Installing and using tag

The easiest way to install tag is with the pip command. By default, pip installs the most recent stable release from the Python Package Index (PyPI).

pip install tag

To install the latest unreleased code, install directly from the development repository at GitHub.

pip install git+


We recommend installing tag and its prerequisites in a virtual environment.

tag is implemented in pure Python and requires no compilation. It has only a single runtime dependency (the intervaltree library) which is also pure Python.

Using tag interactively

If you want to analyze or explore your data interactively, fire up the Python interpreter by invoking the python command in your terminal. Please see the API documentation for a description of the data structures and objects available to you.

>>> import tag
>>> reader = tag.reader.GFF3Reader(infilename='/data/genomes/mybug.gff3.gz')
>>> for entry in, type='intron'):
...     if len(entry) > 100000:
...         print(entry.slug)
intron@scaffold3[37992, 149255]
intron@scaffold55[288477, 389001]
intron@scaffold192[1057, 196433]

Using the tag command-line interface

The tag package has a command-line interface for common processing workflows. Execute tag -h to see a list of available commands and tag <cmd> -h for instructions on running a particular command.