From 23333d253c7adeb697efa558dec3b6e4e57bae77 Mon Sep 17 00:00:00 2001
From: Amandine PERRIN <amandine.perrin@pasteur.fr>
Date: Thu, 5 Dec 2019 12:26:07 +0100
Subject: [PATCH] Write absolute path for annotate_path in LSTINFO file
---
PanACoTA/utils.py | 5 +----
1 file changed, 1 insertion(+), 4 deletions(-)
diff --git a/PanACoTA/utils.py b/PanACoTA/utils.py
index 162c00ce..1931a792 100755
--- a/PanACoTA/utils.py
+++ b/PanACoTA/utils.py
@@ -484,16 +484,13 @@ def write_lstinfo(list_file, genomes, outdir):
"""
_, name_lst = os.path.split(list_file)
-
outlst = os.path.join(outdir, "LSTINFO-" + ".".join(name_lst.split(".")[:-1]) + ".lst")
with open(outlst, "w") as outf:
outf.write("\t".join(["gembase_name", "orig_name", "to_annotate", "gsize",
"nb_conts", "L90"]) + "\n")
for genome, values in sorted(genomes.items(), key=sort_genomes_byname_l90_nbcont):
gembase, _, to_annote, gsize, nbcont, l90 = [str(x) for x in values]
- to_annote_file = os.path.basename(to_annote)
- outf.write("\t".join([gembase, genome, to_annote_file, gsize, nbcont, l90]) + "\n")
-
+ outf.write("\t".join([gembase, genome, to_annote, gsize, nbcont, l90]) + "\n")
def sort_genomes_by_name(x):
"""
--
GitLab