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Issue #3387 has been updated by Peter Cock.
<ul>
<li><strong>Status</strong> changed from <i>New</i> to <i>Resolved</i></li>
<li><strong>% Done</strong> changed from <i>0</i> to <i>100</i></li>
</ul>
<p>Replacing this with GitHub issue <a class="external" href="https://github.com/biopython/biopython/issues/357">https://github.com/biopython/biopython/issues/357</a></p>
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<h1><a href="https://redmine.open-bio.org/issues/3387#change-15298">Bug #3387: Generic per column annotation from stockholm alignment are not stored in alignment object</a></h1>
<ul><li>Author: saverio vicario</li>
<li>Status: Resolved</li>
<li>Priority: Normal</li>
<li>Assignee: Biopython Dev Mailing List</li>
<li>Category: Main Distribution</li>
<li>Target version: </li>
<li>URL: </li></ul>
<p>Stockholm format includes 4 types of annotations<br />#=GF <feature> <Generic per-File annotation, free text><br />#=GC <feature> <Generic per-Column annotation, exactly 1 char per column><br />#=GS <seqname> <feature> <Generic per-Sequence annotation, free text><br />#=GR <seqname> <feature> <Generic per-Sequence AND per-Column markup, exactly 1 char per column><br />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.</p>
<p>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.</p>
<fieldset class="attachments"><legend>Files</legend>
<a href="https://redmine.open-bio.org/attachments/download/1741/diff_StockholmIO.py">diff_StockholmIO.py</a>
(4.08 KB)<br />
<a href="https://redmine.open-bio.org/attachments/download/1742/StockholmIO.py">StockholmIO.py</a>
(26.8 KB)<br />
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