Metadata-Version: 1.2
Name: viral-verify
Version: 0.1.1
Summary: viralVerify rewrite/refactor for PyPI packaging and distribution
Home-page: https://github.com/peterk87/viral_verify
Author: Peter Kruczkiewicz
Author-email: peter.kruczkiewicz@gmail.com
License: MIT license
Description: ============
        viral_verify
        ============
        
        
        .. image:: https://img.shields.io/pypi/v/viral_verify.svg
                :target: https://pypi.python.org/pypi/viral_verify
        
        .. image:: https://img.shields.io/travis/peterk87/viral_verify.svg
                :target: https://travis-ci.com/peterk87/viral_verify
        
        .. image:: https://readthedocs.org/projects/viral-verify/badge/?version=latest
                :target: https://viral-verify.readthedocs.io/en/latest/?badge=latest
                :alt: Documentation Status
        
        
        viralVerify_ rewrite/refactor for PyPI packaging and distribution, maintainability and clarity.
        
        **NOTE:** BLAST+ search option has been removed. Results output table will be different than the original viralVerify_. Naive Bayes classifier training script has not been ported yet.
        
        
        * Free software: MIT license
        * Documentation: https://viral-verify.readthedocs.io.
        
        
        Features
        --------
        
        * Gene prediction with Prodigal_ in metagenomic mode
        * HMMer3_ ``hmmsearch`` for protein domains in predicted genes
        * Naive Bayes classification of contigs as viral/not viral based on HMMer3_ results
        * Output of detailed contig classification results table in CSV format
        * Output of contigs based on classification into separate FASTA files
        
        Requirements
        ------------
        
        An HMMer3_ HMM database is required. For example, the latest version of Pfam-A HMM:
        
        * http://ftp.ebi.ac.uk/pub/databases/Pfam/releases/Pfam33.1/Pfam-A.hmm.gz
        
        **NOTE:** Please extract any compressed HMM DB (``$ gunzip Pfam-A.hmm.gz``)
        
        Software dependencies:
        
        * Prodigal_ v2.6.3
        * HMMer3_ v3.3
        * Python v3.6+
        
        Python dependencies:
        
        * attrs_
        * Click_
        * Pandas_
        * Biopython_
        
        Installation
        ------------
        
        Conda
        ~~~~~
        
        It's recommended that you use Conda_ to install the required software (Prodigal_ and HMMer3_) and Python dependencies.
        
        .. code-block::
        
            $ conda env create -f environment.yml
        
        Pip
        ~~~
        
        If you have Prodigal_ and HMMer3_ installed in your ``$PATH``, and Python 3.6 or greater, you can use ``pip`` to install ``viral_verify``:
        
        .. code-block::
        
            $ pip install viral_verify
        
        
        Usage
        -----
        
        .. code-block::
        
            $ viral_verify --help
            Usage: viral_verify [OPTIONS]
        
              HMM and Naive Bayes classification of contig sequences as either viral,
              plasmid or chromosomal.
        
              Requires Prodigal for gene prediction and hmmsearch from HMMer3 for
              searching for Pfam HMM profiles.
        
            Options:
              -i, --input-fasta PATH          Input fasta file  [required]
              -o, --outdir PATH               Output directory  [required]
              -H, --hmm-db PATH               Path to Pfam-A HMM database  [required]
              -t, --threads INTEGER           Number of threads (default=16)
              -p, --output-plasmids-separately
                                              Output predicted plasmids separately?
              --prefix TEXT                   Output file prefix (default: None)
              --uncertainty-threshold FLOAT   Uncertainty threshold (Natural log
                                              probability) (default=3.0)
        
              --naive-bayes-classifier-table PATH
                                              Table of protein domain frequencies to use
                                              for Naive Bayes classification (default="/ho
                                              me/pkruczkiewicz/repos/viral_verify/viral_ve
                                              rify/data/classifier_table.txt")
        
              -v, --verbose                   Logging verbosity
              --version                       Show the version and exit.
              --help                          Show this message and exit.
        
        
        
        Credits
        -------
        
        The original source code, design and conception can be found at viralVerify_. This is merely a rewrite for easier packaging via PyPI, adding some CI with Travis-CI and organizing the code for maintainability and clarity.
        
        This package was created with Cookiecutter_ and the `audreyr/cookiecutter-pypackage`_ project template.
        
        .. _Cookiecutter: https://github.com/audreyr/cookiecutter
        .. _`audreyr/cookiecutter-pypackage`: https://github.com/audreyr/cookiecutter-pypackage
        .. _viralVerify: https://github.com/ablab/viralVerify/
        .. _attrs: https://www.attrs.org/en/stable/
        .. _Click: https://click.palletsprojects.com/en/7.x/
        .. _Pandas: https://pandas.pydata.org/
        .. _Biopython: https://github.com/biopython/biopython
        .. _Conda: https://docs.conda.io/en/latest/
        .. _HMMer3: http://hmmer.org/
        .. _Prodigal: https://github.com/hyattpd/Prodigal
        
        
        =======
        History
        =======
        
        0.1.1 (2020-06-04)
        ------------------
        
        * Fix PyPI release (include ``classifier_table.txt`` in package)
        
        0.1.0 (2020-06-03)
        ------------------
        
        * First release on PyPI.
        
Keywords: viral_verify
Platform: UNKNOWN
Classifier: Development Status :: 2 - Pre-Alpha
Classifier: Intended Audience :: Developers
Classifier: License :: OSI Approved :: MIT License
Classifier: Natural Language :: English
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Requires-Python: >=3.6
