ncbi-taxonomist Documentation

1.2.1+8580b9b :: 2020-11-15

Synopsis

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

ncbi-taxonomist handles and manages phylogenetic data available in NCBI’s Entrez databases .

Functions

• Collect

  collect taxa from the Entrez Taxonomy database

• Map

  map taxids, names, and accessions to related taxonomic information

• Resolve:

  resolve lineages for taxa (taxid and names) and accessions, e.g. sequence or protein

• Import:

  store obtained results locally in a SQLite databases

• Subtree:

  extract a whole lineage, or a specific rank, or a range of ranks, from a taxid or name

• Group:

  create user defined groups for taxa, for example:

• create a group for all taxa specific for a project
• group taxa without a phylogenetic relationship, e.g. group all taxa representing trees inot a group “trees”

The ncbi-taxonomist commands, e.g. map or import, can be chained together using pipes to from more complex tasks. For example, to populate a local database collect will fetch data remotely from Entrez and print it to STDOUT where import will read STDIN and populates the local database (see below).

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

Requirements and Dependencies

Requirements

• Required: Python >= 3.8

  $: python --version

• Optional: To use local databases, SQLite (>= 3.24.0) has to be installed. ncbi-taxonomist works without local databases, but needs to fetch all data remotely for each query.

  $: sqlite3 --version

Dependencies

ncbi-taxonomist has one dependency:

• entrezpy: to handle remote requests to NCBI’s Entrez databases
  • https://gitlab.com/ncbipy/entrezpy.git
  • https://pypi.org/project/entrezpy/
  • https://doi.org/10.1093/bioinformatics/btz385

This is a library maintained by myself and relies solely on the Python standard library. Therefore, ncbi-taxonomist is less prone to suffer dependency hell.

Contact

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

Indices and tables

• Index
• Module Index
• Search Page