[Biopython] Lineage from GenBank files Question

Ara Kooser akooser at unm.edu
Fri Oct 22 18:22:59 UTC 2010


Hello all,

   I've been working on a code to parse information from BLAST .xml  
files and GenBank files. I am interested in adding the taxonomy  
lineage information to the code.

   I was looking for the tag in the on-line documentation here: http://biopython.org/DIST/docs/api/Bio.GenBank.Scanner-module.html

So in the code I am working on I have this line
name_by_source_index =  
index_genbank_features(gb_record,"source","organism")

which grabs the species Yersinia enterocolitica but not the whole  
lineage.

I was wondering how to I grab the rest of the information like this:
1385              Bacteria; Proteobacteria; Gammaproteobacteria;  
Enterobacteriales;
1386              Enterobacteriaceae; Yersinia.
Thank you!

I do have a second question. Once I have a chunk of code running and  
made pretty what is the best way to submit it so it can be posted up  
in the Cookbook section.

Ara





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