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Issue #2532 has been updated by Peter Cock.
<ul>
<li><strong>Description</strong> updated (<a title="View differences" href="https://redmine.open-bio.org/journals/diff/15402?detail_id=1750">diff</a>)</li>
<li><strong>Status</strong> changed from <i>New</i> to <i>Migrated</i></li>
</ul>
<p>Migrated to GitHub as <a class="external" href="https://github.com/biopython/biopython/issues/1716">https://github.com/biopython/biopython/issues/1716</a></p>
<hr />
<h1><a href="https://redmine.open-bio.org/issues/2532#change-15402">Bug #2532: Using IUPAC alphabets in mixed case Seq objects</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: Not Applicable</li>
<li>URL: </li></ul>
<p>Bio.Alphabets.IUPAC defines a number of alphabets with defined lists of valid letters which are in upper case ONLY.</p>
<p>Bio.Nexus and Bio.Sequencing.Phd create Seq objects which use these alphabets even with mixed case sequences.</p>
<p>This contradicts how I think the alphabet's .letters property is intended to be used (although currently this is not enforced by the Seq object).</p>
<p>I suggest either:</p>
<p>(a) Bio.Nexus etc switch to using generic DNA/RNA alphabets for any Seq objects including lower case letters (or more simply, all Seq objects).</p>
<p>(b) We add lower case and mixed case variants of the alphabet objects, and use the mixed case IUPAC alphabets in Bio.Nexus etc for the Seq objects.</p>
<p>There is also the option of (c) Extend the existing upper case only IUPAC alphabets to include lower case too, but I fear this could have unexpected side effects (e.g. where people looping over the expected set of letters).</p>
<fieldset class="attachments"><legend>Files</legend>
<a href="https://redmine.open-bio.org/attachments/download/961/phd_alpha.patch">phd_alpha.patch</a>
(759 Bytes)<br />
<a href="https://redmine.open-bio.org/attachments/download/972/eee.txt">eee.txt</a>
(1.29 KB)<br />
<a href="https://redmine.open-bio.org/attachments/download/1174/nexus_alphabets.patch">nexus_alphabets.patch</a>
(1.83 KB)<br />
<a href="https://redmine.open-bio.org/attachments/download/1176/mixed_case_IUPAC.patch">mixed_case_IUPAC.patch</a>
(2.57 KB)<br />
</fieldset>
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