(str.upper, args_dict['tail_fields']))
# Define assemble_args dictionary for join mode
if args_dict['assemble_func'] is joinAssembly:
args_dict['assemble_args'] = {'gap': args_dict['gap']}
del args_dict['gap']
# Define assemble_args dictionary for align mode