[Biopython] fetching chromosome IDs given the organism ID

[Peter Cock]

On Thu, Nov 17, 2011 at 11:09 PM, Peter Cock <p.j.a.cock at googlemail.com> 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.
>

The NCBI have just made a public announcement by email today
(21 Nov 2011), and apologized for the lack of notice:

http://www.ncbi.nlm.nih.gov/mailman/pipermail/utilities-announce/2011-November/000083.html

Judging from the URL it was also on their news page the day you
found the problem, but I hadn't seen that then:

http://www.ncbi.nlm.nih.gov/About/news/17Nov2011.html

It looks like a sensible long term change to the genome database.

Regards,

Peter