[med-svn] [Git][med-team/seqmagick][master] Add patch to cope with latest BioPython

[Andreas Tille]

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 <tille at 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.cock at 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

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View it on GitLab: https://salsa.debian.org/med-team/seqmagick/commit/9dff6e032852f9121b9067ce306f9d57c808ed76
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