[Bioperl-l] Accession Nuber to Genbank Record (Isolation Source)

[Chris Fields]

Regardless on what you try, it will only limit records returned (e.g.
you will still get full records, unless you take steps to limit those
somehow, by adding sequence start/stop, etc).  

Anyway, this worked to retrieve those with that tag:
"src isolation source"[Properties]

That get a lot of hits.

If you are only interested in that one line you could just parse it out
w/o resorting to bioperl (beleiev it or not, it's not always the best
answer). 

chris

On Fri, 2010-03-05 at 15:43 -0500, Brian Osborne wrote:
> Shalabh,
> 
> I see. I think you could use EUtils then. Take a look at these:
> 
> http://www.bioperl.org/wiki/HOWTO:EUtilities_Cookbook
> 
> http://www.bioperl.org/wiki/HOWTO:EUtilities_Web_Service
> 
> I'm not an expert on these, and I do not know if one can ask for just a tag value ("isolation_source"). Getting a tag value from the downloaded Genbank entry is not difficult though, that Feature-Annotation HOWTO shows you how.
> 
> Brian O.
> 
> 

> On Mar 5, 2010, at 3:29 PM, shalabh sharma wrote:
> 
> > HI Brian,
> >           Thanks for your quick reply.
> > I was reading the document and it think it talks about parsing a GenBank
> > record. What i exactly want is to submit a batch of accession numbers and
> > get "isolation_source" directly without downloading all the Genbank files.
> > I am still reading the document may be i missed something.
> > 
> > Thanks a lot
> > shalabh
> > 
> > 
> > On Fri, Mar 5, 2010 at 3:13 PM, Brian Osborne <bosborne11 at verizon.net>wrote:
> > 
> >> Shalabh,
> >> 
> >> You can start by reading about how Bioperl processes Genbank files and
> >> their annotations:
> >> 
> >> http://www.bioperl.org/wiki/HOWTO:Feature-Annotation
> >> 
> >> 
> >> 
> >> Brian O.
> >> 
> >> On Mar 5, 2010, at 3:06 PM, shalabh sharma wrote:
> >> 
> >>> Hi All,
> >>>       I have a set of accession numbers. Is it possible to get
> >>> "isolation_source" from the GenBank records for all the Accession
> >> numbers.
> >>> 
> >>> I would really appreciate if anyone can help me out.
> >>> 
> >>> Thanks
> >>> Shalabh
> >>> _______________________________________________
> >>> Bioperl-l mailing list
> >>> Bioperl-l at lists.open-bio.org
> >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >> 
> >> 
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> 
> 
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