[Biopython-dev] [Biopython (old issues only) - Bug #2532] (Migrated) Using IUPAC alphabets in mixed case Seq objects

[redmine at redmine.open-bio.org]

Issue #2532 has been updated by Peter Cock.

Description updated
Status changed from New to Migrated

Migrated to GitHub as https://github.com/biopython/biopython/issues/1716

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Bug #2532: Using IUPAC alphabets in mixed case Seq objects
https://redmine.open-bio.org/issues/2532#change-15402

* Author: Peter Cock
* Status: Migrated
* Priority: Normal
* Assignee: Biopython Dev Mailing List
* Category: Main Distribution
* Target version: Not Applicable
* URL: 
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Bio.Alphabets.IUPAC defines a number of alphabets with defined lists of valid letters which are in upper case ONLY.

Bio.Nexus and Bio.Sequencing.Phd create Seq objects which use these alphabets even with mixed case sequences.

This contradicts how I think the alphabet's .letters property is intended to be used (although currently this is not enforced by the Seq object).

I suggest either:

(a) Bio.Nexus etc switch to using generic DNA/RNA alphabets for any Seq objects including lower case letters (or more simply, all Seq objects).

(b) We add lower case and mixed case variants of the alphabet objects, and use the mixed case IUPAC alphabets in Bio.Nexus etc for the Seq objects.

There is also the option of (c) Extend the existing upper case only IUPAC alphabets to include lower case too, but I fear this could have unexpected side effects (e.g. where people looping over the expected set of letters).

---Files--------------------------------
phd_alpha.patch (759 Bytes)
eee.txt (1.29 KB)
nexus_alphabets.patch (1.83 KB)
mixed_case_IUPAC.patch (2.57 KB)


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