Installation
The easiest way to install pyseer and its dependencies is through conda:
conda install pyseer
If you need conda, download miniconda and add the necessary channels:
conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge
pyseer can also be installed through pip:
python -m pip install pyseer
If you want multithreading make sure that you are using a version 3 python interpreter:
python3 -m pip install pyseer
Prerequisites
These modules are installed through the pip command above, but if you have cloned the repository you will need to install the depdencies yourself.
We used the following versions, though higher should also work:
python 3+ (3.5.3)
numpy
(1.13.3)scipy
(1.0.0)pandas
(0.21.0)scikit-learn
(0.19.1)statsmodels
(0.8.0)pysam
(0.13)glmnet_py
(commit946b65c
)matplotlib
(2.1.0) – for scree plotsDendroPy
(4.3.0) – for phylogeny distancespybedtools
(0.7.10) – for annotating k-mersbedtools
(2.27.0) – for annotating k-mersbedops
(2.4.9) – for annotating k-mers
Test installation
Run unit tests:
pytest -v tests
Test functions and output:
cd tests/ && bash run_test.sh && cd ../
Other software
To count k-mers, you may find fsm-lite or the original seer package useful. These can easily be installed with conda, set up as above:
conda install fsm-lite
conda install seer
Packages to count unitigs and help with their interpretation are also available on bioconda:
conda install unitig-counter unitig-caller