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Issue #3060 has been updated by Peter Cock.
<ul>
<li><strong>Description</strong> updated (<a title="View differences" href="https://redmine.open-bio.org/journals/diff/15387?detail_id=1717">diff</a>)</li>
<li><strong>Status</strong> changed from <i>New</i> to <i>Migrated</i></li>
<li><strong>URL</strong> set to <i>https://github.com/biopython/biopython/issues/1017</i></li>
</ul>
<p>Moved to GitHub as <a class="external" href="https://github.com/biopython/biopython/issues/1017">https://github.com/biopython/biopython/issues/1017</a></p>
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<h1><a href="https://redmine.open-bio.org/issues/3060#change-15387">Bug #3060: Add ungap method to the SeqRecord?</a></h1>
<ul><li>Author: Peter Cock</li>
<li>Status: Migrated</li>
<li>Priority: Normal</li>
<li>Assignee: Biopython Dev Mailing List</li>
<li>Category: Main Distribution</li>
<li>Target version: 1.54b</li>
<li>URL: https://github.com/biopython/biopython/issues/1017</li></ul>
<p>Biopython 1.53 added an ungap method to the Seq object.</p>
<p>This is a possible enhancement request to add a matching ungap method to the SeqRecord object, where the per-letter-annotation and features should be adjusted to match.</p>
<p>My motivating example is to take an ACE file loaded with SeqIO, remove the gaps, and output the contigs as FASTQ or QUAL files. This requires the per-letter-annotation to be sliced to match the ungapped sequence.</p>
<p>Likewise any features fully contained within ungapped regions should be retained and their co-ordinates shifted. I'm not sure if we should do anything about features spanning a gap - the simple option which I have implemented is they are lost. This is done via the existing SeqRecord slicing and addition code.</p>
<p>Patch to follow...</p>
<p>See also Bug 3054 for adding upper and lower methods to the SeqRecord, and the broader discussion on Bug 2351 about strings, Seq and SeqRecord objects.</p>
<fieldset class="attachments"><legend>Files</legend>
<a href="https://redmine.open-bio.org/attachments/download/1482/seqrecord_ungap.patch">seqrecord_ungap.patch</a>
(4.74 KB)<br />
</fieldset>
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