1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
|
Description: fix test failure due to call to deprecated ungap.
Author: Étienne Mollier <emollier@debian.org>
Bug-Debian: https://bugs.debian.org/1066772
Forwarded: https://github.com/fhcrc/seqmagick/pull/101
Last-Update: 2024-03-17
---
This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
--- seqmagick.orig/seqmagick/subcommands/backtrans_align.py
+++ seqmagick/seqmagick/subcommands/backtrans_align.py
@@ -102,7 +102,7 @@
prot_seq.id, nucl_seq.id)
# Ungap nucleotides
- codons = batch(str(nucl_seq.seq.ungap('-')), 3)
+ codons = batch(str(nucl_seq.seq.replace('-', '')), 3)
codons = [''.join(i) for i in codons]
codon_iter = iter(codons)
|
