[Bioperl-guts-l] [Bug 2575] New: Easy request - a frac_identical_total column in HSPTableWriter.pm?

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

http://bugzilla.open-bio.org/show_bug.cgi?id=2575

           Summary: Easy request - a frac_identical_total column in
                    HSPTableWriter.pm?
           Product: BioPerl
           Version: 1.5 branch
          Platform: Macintosh
        OS/Version: All
            Status: NEW
          Severity: enhancement
          Priority: P2
         Component: Bio::Search/Bio::SearchIO
        AssignedTo: bioperl-guts-l at bioperl.org
        ReportedBy: jayoung at fhcrc.org
                CC: jayoung at fhcrc.org


Hi there,

I have a request that should be really easy to do.

Is it possible to add another possible column output to HSPTableWriter.pm?  The
column I'm interested in would be frac_identical_total (by analogy to the two
that are already available, frac_identical_query and frac_identical_hit)? I
guess it would also make sense to add frac_conserved_total.

Adding those two columns would make it easier to make the percent identities
I'm getting from parsed blast via Writer/write_result  match up with percent
identities that blast gives, or those that I get if I use bioperl to examine
hsp  objects.

I almost know how to do this one myself - I just don't understand whether the
column numbers have any siginificance.

thanks!

Janet

------------------------------------------------------------------- 

Dr. Janet Young (Trask lab)

Fred Hutchinson Cancer Research Center
1100 Fairview Avenue N., C3-168, 
P.O. Box 19024, Seattle, WA 98109-1024, USA.

tel: (206) 667 1471 fax: (206) 667 6524
email: jayoung at fhcrc.org

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