Add patch to cope with latest BioPython

seqmagick (0.7.0-1) UNRELEASED; urgency=medium

  * Initial release (Closes: #<bug>)

  TODO: https://github.com/fhcrc/seqmagick/issues/73

 -- Andreas Tille <tille@debian.org>  Thu, 22 Jun 2017 12:03:20 +0200

From: peterjc <p.j.a.cock@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

biopython_1.71_dual_coding_support.patch