Introduction¶
Installation¶
With pip¶
ngs_toolkit
is available for Python 3 only. Is is tested in Python 3.6 and 3.7.
To install, simply do:
pip install ngs-toolkit
you might need to add a --user
flag if not root or running in a virtual environment.
This will install all the Python dependencies needed too. See here a list of all Python dependencies used.
To install the latest development version:
pip install git+https://github.com/afrendeiro/toolkit.git#egg=ngs-toolkit
Using a conda environment¶
Get the latest Python 3 installation of miniconda from the conda website and follow the instructions for installation and activation of the environment.
Setup the bioconda channel:
conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge
Install non-Python dependencies:
conda install -y bedtools==2.20.1
conda install -y ucsc-twobittofa
conda install -y bioconductor-deseq2
conda install -y bioconductor-cqn
And then install the ngs-toolkit
library with pip (available only through PyPi).
pip install ngs-toolkit
Non-Python requirements¶
ngs_toolkit
makes use of some non-Python dependencies.
The following are highly recommended only for some data or analysis types:
- bedtools: required for some ATAC/ChIP-seq functions. It is underlying the Python interface library to bedtools (pybedtools) which can be installed without bedtools.
- R and some bioconductor libraries (optional):
- Kent tools (optional): the ‘twoBitToFa’ binary from UCSC’s Kent bioinformatics toolkit is used to convert between the 2bit and FASTA formats.
Note
bedtools
version should be below 2.24.0 (2.20.1 is used for testing)
Testing¶
To make sure everything is correctly configured, the user is encouraged to test the library prior to use.
In order to do this, install testing requirements and simply run pytest
:
pip install ngs-toolkit[testing]
pytest --pyargs ngs_toolkit
Pytest will output summary results (see for example) and further outputs can be seen in ${TMPDIR}/pytest-of-${USER}/
or /tmp/pytest-of-${USER}/
if $TMPDIR is not defined.
API usage¶
To use a particular class or function from the toolkit, import it like this from within Python/iPython:
from ngs_toolkit import ATACSeqAnalysis
from ngs_toolkit.utils import log_pvalues