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        "author": "Marco Galardini and John Lees",
        "author_email": "marco@ebi.ac.uk",
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            "Development Status :: 4 - Beta",
            "Intended Audience :: Science/Research",
            "License :: OSI Approved :: Apache Software License",
            "Programming Language :: Python :: 2.7",
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            "Programming Language :: Python :: 3.5",
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        "description": "pyseer\n======\n\n[SEER](https://github.com/johnlees/seer), reimplemented in python by\n[Marco Galardini](https://github.com/mgalardini) and [John Lees](https://github.com/johnlees)\n\n    pyseer --phenotypes phenotypes.tsv --kmers kmers.gz --distances structure.tsv --min-af 0.01 --max-af 0.99 --cpu 15 --filter-pvalue 1E-8\n\n[![Build Status](https://travis-ci.org/mgalardini/pyseer.svg?branch=master)](https://travis-ci.org/mgalardini/pyseer)\n[![Documentation Status](https://readthedocs.org/projects/pyseer/badge/?version=master)](http://pyseer.readthedocs.io/)\n[![PyPI version](https://badge.fury.io/py/pyseer.svg)](https://pypi.org/project/pyseer/)\n[![Anaconda package](https://anaconda.org/bioconda/pyseer/badges/version.svg)](https://anaconda.org/bioconda/pyseer)\n\nMotivation\n----------\n\nKmers-based GWAS analysis is particularly well suited for bacterial samples,\ngiven their high genetic variability. This approach has been\nimplemented by [Lees, Vehkala et al.](https://www.nature.com/articles/ncomms12797),\nin the form of the [SEER](https://github.com/johnlees/seer) software.\n\nThe reimplementation presented here should be consistent with the\ncurrent version of the C++ seer (though we do not guarantee this for all\npossible cases).\n\nIn this version, as well as all the original features, many new features (input types,\nassociation models and output parsing) have been implemented. See the\n[documentation](http://pyseer.readthedocs.io/) and\n[paper](https://doi.org/10.1093/bioinformatics/bty539) for full details.\n\nCitation\n--------\n\n``Lees, John A., Galardini, M., et al. \"pyseer: a comprehensive tool for microbial\npangenome-wide association studies\". Bioinformatics 34:4310\u20134312 (2018).``\n\n``doi: 10.1093/bioinformatics/bty539``\n\n``Lees, John A., et al. \"Sequence element enrichment analysis to determine\nthe genetic basis of bacterial phenotypes.\" Nature communications 7:12797 (2016).``\n\n``doi: 10.1038/ncomms12797``\n\nDocumentation\n--------------------\n\nFull documentation is available at [readthedocs](http://pyseer.readthedocs.io/).\n\nYou can also build the docs locally (requires `sphinx`) by typing:\n\n    cd docs/\n    make html\n\nPrerequisites\n-------------\n\nBetween parenthesis the versions the script was tested against:\n\n* `python` 3+ (3.6.6)\n* `numpy` (1.15.2)\n* `scipy` (1.1.0)\n* `pandas` (0.23.4)\n* `scikit-learn` (0.20.0)\n* `statsmodels` (0.9.0)\n* `pysam` (0.15.1)\n* `glmnet_python` (commit `946b65c`)\n* `DendroPy` (4.4.0)\n\nIf you would like to use the `scree_plot_pyseer` script you will also need to have\n`matplotlib` installed.\nIf you would like to use the scripts to map and annotate kmers, you will also need\n`bwa`, `bedtools`,\n`bedops` and `pybedtools` installed.\n\nInstallation\n------------\n\nThe easiest way to install pyseer and its dependencies is through `conda`::\n\n    conda install pyseer\n\nIf you need `conda`, download [miniconda](https://conda.io/miniconda.html)\nand add the necessary channels::\n\n    conda config --add channels defaults\n    conda config --add channels bioconda\n    conda config --add channels conda-forge\n\n`pyseer` can also be installed through `pip`:\n\n   `python -m pip install pyseer`\n\nIf you want multithreading make sure that you are using a version 3 python interpreter::\n\n   `python3 -m pip install pyseer`\n\n**If you want the next pre-release**, just clone/download this repository and run:\n\n    python pyseer-runner.py\n\nCopyright\n---------\n\nCopyright 2017 EMBL-European Bioinformatics Institute\n\nLicensed under the Apache License, Version 2.0 (the \"License\");\nyou may not use this file except in compliance with the License.\nYou may obtain a copy of the License at\n\n    http://www.apache.org/licenses/LICENSE-2.0\n\nUnless required by applicable law or agreed to in writing, software\ndistributed under the License is distributed on an \"AS IS\" BASIS,\nWITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.\nSee the License for the specific language governing permissions and\nlimitations under the License.",
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