[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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