<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 #3162 has been updated by Peter Cock.
<ul>
<li><strong>Description</strong> updated (<a title="View differences" href="https://redmine.open-bio.org/journals/diff/15398?detail_id=1741">diff</a>)</li>
<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>Reading the code in the current MEME parser, it looks to record the llr field:</p>
<p><a class="external" href="https://github.com/biopython/biopython/blob/master/Bio/motifs/meme.py">https://github.com/biopython/biopython/blob/master/Bio/motifs/meme.py</a></p>
<p>Closing this old issue.</p>
<hr />
<h1><a href="https://redmine.open-bio.org/issues/3162#change-15398">Bug #3162: Recording log-likelihood ratio of MEME motifs</a></h1>
<ul><li>Author: Leighton Pritchard</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>The MEMEMotif object in Bio.Motif.MEME does not currently have an attribute for recording log likelihood ratio. This is perhaps a more reliable metric for ranking motifs after parsing, since the E-value may be truncated to zero for very small E-values, e.g.</p>
*<strong><b></strong>*</b>**<strong>**</strong>******************************************************************<br />MOTIF 1 width = 11 sites = 331 llr = 4357 E-value = 3.1e-554
<hr />
<p>has reported E-value after parsing of zero:</p>
<p>In [24]: data<sup><a href="#fn0">0</a></sup>.name<br />Out<sup><a href="#fn24">24</a></sup>: 'Motif 1'</p>
<p>In [25]: data<sup><a href="#fn0">0</a></sup>.length<br />Out<sup><a href="#fn25">25</a></sup>: 11</p>
<p>In [26]: data<sup><a href="#fn0">0</a></sup>.num_occurrences<br />Out<sup><a href="#fn26">26</a></sup>: 331</p>
<p>In [27]: data<sup><a href="#fn0">0</a></sup>.evalue<br />Out<sup><a href="#fn27">27</a></sup>: 0.0</p>
<p>As does the next motif:</p>
*<strong><b></strong>*</b>**<strong>**</strong>******************************************************************<br />MOTIF 2 width = 15 sites = 259 llr = 4456 E-value = 3.1e-743
<hr />
<p>This can easily be handled in __create_motif with the addition at line 265 of</p>
<p>motif.llr = int(ls<sup><a href="#fn9">9</a></sup>)</p>
<p>but it may be more elegantly handled by a method in MEMEMotif.</p>
<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>