[Bioperl-guts-l] [Bug 2098] New: Bug in Bio::Matrix::PSM SiteMatrixI

bugzilla-daemon at newportal.open-bio.org bugzilla-daemon at newportal.open-bio.org
Mon Sep 18 16:18:07 EDT 2006


           Summary: Bug in Bio::Matrix::PSM SiteMatrixI
           Product: Bioperl
           Version: 1.5 branch
          Platform: All
        OS/Version: Linux
            Status: NEW
          Severity: normal
          Priority: P2
         Component: Core Components
        AssignedTo: bioperl-guts-l at bioperl.org
        ReportedBy: shenorr at gmail.com

>From SiteMatrixI description: "When creating the object the constructor will
check for positions that equal 0. If such is found it will increase the count
for all
positions by one and recalculate the frequency. Potential bug- if you
are using frequencies and one of the positions is 0 it will change
significantly. However, you should never have frequency that equals

This becomes a problem when used in conjunction with
Bio::Matrix::PSM::IO(-format=>'meme', -file=>$file); 
as meme often returns matrices with positions equal to 0.

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