[Biopython] searching homologene database

[Wibowo Arindrarto]

Hi Sheila,

You can set the 'retmode' parameter in order to specify your preferred
format. I'm not sure if NCBI provides an output format exactly like
the one you see on their site, but instead of ASN.1 you can specify a
more common
format like XML.

In your case, the call would be this (for XML, let's say):

handle = Entrez.efetch(db="homologene", id=record['IdList'], retmode="xml")

For a list of possible retmode values, you can look them up here:
http://www.ncbi.nlm.nih.gov/books/NBK25499/#chapter4.EFetch (see the
explanation about 'retmode').

If you want to format the output further, you can use modules like the
built-in elementtree or 3rd party modules like lxml to extract the tag
values and feed them to your script / program.

Hope that helps,
Bow


On Mon, Jul 2, 2012 at 2:21 PM, Sheila the angel <from.d.putto at gmail.com> wrote:
> To search tp53 homolog in homologene database -
>
> handle = Entrez.esearch(db="homologene", term="tp53[gene name] AND Homo
> sapiens[orgn]")
> record = Entrez.read(handle)
> handle = Entrez.efetch(db="homologene", id=record['IdList'])
> record = handle.read()
> print record
>
> I think record is asn.1 format !! how can I read or convert it in the genes
> protein table (as we see in the web result)
> http://www.ncbi.nlm.nih.gov/homologene/460
>
> Thanks
>
> --
> Sheila
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