[Biopython-dev] [Biopython (old issues only) - Bug #3066] (Migrated) Iterating/looping over colums/rows of a MultipleSeqAlignment

[redmine at redmine.open-bio.org]

Issue #3066 has been updated by Peter Cock.

Description updated
Status changed from New to Migrated
URL set to https://github.com/biopython/biopython/issues/1722

Migrated to GitHub as https://github.com/biopython/biopython/issues/1722

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Bug #3066: Iterating/looping over colums/rows of a MultipleSeqAlignment
https://redmine.open-bio.org/issues/3066#change-15413

* Author: Peter Cock
* Status: Migrated
* Priority: Normal
* Assignee: Biopython Dev Mailing List
* Category: Main Distribution
* Target version: 1.54b
* URL: https://github.com/biopython/biopython/issues/1722
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The new MultipleSeqAlignment object (like the old Alignment object it replaces)
stores the rows of the alignment as SeqRecord objects. This means column based
access is slow.

It can often be useful to be able to iterate over the columns, and a dedicated
method to do this should be faster than repeatedly accessing columns by index
(either via slicing with __getitem__ or the old get_column method).

A related question here is should the columns be returned as strings or as Seq objects? Possible implementation to follow as a patch...

---Files--------------------------------
align_row_col_iter.patch (3.89 KB)


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