Added signalp module

bin/module_signalp.py

+#!/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)

bin/module_signalp_convert.py

+#!/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]))