run_signalp.py 662 Bytes
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#!/usr/bin/env python3
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import env
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import argparse
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from psot import config
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from os import system

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signalp_tool = config.load_config()['tools'].get('signalp', 'signalp')
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parser = argparse.ArgumentParser(description='Find signal peptides in amino acid sequences')
parser.add_argument('--fasta', '-f', required=True, help='A fasta file with aminoacid sequences')
parser.add_argument('--organism', '-o', choices=['euk', 'gram+', 'gram-'], default='euk', help='The organism type')
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parser.add_argument('--output', required=True, help='The output file')
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args = parser.parse_args()

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system(signalp_tool + " -t " + args.organism + " " + args.fasta + " > " + args.output)