[Bioperl-guts-l] [Bug 2689] New: LocatableSeq::subseq with mapping and frameshift functionality

bugzilla-daemon at portal.open-bio.org bugzilla-daemon at portal.open-bio.org
Thu Nov 27 01:18:00 EST 2008


           Summary: LocatableSeq::subseq with mapping and frameshift
           Product: BioPerl
           Version: main-trunk
          Platform: PC
        OS/Version: All
            Status: NEW
          Severity: enhancement
          Priority: P2
         Component: Core Components
        AssignedTo: bioperl-guts-l at bioperl.org
        ReportedBy: maj at fortinbras.us

I am uploading some (pretty hairy, C-like) code for a subseq() that
(apparently..) correctly tracks frameshifts in [1 => 3] mappings. It carries
gaps along in their original positions, but doesn't count them in the
coordinate calculations. A bonus is a complete generalization of the mapping
principle, so that all combinations of [ $a => $b ] can be handled (though the
.t right now tests only [1 => 3] and [3 => 1]). I believe there could be cool
specialized uses for this (for example, mapping constant-length VNTRs to single
letter names, or for analysis of sequences on Planet Goob, where codons of 5
nts encode pairs of amino acids).

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