[Biopython-dev] [Biopython (old issues only) - Bug #2653] (Migrated) Bio.SeqUtils.CodonUsage is not translation table aware

[redmine at redmine.open-bio.org]

Issue #2653 has been updated by Peter Cock.

Description updated
Status changed from New to Migrated
URL set to https://github.com/biopython/biopython/issues/1720

Migrated to GitHub as https://github.com/biopython/biopython/issues/1720

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Bug #2653: Bio.SeqUtils.CodonUsage is not translation table aware
https://redmine.open-bio.org/issues/2653#change-15410

* Author: Peter Cock
* Status: Migrated
* Priority: Normal
* Assignee: Biopython Dev Mailing List
* Category: Main Distribution
* Target version: Not Applicable
* URL: https://github.com/biopython/biopython/issues/1720
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Looking at Bio/SeqUtils/CodonUsage.py there is a hard coded dictionary SynonymousCodons, presumably for the standard genetic code.

Ideally Bio.SeqUtils.CodonUsage should support any of the genetic code tables defined in Bio.Data.CodonTable, perhaps via an optional initiation argument to the CodonAdaptationIndex object.



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