Commit a6cb14bf authored by Lukas Jelonek's avatar Lukas Jelonek
Browse files

Added signalp module

parent 7f09a528
#!/usr/bin/env python3
import argparse
from os import system
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')
args = parser.parse_args()
system("/vol/biotools/bin/signalp -t " + args.organism + " " + args.fasta)
#!/usr/bin/python3
import sys
import json
filename = sys.argv[1]
documents = {}
with open(filename) as f:
tool = None
for line in f:
if not line.startswith("#"):
split = line.split()
if not split[0] in documents:
documents[split[0]] = {"id": split[0], "computations": [{'tool': tool, 'results':[]}]}
results = documents[split[0]]['computations'][0]["results"]
print(split)
if split[9] == "Y":
results.append({
'signalpeptide': True,
'score': float(split[8]),
'start':1,
'end': int(split[2])-1
})
else:
results.append({'signalpeptide': False})
else:
if line.startswith('# SignalP'):
split = line.split()
tool = {'name': 'SignalP',
'version': split[1].split('-')[1],
'mode': split[2]}
for key in documents:
print(json.dumps(documents[key]))
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