Make signalp run script accept optional include_mature flag.

scripts/convert_signalp.py

 #!/usr/bin/python3
+
 import sys
 import json
 import argparse
 
-parser = argparse.ArgumentParser(description='Convert signalp results to json documents')
-parser.add_argument('--result', '-r', required=True, help='The signalp result file')
+parser = argparse.ArgumentParser(description='Convert signalp results to json document')
+parser.add_argument('--result', '-r', required=True, help='The signalp result directory')
 parser.add_argument('--output', '-o', required=True, help='The converted results json file')
 args = parser.parse_args()
 
-filename = args.result
+# Check wether args.result + '/mature.fas' exists and if so read into id:seq dict
+
+filename = args.result + '/results.txt'
 documents = {}
+
 with open(filename) as f:
     tool = None
     for line in f:
@@ -36,5 +40,6 @@ with open(filename) as f:
                         'mode': split[2]}
 
 output_filename = args.output
+
 with open(output_filename, 'w') as o:
     json.dump(documents, o)

scripts/run_signalp.py

 #!/usr/bin/env python3
+
 import env
 import argparse
 from psot import config
-from os import system
+from os import system,makedirs
 
 signalp_tool = config.load_config()['tools'].get('signalp', 'signalp')
 
 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')
-parser.add_argument('--output', required=True, help='The output file')
+parser.add_argument('--include_mature', '-m', action='store_true', help='Include mature sequences of proteins with signal peptide')
+parser.add_argument('--output', required=True, help='The result directory. Will contain results.txt and optionally mature.fas.')
 args = parser.parse_args()
 
-system(signalp_tool + " -t " + args.organism + " " + args.fasta + " > " + args.output)
+makedirs(args.output, exist_ok=True)
+
+mature_param = " -m {}/mature.fas ".format(args.output) if args.include_mature else " "
+results_file = args.output + '/results.txt'
+system(signalp_tool + " -t " + args.organism + mature_param + args.fasta + " > " + results_file)