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 (commit 946b65c)
  • matplotlib (2.1.0) – for scree plots
  • DendroPy (4.3.0) – for phylogeny distances
  • pybedtools (0.7.10) – for annotating k-mers
  • bedtools (2.27.0) – for annotating k-mers
  • bedops (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

A package to count unitigs and help with their interpretation is also available on bioconda:

conda install unitig-counter