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

shalabh sharma shalabh.sharma7 at gmail.com
Fri Mar 5 17:06:41 EST 2010


Thanks Bran and Chris,
           I followed the example given here :
http://www.bioperl.org/wiki/HOWTO:EUtilities_Cookbook
to retrieve raw data records from genbank.
For example i used the id : 157091572 to  get the genbank record, but the
downloaded file does not contain "isolation_source" which is there when you
look for the record online:
http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=nucleotide&dopt=GenBank&RID=T2S9N0PJ01N&log%24=nuclalign&blast_rank=1&list_uids=157091572

Thanks
Shalabh


On Fri, Mar 5, 2010 at 4:22 PM, Chris Fields <cjfields at illinois.edu> wrote:

> 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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>
>
>


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