[Biopython] From genome to lineage with Entrez

[Peter Cock]

On Wed, Mar 23, 2011 at 5:43 PM, Fabio Gori <gori at cs.ru.nl> wrote:
> Hi all,
>
> I have downloaded all the bacterial genomes
> (ftp://ftp.ncbi.nih.gov/genomes/Bacteria/all.fna.tar.gz) and I want to compare
> their taxonomic lineages.
>
> I'm looking for a way to get their lineages with Entrez. From the files I can
> get the accession numbers and GIs, but I don't know how to get their taxonomic
> ids.
> I know that I can step from GIs to Taxids processing the file
> gi_taxid_nucl.dmp, but I'd prefer to use Entrez.
>

I think you can do it with ELink, but personally I'd use the taxid dump file,
since it sounds like you'll want to process hundreds of lineages.

Peter