Andreas Tille pushed to branch master at Debian Med / seqmagick
Commits: 9dff6e03 by Andreas Tille at 2018-05-30T09:30:27+02:00 Add patch to cope with latest BioPython - - - - - 3 changed files: - debian/changelog - + debian/patches/biopython_1.71_dual_coding_support.patch - + debian/patches/series Changes: ===================================== debian/changelog ===================================== --- a/debian/changelog +++ b/debian/changelog @@ -1,6 +1,5 @@ seqmagick (0.7.0-1) UNRELEASED; urgency=medium * Initial release (Closes: #<bug>) - TODO: https://github.com/fhcrc/seqmagick/issues/73 -- Andreas Tille <ti...@debian.org> Thu, 22 Jun 2017 12:03:20 +0200 ===================================== debian/patches/biopython_1.71_dual_coding_support.patch ===================================== --- /dev/null +++ b/debian/patches/biopython_1.71_dual_coding_support.patch @@ -0,0 +1,32 @@ +From: peterjc <p.j.a.c...@googlemail.com> +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. +--- + seqmagick/transform.py | 4 ++++ + 1 file changed, 4 insertions(+) + +--- a/seqmagick/transform.py ++++ b/seqmagick/transform.py +@@ -668,6 +668,10 @@ class CodonWarningTable(object): + else: + return self.wrapped.__getitem__(codon) + ++ def __contains__(self, value): ++ return value in self.wrapped ++ ++ + def translate(records, translate): + """ + Perform translation from generic DNA/RNA to proteins. Bio.Seq ===================================== debian/patches/series ===================================== --- /dev/null +++ b/debian/patches/series @@ -0,0 +1 @@ +biopython_1.71_dual_coding_support.patch View it on GitLab: https://salsa.debian.org/med-team/seqmagick/commit/9dff6e032852f9121b9067ce306f9d57c808ed76 -- View it on GitLab: https://salsa.debian.org/med-team/seqmagick/commit/9dff6e032852f9121b9067ce306f9d57c808ed76 You're receiving this email because of your account on salsa.debian.org.
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