ncbi-taxonomist

Version: 0.5.0+15329cb / https://pypi.org/project/ncbi-taxonomist/0.5.0.HEAD133

Docs updated: 2020-01-28

Licence: ncbi-taxonomist is licensed under the GNU General Public License v3 (GPLv3) or later.

Synopsis

$ pip install ncbi-taxonomist --user
$ ncbi-taxonomist collect -n human -r

ncbi-taxonomist handles and manages phylogenetic data from NCBI Entrez [Entrez2016]. It can:

  • map between taxids, names, and accessions to related taxonomic information
  • resolve lineages
  • store obtained taxa and their data locally in a SQLite databases

ongoing:

  • group taxa into user defined groups (locally)
  • collect metadata for specific taxonomies
  • import the whole predownloaded NCBI taxonomy database

ncbi-taxonomist has several simple operations, e.g. map or import, which can be chained together using pipes to from more complex tasks. For example, to populate a local database (on the machine running ncbi-taxonomist), collect will fetch data remotely from Entrez and print it to STDOUT. import reads the STDIN and populates the local database (see below).

ncbi-taxonomist collect -r -n human | ncbi-taxonomist import -db taxo.db

Install

pip install ncbi-taxonomist --user

For more details, see Installation.

Source code

git clone https://gitlab.com/jpb/ncbi-taxonomist.git

Dependencies

ncbi-taxonomist has two dependencies:

These are libraries maintained by myself and rely solely on the Python standard library. Therefore, ncbi-taxonomist is less prone to suffer [dependency hell](https://en.wikipedia.org/wiki/Dependency_hell).

Local databases

To use local databases, [SQLite](https://sqlite.org/index.html) (>= 3.29.0) has to be installed. ncbi-taxonomist works without local databases, but needs to fetch all data remotely.

Contact

To report bugs and/or errors, please open an issue at https://gitlab.com/ncbi-taxonomist or contact me at: jan.buchmann@sydney.edu.au Of course, feel free to fork the code, improve it, and/or open a pull request.