NCBI installation updates

[ghost]

Dear MitoZ team,
Thanks for updating and maintaining the repository.
I have a question regarding installing NCBI database inside ete3 package command:

from ete3 import NCBITaxa
ncbi = NCBITaxa()
ncbi.update_taxonomy_database()

Many HPC actually refuse to give FTP right to the users.However the NCBI database are all already installed locally.
I went through the source codes and it seems mitoz actually need FTP connection for creating populating database when first executed. I see we can change the database later on but i don't see how we can feed a local NCBI database to the function "ncbi = NCBITaxa()".
I am wondering if you have any suggestions regarding solving the issue.
Thanks in advance

[linzhi2013]

Dear aremkho,

This is a very good question.

I noticed this problem during the development of MitoZ. MitoZ relies on the ETE3 pakcage, which must install the NCBI taxonomy database into ~/.etetoolkit/ directory:

.etetoolkit/
├── taxa.sqlite
└── taxa.sqlite.traverse.pkl

As you can see, the ETE3 package will transform the ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump.tar.gz into two files: taxa.sqlite and taxa.sqlite.traverse.pkl under the ~/.etetoolkit/ directory. So the taxonomy database on your HPC
will not work for ETE3 package.

My goal was to install the database into somewhere else, then I checked the ETE3's source code, and found that I cannot do it easily, because one has to modify much of the ETE3's source code.

Since I want to make it more easily to distribute MiotZ, for example, use conda to install all relevant dependencies automatically, so I gave up on this.

NB: I am currently updating MitoZ, but the version 2.2 is still testing: the algorithm is the same as verion 1.0, changes only invoked to make it more user-friendly. The testing will be done in one or two weeks, I hope.

Cheers,
Guanliang Meng

[ghost]

Dear Guanliang,
Thanks for your kind answer. The MitoZ is actually very well written and I don't have any issue running it locally. ete3 FTP issue is an issue that we need to address to ete3 team.
Looking forward to test version2.
Cheers
Arsalan

[linzhi2013]

Dear Arsalan,

Thank you very much!

Now I'm going to close the issue. Please open new issues if you have questions.

[linzhi2013]

Closed since the limitation is from ETE3 package.