[Biopython-dev] [Biopython (old issues only) - Feature #3388] (Closed) add annotation and letter_annotations attributed for Bio.Align.MultipleSeqAlignment. object

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Issue #3388 has been updated by Peter Cock.

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

General annotation was included in Biopython 1.61

Closing in favour of https://github.com/biopython/biopython/issues/516 for per-column annotation.


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Feature #3388: add annotation and letter_annotations attributed for Bio.Align.MultipleSeqAlignment. object
https://redmine.open-bio.org/issues/3388#change-15276

* Author: saverio vicario
* Status: Closed
* Priority: Normal
* Assignee: Biopython Dev Mailing List
* Category: Main Distribution
* Target version: 
* URL: 
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At the moment I could not add annotation at alignment level.  annotation could be usefull for tracking info linked to the loci ( i.e. name of domain), while letter annotation could be usefull to track quality score of alignment or if the sites belong to a given character set.
In particular when to alignment are merged it would be usefull tha the bounduary of the merge is tracked
for example in Letter annotation of the merge of an alignment a with 10 sites and b of 5 sites the letter_annotations would be as following 

{locus1:'111111111100000',locus2:'000000000011111'} 
this could be usefull also to annotate the 3 position of codons
{pos1:'1001001001',pos2:'0100100100', pos3:'0010010010'}

If this letter_annotation would be supported the annotation could be kept across merging and splitting of the alignment



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