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| author | peterjc <p.j.a.cock@googlemail.com> | 2018-05-29 15:05:22 +0100 |
|---|---|---|
| committer | Étienne Mollier <emollier@debian.org> | 2024-03-17 18:11:48 +0100 |
| commit | 85ae91140bd7f98445d6533e3452d2f0b444993b (patch) | |
| tree | 00605667915ef7932a05e57e6964fa021105d10b | |
| parent | 276b39582de02130980fc604299ff0899379e68e (diff) | |
[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
| -rw-r--r-- | seqmagick/transform.py | 4 |
1 files changed, 4 insertions, 0 deletions
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 |