[Bioperl-guts-l] [Bug 2842] New: add mask_columns to SimpleAlign.pm

bugzilla-daemon at portal.open-bio.org bugzilla-daemon at portal.open-bio.org
Wed May 27 17:40:21 EDT 2009


http://bugzilla.open-bio.org/show_bug.cgi?id=2842

           Summary: add mask_columns to SimpleAlign.pm
           Product: BioPerl
           Version: 1.6 branch
          Platform: PC
        OS/Version: Linux
            Status: UNCONFIRMED
          Severity: enhancement
          Priority: P2
         Component: Core Components
        AssignedTo: bioperl-guts-l at bioperl.org
        ReportedBy: tristan.lefebure at gmail.com


Hi there,

I'm hoping I'm not re-inventing the wheel. So, I was looking for a method to
mask a portion of an alignment, e.g. low quality alignment regions or
duplicated regions. I did not find such a thing in Bioperl, so I added a simple
one in SimpleAlign.pm called mask_columns(). It's almost a copy paste of
slice(), except that I was not sure what the Bio::Seq::Meta sections was used
for, so I removed them.

I will attach a diff file, as well as an example.

(this is my first real patch, be kind!)

Cheers,

--Tristan


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