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cli.py
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cli.py
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#!/usr/bin/env python
# -*- coding: utf-8 -*-
# ------------------------------------------------------------------------------
"""
Function used to parse argument when digestool is run with CLI
"""
# ------------------------------------------------------------------------------
import argparse
# ------------------------------------------------------------------------------
def parse_args():
""" Parse command line arguments to run a cleave protein of the given
fasta file"""
parser = argparse.ArgumentParser(description='Digest proteins of a given fasta file')
parser.add_argument(
'fasta_file',
metavar='</path/to/file.fasta>'
)
parser.add_argument(
'-l', '--min_length',
metavar='',
default=7,
help='minimal length of peptide sequences (default: 7)'
)
parser.add_argument(
'-L', '--max_length',
metavar='',
default=None,
help='maximal length of peptide sequences (default: None)'
)
parser.add_argument(
'-M', '--miscleavages',
metavar='',
default=2,
help='maximum of miscleavages allowed (default: 2)'
)
parser.add_argument(
'-m', '--mass',
metavar='',
default=4600,
help='maximal molecular mass of peptide sequences (default: 4600 dalton)'
)
parser.add_argument(
'-u ', '--unique',
action='store_true',
help='add flag to inform if the peptides are unique or not'
)
parser.add_argument(
'-e', '--enzyme',
metavar='',
default='trypsin',
help='enzyme used to perform digestion (default: trypsin)'
)
parser.add_argument(
'-o', '--output',
metavar='',
help='output directory (default: /path/to/file.fasta_digestedPeptides.csv)'
)
args = parser.parse_args()
return args