Edit the NCBI Taxonomy with ete3 toolkit ?

Question

[Pierre]

Hi everyone,

I want to use the whole NCBI taxonomy ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/

I found an excellent library on python called http://etetoolkit.org/

Ete3 can load NCBI taxonomy with this command:

ncbiTaxa = NCBITaxa(taxdump_file=path.abspath(localTaxdumpArchive))

Is it possible to edit the ncbiTaxa object and then extract the whole new edited ncbi taxonomy ? I would like to add nodes of custom species this way.

[Joe]

Take a look at the object model of the tree that ETE produces. It simply parses the NCBI taxonomy in to its standard tree representation, so you should in principle be able to do anything and everything to it that you'd do with a 'regular' tree, such as add nodes, prune leaves etc.