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Issue #2597 has been updated by Peter Cock.
<ul>
<li><strong>Assignee</strong> changed from <i>Biopython Dev Mailing List</i> to <i>Peter Cock</i></li>
</ul>
<p>Moved to GitHub as <a class="external" href="https://github.com/biopython/biopython/issues/1040">https://github.com/biopython/biopython/issues/1040</a></p>
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<h1><a href="https://redmine.open-bio.org/issues/2597#change-15389">Bug #2597: Enforce alphabet letters in Seq objects</a></h1>
<ul><li>Author: Peter Cock</li>
<li>Status: In Progress</li>
<li>Priority: Normal</li>
<li>Assignee: Peter Cock</li>
<li>Category: Main Distribution</li>
<li>Target version: Not Applicable</li>
<li>URL: </li></ul>
<p>If a Seq object is created with an alphabet with a pre-defined set of letters (e.g. the IUPAC alphabets) then I think Biopython should validate that the sequence does indeed only use those letters.</p>
<p>This will catch mis-use of ambiguous sequences with non-ambiguous alphabets, letters in an unexpected case, and most importantly any unexpected symbols (e.g. from a parsing problem).</p>
<p>This will impose a performance overhead - which can be avoided if the user instead chooses to use a generic dna/rna/protein alphabet which does not list the letters expected.</p>
<p>Note that we will have to resolve Bug 2532 before doing this, as currently some parts of Biopython are mis-using the upper case only IUPAC alphabet objects with mixed case sequences.</p>
<fieldset class="attachments"><legend>Files</legend>
<a href="https://redmine.open-bio.org/attachments/download/1175/bug2597.patch">bug2597.patch</a>
(459 Bytes)<br />
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