Installing and using **tag** ============================ The easiest way to install **tag** is with the :code:`pip` command. By default, :code:`pip` installs the most recent stable release from the Python Package Index (PyPI). .. code:: pip install tag To install the latest unreleased code, install directly from the development repository at GitHub. .. code:: pip install git+https://github.com/standage/tag.git .. note:: 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 :code:`python` command in your terminal. Please see the :doc:`API documentation ` for a description of the data structures and objects available to you. .. code:: python >>> import tag >>> reader = tag.reader.GFF3Reader(infilename='/data/genomes/mybug.gff3.gz') >>> for entry in tag.select.features(reader, 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 :code:`tag -h` to see a list of available commands and :code:`tag -h` for instructions on running a particular command.