[Bioperl-l] Taxonomy DB problem

Chris Fields cjfields at illinois.edu
Mon Aug 30 09:36:41 EDT 2010


Regarding a fix for that script, we would have to see your modified script and the error.  However, there are modules within BioPerl to essentially do what you want, in particular, Bio::DB::Taxonomy.


On Aug 30, 2010, at 7:55 AM, J. Christopher Ellis wrote:

> Hi All,
> 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!
> Chris 
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