From b074f0dc939b503dd25fc640e2bf44bd901c0545 Mon Sep 17 00:00:00 2001
From: Amandine PERRIN <amandine.perrin@pasteur.fr>
Date: Wed, 31 Jul 2019 13:32:50 +0200
Subject: [PATCH] add path to sequence formatted
---
PanACoTA/annotate_module/prokka_prodigal_functions.py | 5 +++--
1 file changed, 3 insertions(+), 2 deletions(-)
diff --git a/PanACoTA/annotate_module/prokka_prodigal_functions.py b/PanACoTA/annotate_module/prokka_prodigal_functions.py
index f690cab3..58bc450d 100755
--- a/PanACoTA/annotate_module/prokka_prodigal_functions.py
+++ b/PanACoTA/annotate_module/prokka_prodigal_functions.py
@@ -31,7 +31,7 @@ def run_annotation_all(genomes, threads, force, annot_folder, prodigal_only=Fals
Parameters
----------
genomes : dict
- {genome: [name, gpath_cut_gembase, size, nbcont, l90]}
+ {genome: [gembase_name, path_to_origfile, path_split_gembase, gsize, nbcont, L90]}
threads : int
max number of threads that can be used
force : bool
@@ -126,7 +126,7 @@ def run_prokka(arguments):
Parameters
----------
arguments : tuple
- (gpath, prok_folder, cores_annot, name, force, nbcont, q) with:
+ (gpath, prok_folder, cores_annot, name, force, nbcont, small, q) with:
* gpath: path and filename of genome to annotate
* prok_folder: path to folder where all prokka folders for all genomes are saved
@@ -134,6 +134,7 @@ def run_prokka(arguments):
* name: output name of annotated genome
* force: True if force run (override existing files), False otherwise
* nbcont: number of contigs in the input genome, to check prokka results
+ * small: used for prodigal, if sequences to annotate are small. Not used here
* q : queue where logs are put
Returns
--
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