[Biopython (old issues only) - Bug #3387] (Resolved) Generic per column annotation from stockholm alignment are not stored in alignment object
| Newsgroups | gmane.comp.python.bio.devel |
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| Message-ID | <redmine.journal-15298.20160722155136.d7b2c70bd3347e85@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 ---------------------------------------- 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: ---------------------------------------- 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) -- You have received this notification because you have either subscribed to it, or are involved in it. To change your notification preferences, please click here and login: http://redmine.open-bio.org _______________________________________________ Biopython-dev mailing list [email protected] http://mailman.open-bio.org/mailman/listinfo/biopython-dev