From 85ae91140bd7f98445d6533e3452d2f0b444993b Mon Sep 17 00:00:00 2001 From: peterjc Date: Tue, 29 May 2018 15:05:22 +0100 Subject: [PATCH] Fix for Biopython 1.71 dual coding support. Origin: https://github.com/fhcrc/seqmagick/pull/76 This closes issue #73, indirectly triggered by changes in Biopython to support recent NCBI codon tables with codons which can be amino acids of stop codons. Previously the monkey-patched sub-class was breaking here: dual_coding = [c for c in stop_codons if c in forward_table] This change adds direct support for __contains__ by forwarding this to the wrapped forward table. Gbp-Pq: Name biopython_1.71_dual_coding_support.patch --- seqmagick/transform.py | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/seqmagick/transform.py b/seqmagick/transform.py index 3150d1d..4478786 100644 --- a/seqmagick/transform.py +++ b/seqmagick/transform.py @@ -670,6 +670,10 @@ class CodonWarningTable(object): return value in self.wrapped + def __contains__(self, value): + return value in self.wrapped + + def translate(records, translate): """ Perform translation from generic DNA/RNA to proteins. Bio.Seq -- cgit v1.2.3