[BioPython] Entrez.read

[Bruno Santos]

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 I'd guess your biopython is outdated.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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