run_tmhmm.py 557 Bytes
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#!/usr/bin/env python3
import env
import argparse
from psot import config
from os import system
import subprocess

tmhmm_tool = config.load_config()['tools'].get('tmhmm', 'tmhmm')

parser = argparse.ArgumentParser(description='Find transmembrane helices in amino acid sequences')
parser.add_argument('--fasta', '-f', required=True, help='A fasta file with aminoacid sequences')
parser.add_argument('--output', required=True, help='The output file')
args = parser.parse_args()

system("cat " + args.fasta + " | " + tmhmm_tool + " -short > " + args.output) #