[Biopython-dev] [Biopython (old issues only) - Feature #3326] (Closed) MultipleSeqAlignment should support iterators, not only slice objects

[redmine at redmine.open-bio.org]

Issue #3326 has been updated by Peter Cock.

Status changed from New to Closed
% Done changed from 0 to 100

As part of retiring the old RedMine issue tracker, I'm closing this but would welcome a pull request on GitHub if you think it would be useful.
https://github.com/biopython/biopython/

Thanks.

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Feature #3326: MultipleSeqAlignment should support iterators, not only slice objects
https://redmine.open-bio.org/issues/3326#change-15325

* Author: Fabio Zanini
* Status: Closed
* Priority: Normal
* Assignee: Biopython Dev Mailing List
* Category: Main Distribution
* Target version: 
* URL: 
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Currently, the MultipleSeqAlignment object supports slicing via various syntaxes, e.g.:

- alignment[4,6]
- alignment[2:4,3:6]
- alignment[3:4:5]

In the latter case, the indices build a so-called slice, a pure Python object, and MultipleSeqAlignment has an explicit if clause for dealing with this case.

However, the user might want to iterate over the MSA using the more general *iterators*, e.g. from itertools, rather than simple slice objects. An extension that includes iterators looks easy:

# Check whether the index is an iterator
if (hasattr(index, 'next')) and (hasattr(index:, '__iter__')):
    return MultipleSeqAlignment([self._records[i] for i in index], self._alphabet)

Would you think this is useful?





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