[Biopython] fetching chromosome IDs given the organism ID

[Peter Cock]

On Thu, Nov 17, 2011 at 10:51 PM, Vladislav Petyuk <petyuk at gmail.com> wrote:
> I am trying to fetch the chromosome IDs for a given genome.
> For example Cyanothece sp 51142 has 2 chromosomes and 4 plasmids
> http://www.ncbi.nlm.nih.gov/genome?term=1608%5Buid%5D#tabs-1608-2
> The piece of Biopython code that used to work for me is:
> #---------------------
> url = Entrez.esearch(db="genome", term="txid43989")
> record = Entrez.read(url)
> chromosomeIDs = record["IdList"]
> #---------------------
> Not anymore. Now it returns the organism id, which is 1608.

That's annoying of the NCBI to change things.

> Please point in the right direction how to get the chromosome ids given the
> organism id.

Try searching the nucleotide database directly, with
term txid43989[orgn] to restrict the species, and I think
there is another field to restrict to complete genomes.
Have a look at the field list with EInfo (see the Biopython
tutorial for EInfo which explains how to do this).

I would try it myself right now, but the Entrez website
seems very slow from here tonight.

Peter