[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...

	Thanks!
	--Nancy

*************************************
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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