Question: How to get list of GenBank accession Ids by a Taxonomy Id?
0
gravatar for genebow
3.3 years ago by
genebow160
USA/Chicago
genebow160 wrote:

In NCBI genbank, one Taxonomy Id corresponds a list of GenBank accession Ids, how do I retrieve these geneBank Ids by Python per a given Taxonomy Id? Thank you in advance.

genbank sequence • 1.5k views
ADD COMMENTlink modified 3.3 years ago • written 3.3 years ago by genebow160

Thanks! But what is the file? I tried to download that file, it is about 1GB. I wish to use Biopython to retrieve GeneBank Ids from a given Taxonomy Id automatically. Is that possible?

ADD REPLYlink written 3.3 years ago by genebow160

If you must use biopython then see this: Retrieve Genbanks From Taxid

BTW: Use ADD REPLY/ADD COMMENT when responding to existing posts to keep threads logically organized.

ADD REPLYlink modified 3.3 years ago • written 3.3 years ago by genomax85k
0
gravatar for genomax
3.3 years ago by
genomax85k
United States
genomax85k wrote:

Get this file (it is large), uncompress and parse out the ID's you need.

For example for taxID 964: awk '{FS="\t";OFS="\t"}{if ($1 == 964) print $1,$6,$8;}' gene2accession

ADD COMMENTlink modified 3.3 years ago • written 3.3 years ago by genomax85k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 778 users visited in the last hour