[Biopython-dev] [Biopython (old issues only) - Bug #3162] (Resolved) Recording log-likelihood ratio of MEME motifs

[redmine at redmine.open-bio.org]

Issue #3162 has been updated by Peter Cock.

Description updated
Status changed from New to Resolved
% Done changed from 0 to 100

Reading the code in the current MEME parser, it looks to record the llr field:

https://github.com/biopython/biopython/blob/master/Bio/motifs/meme.py

Closing this old issue.

----------------------------------------
Bug #3162: Recording log-likelihood ratio of MEME motifs
https://redmine.open-bio.org/issues/3162#change-15398

* Author: Leighton Pritchard
* Status: Resolved
* Priority: Normal
* Assignee: Biopython Dev Mailing List
* Category: Main Distribution
* Target version: Not Applicable
* URL: 
----------------------------------------
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.

********************************************************************************
MOTIF  1	width =   11   sites = 331   llr = 4357   E-value = 3.1e-554
********************************************************************************

has reported E-value after parsing of zero:


In [24]: data[0].name
Out[24]: 'Motif 1'

In [25]: data[0].length
Out[25]: 11

In [26]: data[0].num_occurrences
Out[26]: 331

In [27]: data[0].evalue
Out[27]: 0.0

As does the next motif:

********************************************************************************
MOTIF  2	width =   15   sites = 259   llr = 4456   E-value = 3.1e-743
********************************************************************************

This can easily be handled in __create_motif with the addition at line 265 of 

motif.llr = int(ls[9])

but it may be more elegantly handled by a method in MEMEMotif.



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