[Bioperl-l] Can't parse bacterial strain from EMBL OS or RC lines

[Mark A. Miller]

Thanks for your responses, Jason and Brian.

Brian, you suggestion works great.  I had really hoped that by parsing
the OS line as well, I could be sure I wasn't missing any sequences
from my organisms.  Well, I gave up on that and just obtained the NCBI
taxonomy values.  I find it pretty easy to work with them in bioperl. 
Unfortunately, walking through all of Trembl takes a while, and I'm
getting this error:

  Can't call method "ncbi_taxid" on an undefined value at ./ga2.pl line
55, <GEN0> line 3253682.

When I try to extract annotations, etc., from entries like:

  DHE4_UNKP

with:

  my $species_object = $seq->species;
  my $taxid_string = $species_object->ncbi_taxid;

I guess I have to write an error handler for incomplete taxonomy
values.

Bye for now,
Mark


--- Brian Osborne <osborne1 at optonline.net> wrote:

> Mark,
> 
> The RC line is part of the description of a reference, I'm guessing
> 'RC'
> stands for Reference Comment. In order to get the attributes of a
> reference
> you'll first do something like:
> 
> my $anno_collection = $seq->annotation;
> my @references = $anno_collection->get_Annotations('reference');
> 
> To get the comment field for a specific reference you can do:
> 
> $references[0]->comment;
> 
> See the Feature-Annotation HOWTO for more information on Annotations,
> the
> Reference object is a kind of Annotation object.
> 
> Brian O.
> 
> 
> On 5/3/06 3:34 PM, "Mark A. Miller" <mamillerpa at yahoo.com> wrote:
> 
> > Yeah.  Do you have any experience with that?
> > 
> > Mark
> > 
> > --- Brian Osborne <osborne1 at optonline.net> wrote:
> > 
> >> Mark,
> >> 
> >> So you're trying to get the information in the RC line from a
> >> Swissprot
> >> format file?
> >> 
> >> Brian O.
> > 
> > 
> > ---   ---   ---   ---   ---   ---   ---   ---
> > 
> > Mark A. Miller
> > 
> > __________________________________________________
> > Do You Yahoo!?
> > Tired of spam?  Yahoo! Mail has the best spam protection around
> > http://mail.yahoo.com 
> 
> 
> 


---   ---   ---   ---   ---   ---   ---   ---

Mark A. Miller

__________________________________________________
Do You Yahoo!?
Tired of spam?  Yahoo! Mail has the best spam protection around 
http://mail.yahoo.com