This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Manipulating Ncbi Dumped Files

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

taxonomy
• 3,452 views • link
updated by Chris Fields Chris Fields • written by Lhl Lhl

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

Cheers

Lhl

• 0 views • link
written by Lhl 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

• 0 views • link
written by Lhl Lhl

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

• 0 views • link
written by Neilfws Neilfws

1 answer

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

• 0 views • link
written by Chris Fields Chris Fields

Log in to answer this question.

More posts like this