<html>
<head>
<style>
body {
font-family: Verdana, sans-serif;
font-size: 0.8em;
color:#484848;
}
h1, h2, h3 { font-family: "Trebuchet MS", Verdana, sans-serif; margin: 0px; }
h1 { font-size: 1.2em; }
h2, h3 { font-size: 1.1em; }
a, a:link, a:visited { color: #2A5685;}
a:hover, a:active { color: #c61a1a; }
a.wiki-anchor { display: none; }
fieldset.attachments {border-width: 1px 0 0 0;}
hr {
width: 100%;
height: 1px;
background: #ccc;
border: 0;
}
span.footer {
font-size: 0.8em;
font-style: italic;
}
</style>
</head>
<body>
Issue #2818 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>Resolved with changes to Biopython since, including the new CompoundLocation object for joins, and making the position objects more integer like.</p>
<hr />
<h1><a href="https://redmine.open-bio.org/issues/2818#change-15388">Bug #2818: Add start and end properties to SeqFeature object</a></h1>
<ul><li>Author: Peter Cock</li>
<li>Status: Resolved</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>An enhancment proposed on the mailing list would add start and end properties to the SeqFeature returning plain integers (non-fuzzy approximations to the start and end locations) suitable for slicing most parent sequences. Dealing with a join location would still be tricky.</p>
<p>Example usage:</p>
<blockquote><blockquote><blockquote>
<p>from Bio import SeqIO<br />record = SeqIO.read(open("NC_005816.gb"),"gb")<br />feature = record.features<sup><a href="#fn2">2</a></sup><br />print feature</p>
</blockquote></blockquote></blockquote>
<p>type: gene<br />location: [86:1109]<br />ref: None:None<br />strand: 1<br />qualifiers: <br /> Key: db_xref, Value: ['GeneID:2767718']<br /> Key: locus_tag, Value: ['YP_pPCP01']</p>
<blockquote><blockquote><blockquote>
<p>record[feature.start:feature.end]</p>
</blockquote></blockquote></blockquote>
<p>SeqRecord(seq=Seq('ATGGTCACTTTTGAGACAGTTATGGAAATTAAAATCCTGCACAAGCAGGGAATG...TGA', IUPACAmbiguousDNA()), id='NC_005816.1', name='NC_005816', description='Yersinia pestis biovar Microtus str. 91001 plasmid pPCP1, complete sequence.', dbxrefs=[])</p>
<blockquote><blockquote><blockquote>
<p>record.seq[feature.start:feature.end]</p>
</blockquote></blockquote></blockquote>
<p>Seq('ATGGTCACTTTTGAGACAGTTATGGAAATTAAAATCCTGCACAAGCAGGGAATG...TGA', IUPACAmbiguousDNA())</p>
<p>Patch to follow.</p>
<fieldset class="attachments"><legend>Files</legend>
<a href="https://redmine.open-bio.org/attachments/download/1281/sf_start_end.patch">sf_start_end.patch</a>
(519 Bytes)<br />
</fieldset>
<hr />
<span class="footer"><p>You have received this notification because you have either subscribed to it, or are involved in it.<br />To change your notification preferences, please click here and login: <a class="external" href="http://redmine.open-bio.org">http://redmine.open-bio.org</a></p></span>
</body>
</html>