[Bioperl-guts-l] [Bug 1975] New: request to add "-validate" option to Bio::Species->new()

bugzilla-daemon at newportal.open-bio.org bugzilla-daemon at newportal.open-bio.org
Tue Mar 28 20:01:48 EST 2006


http://bugzilla.open-bio.org/show_bug.cgi?id=1975

           Summary: request to add "-validate" option to Bio::Species->new()
           Product: Bioperl
           Version: unspecified
          Platform: All
        OS/Version: Windows XP
            Status: NEW
          Keywords: Bioperl
          Severity: enhancement
          Priority: P2
         Component: Core Components
        AssignedTo: bioperl-guts-l at bioperl.org
        ReportedBy: dwaner at scitegic.com


I would like to request the addition of a "-species_validate" option to
Bio::Species->new().

The problem is that Bio::Species->new() calls classification(),
which calls validate_species_name(), which then throws an exception on
some species names.  As far as I can see, there is no way to turn off
this (over-aggressive) validation in the Species constructor.

I guess that instead of this:

    $species = Bio::Species->new(-classification => \@classificationArray);

I could do this:

    $species = Bio::Species->new();
    $species->classification(\@classificationArray, 'no validation');

but it would make a nicer interface to have a validation option in the
Species constructor.


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