[Biopython-dev] [Bug 3162] New: Recording log-likelihood ratio of MEME motifs

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=3162

           Summary: Recording log-likelihood ratio of MEME motifs
           Product: Biopython
           Version: Not Applicable
          Platform: PC
        OS/Version: Mac OS
            Status: NEW
          Severity: enhancement
          Priority: P2
         Component: Main Distribution
        AssignedTo: biopython-dev at biopython.org
        ReportedBy: lpritc at scri.sari.ac.uk


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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