[Bioperl-l] SeqIO::genbank

[Jason Stajich]

I checked in the change to handle featureless files, I won't have time to
look at the rest of the problems until tomorrow so send a note if you get
started on it, otherwise I'll take a look at it in the morning.

-Jason

On Thu, 13 Jul 2000, Ewan Birney wrote:

> 
> 
> 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
> > 
> 

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/