[Bioperl-l] SeqIO::genbank

[Ewan Birney]

On Wed, 12 Jul 2000, Jason Stajich wrote:

> In addition to Chris' email
> I also noticed that if you have a gb sequence file that does not have any
> features it will not read the sequence.  I'm not sure if the COMMENT and
> FEATURE tag are required by thethe Genbank spec but this doesn't seem
> to be expected behavior.  

Yup. GenBank parser is not in good shape.

I suspect that some of what chris is seeing is things not be transfered
from the branch to the main trunk.

Jason - if you have the time, could you check in this fix and see what's
up between the branches. If you don't do it I will try to get around to
this tomorrow.


> 
> 
> Added the following - can check it in if you agree.
> RCS file: /home/repository/bioperl/bioperl-live/Bio/SeqIO/genbank.pm,v
> retrieving revision 1.12
> diff -r1.12 genbank.pm
> 272c272
> <           
> ---
> >           goto ORIGIN if( /^ORIGIN/ );
> 283a284
> > 
> 302c303
> < 
> ---
> >   ORIGIN:
> 309d309
> < 
> 
> Jason Stajich
> Center for Human Genetics
> Duke University Medical Center
> jason@chg.mc.duke.edu
> (919)684-1806 (office)
> (919)684-2275 (fax)
> http://wwwchg.mc.duke.edu/
> http://galton.mc.duke.edu/~jason/
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@bioperl.org
> http://bioperl.org/mailman/listinfo/bioperl-l
>