Refgenie from within Python

Third-party python tools can rely on our Python object for access to refgenie assets. refgenie CLI relies on Refgenie object that provides a Python API for accessing and managing genome assets.

Installing

No additional installation is required if you have refgenie installed.

Quick start

Create a RefGenConf object, which is the package’s main data type. You just need to give it a refgenie genome configuration file (in YAML format). You can create a template using refgenie init.

As a general rule, the CLI functions are available from within Python under the same names, e.g. refgenie list ... is available as Refgenie.list() method.

from refgenie import Refgenie
r = Refgenie()

Now, you can interact with it:

print(r)

Use this to show all available remote assets:

r.listr()

In a tool, you’re probably most interested in using refgenie to locate reference genome assets, for which you want to use the get_asset function. For example:

# identify genome (perhaps provided by user)
genome = "hg38"

# get the local path to bowtie2 indexes:
bt2idx = r.seek(genome, "bowtie2_index")

# run bowtie2...

This enables you to write python software that will work on any computing environment without having to worry about passing around brittle environment-specific file paths. See this tutorial for more comprehensive example of how to work with refgenconf as a tool developer.