Introduction

ensembl-tui provides a textual interface to localised ensembl genomic data.

Installing The Software

ensembl-tui can be installed from PyPI as follows

pip install ensembl-tui

Note

If you experience any errors during installation, we recommend using uv pip. This command provides much better error messages than the standard pip command. If you cannot resolve the installation problem, please open an issue.

Note

The first usage of ensembl-tui is slow because both cogent3 and ensembl-tui are compiling some functions. This is a one-time cost.

Installation And Usage With uv

Speaking of uv (see the uv installation guide), it provides a simplified approach to install eti as a command-line only tool as

uv tool install ensembl-tui

For the examples in this documentation, you can access the eti command as

uvx --from ensembl-tui eti

without having to activate a virtual environment.

Getting Help

To see the options for eti or one of its subcommands, just enter the expression in the terminal and press return. For example,

$ eti
Usage: eti [OPTIONS] COMMAND [ARGS]...

  Tools for obtaining and interrogating subsets of https://ensembl.org genomic
  data.

Options:
  --version  Show the version and exit.
  --help     Show this message and exit.

Commands:
  tui              Open Textual TUI.
  demo-config      exports sample config and species table to the...
  download         download data from Ensembl's ftp site
  install          create the local representations of the data
  installed        show what is installed
  species-summary  genome summary data for a species
  dump-genes       export meta-data table for genes from one species to...
  compara-summary  summary data for compara
  homologs         exports CDS sequence data in fasta format for homology...
  alignments       export multiple alignments in fasta format for named...

lists all of the subcommands. While

$ eti download
Usage: eti download [OPTIONS]

  download data from Ensembl's ftp site

Options:
  -c, --configpath PATH    Path to config file specifying databases, (only
                           species or compara at present).
  -d, --debug              Maximum verbosity, and reduces number of downloads,
                           etc...
  -sm, --species_map TEXT  Tsv file with species names, abbreviations etc..
                           [default: main]
  -v, --verbose
  --help                   Show this message and exit.

shows the options for the download command.