[Bioperl-l] Taxonomy DB problem
J. Christopher Ellis
J.Christopher.Ellis at duke.edu
Mon Aug 30 08:55:04 EDT 2010
I am trying to extract the entire taxonomy of an organism including the
classifications. Some thing like...
Phylum:Proteobacteria, Class:Gammaproteobacteria, Order:Enterobacteriales, Family:Enterobacteriaceae, Genus:Escherichia
I am not worried about format just that I get the information and the associated level of hierarchy. The script found at http://bioperl.org/wiki/Species_names_from_accession_numbers seemed like a good starting point so I copied it and tried run it but got an error.
My first question is "Is there a known fix for this?" and my second question is how do I get the full hierarchical information (as seen above) with the taxonomy db?
Thanks for all your help in advance!
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