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

Chris Fields cjfields at illinois.edu
Fri Mar 5 16:22:47 EST 2010


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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