Commit 193e2cef authored by hmueller's avatar hmueller
Browse files

Add run_targetp.py script.

parent 51c09db6
#!/usr/bin/env python3
import env
import argparse
from psot import config
from os import system
targetp_tool = config.load_config()['tools'].get('targetp', 'targetp')
parser = argparse.ArgumentParser(description = 'Determine subcellular locations of eukaryotic amino acid sequences')
parser.add_argument('--fasta', '-f', required = True, help = 'A fasta file with amino acid sequences')
parser.add_argument('--plant', '-p', action = 'store_true', help = 'Wether sequences originate from plants')
parser.add_argument('--output', required = True, help = 'The output file')
args = parser.parse_args()
plant_flag = '-P' if args.plant else '-N'
system(targetp_tool + " " + plant_flag + " " + args.fasta + " > " + args.output)
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