Documentation¶
Overview of Cortexpy¶
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Cortexpy is a Python package for sequence analysis using linked and colored De Bruijn graphs such as the ones created by Cortex and Mccortex. This project aims to mirror many of the features contained in CortexJDK.
Cortexpy also comes with a command-line tool for basic inspection and manipulation of Cortex graphs with and without links.
Audience¶
The audience of cortexpy is researchers working with colored De Bruijn graphs and link information in Cortex and Mccortex format.
Free software¶
Cortexpy is free software; you can redistribute it and/or modify it under the terms of the Apache License version 2.0. Contributions are welcome. Please join us on GitHub.
Installation¶
pip install cortexpy
Documentation¶
For more information, please see cortexpy documentation.
Bugs¶
Please raise a github issue for any bugs.
Development¶
Install conda.
Download development and testing tools:
conda env create -f environment.yml -n my-dev-environment
Activate development environment:
conda activate my-dev-environment
All remaining commands in the development section need to be run in an activated conda dev environment.
Tests¶
make test
Building the docs¶
The documentation is automatically built by read-the-docs on push to master. To build the documentation manually:
# install sphinx dependencies
pip install docs/requirements.txt
make docs
Update the dev environment¶
This section is experimental because it does not work on travis-CI yet.
# Create a new env from the high-level requirements file
conda env create -f environment.yml -n another-dev-env
# activate the new environment
conda activate another-dev-env
# save new env to environment.lock.yml
make lock
Usage examples¶
Python API¶
Check if a cortex graph contains a kmer¶
We can use the After you have installed cortexpy, you can start using it to access cortex files from python:
from cortexpy.graph.parser.random_access import RandomAccess
# make sure to open the cortex graph in binary mode
with open('my_graph.ctx', 'rb') as fh:
ra = RandomAccess(fh)
# let's see if our favorite kmer is in the graph
if 'AAA' in ra:
print('AAA exists in my_graph.ctx!')
The cortexpy API reference¶
Random access of cortexpy graphs¶
This module contains classes for inspecting cortex graphs with random access to their kmers.
-
class
cortexpy.graph.parser.random_access.RandomAccess(graph_handle, kmer_cache_size=None)[source]¶ Provide fast k-mer access to Cortex graph in log(n) time (n = number of kmers in graph)
-
__getitem__(lexlo_string)[source]¶ Return kmer associated with kmer string
No check is performed to make sure that the input string is a lexicographically-lowest kmer string. Use
get_kmer_for_string()in order to convert a kmer string to its lexlo form before retrieving it from the cortex object.
-
Utility functions¶
This module contains utility functions that are used inside cortexpy. These functions may also be useful outside of cortexpy.
License¶
Cortexpy is distributed under the Apache Lincense version 2.0:
Apache License
Version 2.0, January 2004
http://www.apache.org/licenses/
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