[Biopython-dev] [Biopython - Bug #3387] 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.


The underlying alignment class would need a per-column-annotation dictionary (as well as an annotations dictionary, also on the TODO list), to match the per-letter-annotation and annotations dictionaries of the SeqRecord.

Parsing this and putting it in alignment._letter_annotation (dictionary as a private variable) would be a reasonable short term hack if you'd like to work on that.
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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

Author: saverio vicario
Status: New
Priority: Normal
Assignee: Biopython Dev Mailing List
Category: Main Distribution
Target version: 
URL: 


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. 




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