Fix bug: adapt targetp runner to new helpers path

psot/scripts/convert_targetp.py

@@ -4,6 +4,7 @@ import sys
 import json
 import argparse
 from os import path
+from psot import config
 import subprocess
 
 parser = argparse.ArgumentParser(description='Convert targetp results to json document')
@@ -57,5 +58,5 @@ with open(output_filename, 'w') as o:
     json.dump(documents, o)
 
 # Replace sequences' enumerated ids with their original ids
-restore_seq_ids_tool = path.dirname(__file__) + '/restore_seq_id_from_enumeration.py'
+restore_seq_ids_tool = config.load_config()['helpers_path'] + '/restore_seq_id_from_enumeration.py'
 subprocess.run([restore_seq_ids_tool, '-j', output_filename, '-e', args.result + '/enum_headers.tsv'])

psot/scripts/run_targetp.py

@@ -5,7 +5,8 @@ from psot import config
 from os import system,makedirs,path
 import subprocess
 
-targetp_tool = config.load_config()['tools'].get('targetp', 'targetp')
+cfg = config.load_config()
+targetp_tool = cfg['tools'].get('targetp', 'targetp')
 
 org_flags = {'plant': '-P', 'non-plant': '-N'}
 
@@ -18,7 +19,7 @@ args = parser.parse_args()
 makedirs(args.output, exist_ok=True)
 
 # Swap fasta headers for unique numbers to avoid truncation
-reduce_headers_tool = path.dirname(__file__) + '/reduce_fasta_headers_to_enumeration.py'
+reduce_headers_tool = cfg['helpers_path'] + '/reduce_fasta_headers_to_enumeration.py'
 subprocess.run([reduce_headers_tool, "-f", args.fasta, "-e", args.output + '/enum_headers.tsv'])
 
 results_file = args.output + '/results.txt'