[Biopython-dev] [Biopython (old issues only) - Bug #3387] (Resolved) Generic per column annotation from stockholm alignment are not stored in alignment object

[redmine at redmine.open-bio.org]

Issue #3387 has been updated by Peter Cock.

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

Replacing this with GitHub issue https://github.com/biopython/biopython/issues/357

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Bug #3387: Generic per column annotation from stockholm alignment are not stored in alignment object
https://redmine.open-bio.org/issues/3387#change-15298

* Author: saverio vicario
* Status: Resolved
* Priority: Normal
* Assignee: Biopython Dev Mailing List
* Category: Main Distribution
* Target version: 
* URL: 
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Stockholm format includes 4 types of annotations
#=GF <feature> <Generic per-File annotation, free text>
#=GC <feature> <Generic per-Column annotation, exactly 1 char per column>
#=GS <seqname> <feature> <Generic per-Sequence annotation, free text>
#=GR <seqname> <feature> <Generic per-Sequence AND per-Column markup, exactly 1 char per column>
GC and GF annotation are not pickup by AlignIO and not supported in Bio.Align.MultipleSeqAlignment because no annotation is available at alignment level. In fact Bio.Align.MultipleSeqAlignment.annotations or Bio.Align.MultipleSeqAlignment.letter_annotations do not exist, only Bio.Align.MultipleSeqAlignment._annotations that is generated from the single records annotations and letter_annotations.

GC annotation in stockholm contain the quality score of the sites (columns of the alignment) that is a quite important parameters to decide if to trim the sites or not. 



---Files--------------------------------
diff_StockholmIO.py (4.08 KB)
StockholmIO.py (26.8 KB)


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