[Biopython] fetching chromosome IDs given the organism ID

[Fields, Christopher J]

On Nov 17, 2011, at 5:09 PM, Peter Cock wrote:

> 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.

...but not unusual (ref: BLAST output over the ages). 

>> 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

I think they are doing a lot of work behind the scenes, particularly with efetch (something to be aware of for all us folks who have modules pulling data from genbank).  

chris