From dd8bed3ce9734bd504edd5603b7113f47c5e2113 Mon Sep 17 00:00:00 2001
From: Amandine PERRIN <amandine.perrin@pasteur.fr>
Date: Wed, 2 Sep 2020 11:49:05 +0200
Subject: [PATCH] update functions
---
PanACoTA/annotate_module/general_format_functions.py | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git a/PanACoTA/annotate_module/general_format_functions.py b/PanACoTA/annotate_module/general_format_functions.py
index 594325e8..023e66ff 100644
--- a/PanACoTA/annotate_module/general_format_functions.py
+++ b/PanACoTA/annotate_module/general_format_functions.py
@@ -26,8 +26,8 @@ import progressbar
import multiprocessing
import threading
import PanACoTA.utils as utils
-# import PanACoTA.annotate_module.format_prokka as fprokka
-# import PanACoTA.annotate_module.format_prodigal as fprodigal
+import PanACoTA.annotate_module.format_prokka as fprokka
+import PanACoTA.annotate_module.format_prodigal as fprodigal
def format_genomes(genomes_ok, res_path, annot_path, prodigal_only, threads=1, quiet=False,
@@ -179,7 +179,7 @@ def handle_genome(args):
logger = logging.getLogger('format.handle_genome')
# Handle genome
ok_format = format_one_genome(gpath, name, annot_path, lst_dir,
- prot_dir, gene_dir, rep_dir, gff_dir, logger)
+ prot_dir, gene_dir, rep_dir, gff_dir)
return ok_format, genome
--
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