Metadata-Version: 2.1
Name: poppunk
Version: 1.2.2
Summary: PopPUNK (POPulation Partitioning Using Nucleotide Kmers)
Home-page: https://github.com/johnlees/PopPUNK
Author: John Lees and Nicholas Croucher
Author-email: john@johnlees.me
License: Apache Software License
Description: # PopPUNK (POPulation Partitioning Using Nucleotide Kmers)
        
        [![Dev build Status](https://dev.azure.com/jlees/PopPUNK/_apis/build/status/johnlees.PopPUNK?branchName=master)](https://dev.azure.com/jlees/PopPUNK/_build/latest?definitionId=1&branchName=master)
        [![Stable build Status](https://travis-ci.org/johnlees/PopPUNK.svg?branch=v1.1.7)](https://travis-ci.org/johnlees/PopPUNK/)
        [![Documentation Status](https://readthedocs.org/projects/poppunk/badge/?version=latest)](https://poppunk.readthedocs.io/)
        [![PyPI version](https://badge.fury.io/py/poppunk.svg)](https://badge.fury.io/py/poppunk)
        [![Anaconda package](https://anaconda.org/bioconda/poppunk/badges/version.svg)](https://anaconda.org/bioconda/poppunk)
        
        See our website: <https://www.poppunk.net>
        
        ## Description
        
        Step 1) Use k-mers to calculate core and accessory distances
        
        Step 2) Use core and accessory distance distribution to define strains
        
        Step 3) Pick references from strains, which can be used to assign new
        query sequences
        
        See the [documentation](http://poppunk.readthedocs.io/en/latest/) and the
        [paper](https://doi.org/10.1101/gr.241455.118).
        
        If you find PopPUNK useful, please cite as:
        
        Lees JA, Harris SR, Tonkin-Hill G, Gladstone RA, Lo SW, Weiser JN, Corander J, Bentley SD, Croucher NJ.
        Fast and flexible bacterial genomic epidemiology with PopPUNK. *Genome Research* **29**:304-316 (2019).
        doi:[10.1101/gr.241455.118](https://doi.org/10.1101/gr.241455.118)
        
        ## Installation
        
        ### Through conda (recommended)
        
        The easiest way is through conda, which is most easily accessed by first
        installing [miniconda](https://conda.io/miniconda.html). PopPUNK can then
        be installed by running:
        ```
        conda install poppunk
        ```
        If the package cannot be found you will need to add the necessary channels:
        ```
        conda config --add channels defaults
        conda config --add channels bioconda
        conda config --add channels conda-forge
        ```
        
        ### Through pip
        If you do not have conda you can also install through pip:
        ```
        python3 -m pip install poppunk
        ```
        You will need to be using Python 3.
        
        Using both of these methods command `poppunk` will then be directly executable.
        Alternatively clone this repository:
        ```
        git clone git@github.com:johnlees/PopPUNK.git
        ```
        Then run with `python poppunk-runner.py`.
        
        ## Quick usage
        Easy run mode, go from assemblies to clusters of strains:
        ```
        poppunk --easy-run --r-files reference_list.txt --output poppunk_db
        ```
        
        Or in two parts. First, create the database:
        ```
        poppunk --create-db \
           --r-files reference_list.txt \
           --output poppunk_db \
           --threads 2 \
           --k-step 2 \
           --min-k 9 \
           --plot-fit 5
        ```
        
        Then fit the model:
        ```
        poppunk --fit-model \
           --ref-db poppunk_db \
           --distances poppunk_db/poppunk_db.dists \
           --output poppunk_db \
           --full-db \
           --K 2
        ```
        
        Once fitted, new query sequences can quickly be assigned:
        ```
        poppunk --assign-query \
           --ref-db poppunk_db \
           --q-files query_list.txt \
           --output query_results \
           --update-db
        ```
        
        If running without having installed through conda or pip,
        run `python poppunk-runner.py` instead of `poppunk`.
        
        See the [documentation](http://poppunk.readthedocs.io/en/latest/) for
        full details.
        
        ## Other installation notes
        
        Installing via conda takes care of all dependencies. For other methods you will
        need to install the packages listed under dependencies.
        
        If you wish to use the [/scripts](https://poppunk.readthedocs.io/en/latest/scripts.html)
        you will need to clone the github.
        
        ### Dependencies
        
        You will need a [mash](http://mash.readthedocs.io/en/latest/) installation
        which is v2.0 or higher.
        
        The following python packages are required, which can be installed
        through `pip`. In brackets are the versions we used:
        
        * python3
        * `DendroPy` (4.3.0)
        * `hdbscan` (0.8.13)
        * `matplotlib` (2.1.2)
        * `networkx` (2.1)
        * `numba` (0.36.2)
        * `numpy` (1.14.1)
        * `pandas` (0.22.0)
        * `scikit-learn` (0.19.1)
        * `scipy` (1.0.0)
        * `sharedmem` (0.3.5)
        
        To install `numba` through pip, you may need `gcc >=v4.8` for it to work correctly.
        
        ### Test installation
        Run the following command:
        ```
        cd test && python run_test.py
        ```
        
        If successful, you can clean the test data by running:
        ```
        cd test && python clean_test.py
        ```
        
        
        
        
        
Keywords: bacteria genomics population-genetics k-mer
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: License :: OSI Approved :: Apache Software License
Classifier: Programming Language :: Python :: 3.7
Requires-Python: >=3.4.0
Description-Content-Type: text/markdown
