From 24e6d5d51bcfa3000e86df46049770664bc4a5b8 Mon Sep 17 00:00:00 2001
From: Amandine PERRIN <amandine.perrin@pasteur.fr>
Date: Sat, 22 Aug 2020 08:53:32 +0200
Subject: [PATCH] get_contigs returned in the wrong way
---
PanACoTA/utils.py | 12 ++++++++----
1 file changed, 8 insertions(+), 4 deletions(-)
diff --git a/PanACoTA/utils.py b/PanACoTA/utils.py
index cb123954..69e51888 100755
--- a/PanACoTA/utils.py
+++ b/PanACoTA/utils.py
@@ -1133,8 +1133,10 @@ def get_genome_contigs_and_rename(gembase_name, gpath, outfile):
# - write header ("<contig name> <size>") to replicon file
if prev_cont:
cont = "\t".join([prev_cont, str(cont_size)]) + "\n"
- sizes[prev_cont] = cont_size
- contigs[prev_cont] = prev_orig_name
+ prevcont_nohead = "".join(prev_cont.split(">")[1:])
+ prev_orig_name_nohead = "".join(prev_orig_name.split(">")[1:])
+ sizes[prevcont_nohead] = cont_size
+ contigs[prev_orig_name_nohead] = prevcont_nohead
grf.write(cont)
grf.write(seq)
prev_cont = ">" + gembase_name + "." + str(contig_num).zfill(4)
@@ -1148,8 +1150,10 @@ def get_genome_contigs_and_rename(gembase_name, gpath, outfile):
cont_size += len(line.strip())
# Write last contig
cont = "\t".join([prev_cont, str(cont_size)]) + "\n"
- sizes[prev_cont] = cont_size
- contigs[prev_cont] = prev_orig_name
+ prevcont_nohead = "".join(prev_cont.split(">")[1:])
+ prev_orig_name_nohead = "".join(prev_orig_name.split(">")[1:])
+ contigs[prev_orig_name_nohead] = prevcont_nohead
+ sizes[prevcont_nohead] = cont_size
grf.write(cont)
grf.write(seq)
return contigs, sizes
--
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