[Bioperl-guts-l] [Bug 2036] New: Bio::SearchIO::hmmer hmmpfam parsing misses model/domain pairs

bugzilla-daemon at newportal.open-bio.org bugzilla-daemon at newportal.open-bio.org
Thu Jun 29 01:26:15 EDT 2006


http://bugzilla.open-bio.org/show_bug.cgi?id=2036

           Summary: Bio::SearchIO::hmmer hmmpfam parsing misses model/domain
                    pairs
           Product: Bioperl
           Version: main-trunk
          Platform: All
        OS/Version: All
            Status: NEW
          Severity: normal
          Priority: P2
         Component: Bio::Search/Bio::SearchIO
        AssignedTo: bioperl-guts-l at bioperl.org
        ReportedBy: cjfields at uiuc.edu


This was reported to the mail list be Selvi Kadirvel.  When parsing hmmpfam
output with alignments set to return a certain number (-A5 parameter, for
instance), HMMER hit/HSP pairs not present in the alignments are skipped even
if they are present in the sequence and domain tables in the report.  However,
if no alignments are returned (-A0), all are parsed normally.  This is in
bioperl-live, run on WinXP with perl 5.8.817 (ActivePerl).


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