[Biopython-dev] [Biopython - Bug #3361] RE: Error finding lineage info for an organism

[redmine at redmine.open-bio.org]

Issue #3361 has been updated by Peter Cock.


You can download the entire taxonomy tree as a bunch of text files from the FTP site. Then assuming you know your species' taxid getting the lineage is trivial. e.g.

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

See also this old thread on mapping GI numbers to taxons, http://lists.open-bio.org/pipermail/biopython/2009-June/005304.html
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Bug #3361: RE: Error finding lineage info for an organism
https://redmine.open-bio.org/issues/3361

Author: James-Alex Matthews
Status: New
Priority: Immediate
Assignee: Biopython Dev Mailing List
Category: Main Distribution
Target version: Not Applicable
URL: 


Though I've successfully used the tool many time, the following code now generates an empty list:

handle = Entrez.efetch(db = "Taxonomy", id = tax_id, retmode = "xml")   #Query taxonomy database with taxon id
lineage_record = Entrez.read(handle)    #Read out handle
>> Problem: Record is empty

I've even run the example code from the Biopython tutorial/cookbook:
handle = Entrez.efetch(db="Taxonomy", id="158330", retmode="xml")
records = Entrez.read(handle)
>> Same problem: Record is empty

Yelp!!!!!!


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