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

Chris Fields cjfields at uiuc.edu
Wed Nov 1 09:39:38 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

You can check them into Bugzilla as a patch to a bug:


There is a HOWTO for patch submission here:


You could also send them to Brian or me.  Bugzilla is probably your best bet
as anyone with a developer account can check in the fix.

You should also write up some tests for your code changes.  You can use the
test file mentioned above (t/scf.t) as a start.


Christopher Fields
Postdoctoral Researcher - Switzer Lab
Dept. of Biochemistry
University of Illinois Urbana-Champaign

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