Manipulating Ncbi Dumped Files

Question

[Lhl]

Hi,

The NCBI taxonomy information is dumped here.

I am wondering if there is a way to get all species under a given genus (scientific name or its taxon ID)? And all genus under a certain family?

Thanks in advance.

Cheers

Lhl

[Pierre Lindenbaum]

http://whathaveyoutried.com/

[Lhl]

Thanks for reminding me. I will improve my coding skills.

Cheers

Lhl

[jhc]

Hey Lhi, this is an old example, but it should still work: http://ete.cgenomics.org/node/58 You could also combine it with the NCBI query script that I mentioned to you in one of your previous questions (Extract Tree Topology From Ncbi Taxonomy Database.

[Lhl]

Thanks for reminding me, Jhc,

I have learned Python for 2 weeks. I am a little bit struggling with using it properly.

But i will do better.

Thanks.

Lhl

[Neilfws]

What information is dumped where? Did you mean to link to something?

[Lhl]

The taxonomy information ftp://ftp.ncbi.nih.gov/pub/taxonomy/

Answer 1

[Chris Fields]

Maybe have a look at BioPerl's Bio::DB::Taxonomy? It can do something like this via the 'flatfile' plugin.