Question: How to get list of GenBank accession Ids by a Taxonomy Id?
0
gravatar for genebow
24 months ago by
genebow150
USA/Chicago
genebow150 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 • 951 views
ADD COMMENTlink modified 24 months ago • written 24 months ago by genebow150

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 24 months ago by genebow150

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 24 months ago • written 24 months ago by genomax64k
0
gravatar for genomax
24 months ago by
genomax64k
United States
genomax64k 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 24 months ago • written 24 months ago by genomax64k
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