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etetoolkit / ete

Python package for building, comparing, annotating, manipulating and visualising trees. It provides a comprehensive API and a collection of command line tools, including utilities to work with the NCBI taxonomy tree.
http://etetoolkit.org
GNU General Public License v3.0
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Problem with custom path to taxdump.tar.gz #623

Open aziele opened 2 years ago

aziele commented 2 years ago

Hi,

I'm trying to specify the custom path for the taxdump.tar.gz file. The file successfully downloads to the path I specify, however I get an error when ete3 tries to open the file (The file does not exist). I think the issue is with the update_db(dbfile, targz_file=None) function.

ncbi = NCBITaxa()
ncbi.update_taxonomy_database('/home/user/Desktop/taxdump.tar.gz')
dengzq1234 commented 2 years ago

I'm afraid that I am not able to reproduce the error you had, would you like to provide more information including the ete version you were using?