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

Mauricio Herrera Cuadra arareko at campus.iztacala.unam.mx
Wed Nov 1 09:30:34 EST 2006


The usual way is to send your modifications as an 'enhancement' through 
the Bugzilla system (please add your patches as attachments after 
creating the report, not into the description field):

http://bugzilla.open-bio.org/

Thanks for contributing!

Regards,
Mauricio.

Nancy Hansen wrote:
> 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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> 

-- 
MAURICIO HERRERA CUADRA
arareko at campus.iztacala.unam.mx
Laboratorio de Genética
Unidad de Morfofisiología y Función
Facultad de Estudios Superiores Iztacala, UNAM



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