[Bioperl-l] Bio::SeqIO::scf header/comments handling

Nancy Hansen nhansen at nhgri.nih.gov
Wed Nov 1 08:43:32 EST 2006

On Tue, 31 Oct 2006, Brian Osborne wrote:

> It looks like a good place to start would be the get_header() and
> _get_header methods in Bio::SeqIO::scf. If you read t/scf.t you can see that
> the author, at some point, wanted get_header to return meaningful
> information but stepping through the test shows it returning a lot of UNDEF.
> Now I don't know if this is due to the method or the source SCF file, but
> you might be able to get these methods to work yourself.
> But to answer your questions, yes, it certainly sounds reasonable that these
> values would be extracted by Bio::SeqIO::scf.

Sounds great!  So, if I make these changes, is there someone I should run
them by before checking them into CVS?  Is Chad Matsalla still involved in
bioperl?  I've never contributed to the project, so I'm not sure how
things work...


Nancy F. Hansen, PhD	nhansen at nhgri.nih.gov
Bioinformatics Group
NIH Intramural Sequencing Center (NISC)
5625 Fishers Lane
Rockville, MD 20852
Phone: (301) 435-1560	Fax: (301) 435-6170

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