[BioPython] Entrez.read

[Iddo Friedberg]

The example *is* limiting your search to the subfamily Cypripedioideae. To
limit to a species you can write along the same lines:

handle = Entrez.esearch(db="nucleotide",term="Escherichia coli[Orgn]")

(With apologies to Brad Chapman. I'm a microbe guy, not a plant guy).

./I


On Thu, Sep 11, 2008 at 9:36 AM, Bruno Santos <bsantos at biocant.pt> wrote:

> Ok this seem to be a completely stupid error, I was playing a little bit
> with the pydev console in eclipse and the Entrez.read raise an exception,
> but if I place this instruction in a script it works fine. No idea why this
> is happening but in fact this method don't appear listed in eclipse auto
> complete.
> Thank you all for your answers.
> No I have another question it is possible to limit the esearch not only to
> database but also to species? Because I only need the ids associated with
> droshophila melanogaster, and have to fetch all the sequences and only than
> check if they belong to this species seems a waste of bandwidth.
>
> Thanks in advance,
> Bruno Santos
>
> -----Mensagem original-----
> De: biopython-bounces at lists.open-bio.org
> [mailto:biopython-bounces at lists.open-bio.org] Em nome de Frank Kauff
> Enviada: quinta-feira, 11 de Setembro de 2008 16:27
> Para: biopython at biopython.org
> Assunto: Re: [BioPython] Entrez.read
>
> Hi Bruno,
>
> from what I see your code should work. Without knowing what version of
> Biopython you are running and what error message you get, it's a bit
> difficult to tackle he problem. I'd guess your biopython is outdated.
>
> Frank
>
> Bruno Santos wrote:
> > No answers?
> > -----Mensagem original-----
> > De: biopython-bounces at lists.open-bio.org
> > [mailto:biopython-bounces at lists.open-bio.org] Em nome de Bruno Santos
> > Enviada: quarta-feira, 10 de Setembro de 2008 22:43
> > Para: biopython at biopython.org
> > Assunto: [BioPython] Entrez.read
> >
> > Hi everyone,
> > I am trying to use Entrez.esearch to find the ids I can then use to fetch
> > the genbank records.
> > For that purpose I went looking for biopython tutorial for more
> information
> > in how to do this, and I get the following information:
> >
> >
> >
> >>>> handle = Entrez.esearch(db="nucleotide",term="Cypripedioideae[Orgn]
> AND
> >>>>
> > matK[Gene]")
> >
> >>>> record = Entrez.read(handle)
> >>>> record["Count"]
> >>>>
> > '25'
> >
> >>>> record["IdList"]
> >>>>
> > ['186972394', '186972384', '186972382', '186972378', ..., '61585484']
> >
> > Unfortunately when I try to follow this instructions I found out that I
> > don't have any Entrez.read
> >  to parse the output of Entrez.esearch. Is this a new option in the last
> > release?
> > Thanks in advance,
> > Bruno Santos
> >
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> >
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-- 

Iddo Friedberg, Ph.D.
CALIT2, mail code 0440
University of California, San Diego
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http://iddo-friedberg.org