Metadata-Version: 2.1
Name: tbvcfreport
Version: 0.1.7.dev20190823
Summary: Parses SnpEff generated VCF and generates an HTML report.
Home-page: https://github.com/COMBAT-TB/tbvcfreport
Author: SANBI
Author-email: help@sanbi.ac.za
License: GPLv3
Project-URL: Project, https://combattb.org
Project-URL: Source, https://github.com/COMBAT-TB/tbvcfreport
Project-URL: Tracker, https://github.com/COMBAT-TB/tbvcfreport/issues
Description: # **tbvcfreport**
        
        [![Build Status](https://travis-ci.org/COMBAT-TB/tbvcfreport.svg?branch=master)](https://travis-ci.org/COMBAT-TB/tbvcfreport)
        [![Anaconda-Server Badge](https://anaconda.org/thoba/tbvcfreport/badges/version.svg)](https://anaconda.org/thoba/tbvcfreport)
        
        A tool to generate an interactive HTML-based report from SnpEff annotated VCF file(s) with links to the Combat-TB-Explorer.
        
        ![test-report-img](img/test-report.png)
        
        ## Usage
        
        **Prerequisites:**
        
        - `python-pip`
        - [SnpEff](http://snpeff.sourceforge.net/SnpEff_manual.html) annotated *M.tuberculosis* VCF file(s).
        - A [Combat-TB-NeoDB](https://github.com/COMBAT-TB/combat-tb-neodb) instance, `tbvcfreport` defaults to [neodb.sanbi.ac.za](https://neodb.sanbi.ac.za).
          - See [combat-tb-neodb](https://github.com/COMBAT-TB/combat-tb-neodb) if you want a local installation and `export DATABASE_URI=localhost` for `tbvcfreport` to use your local instance.
        
        ### Installation
        
        #### Using `pip`
        
        ```sh
        $ pip install -i https://test.pypi.org/simple/ tbvcfreport
        ...
        ```
        
        #### From source
        
        ```sh
        $ git clone https://github.com/COMBAT-TB/tbvcfreport.git
        ...
        $ cd tbvcfreport
        $ virtualenv envname
        $ source envname/bin/activate
        $ pip install -r requirements.txt
        $ pip install -e .
        ```
        
        ### Run `tbvcfreport`
        
        ```sh
        $ tbvcfreport --help
        Usage: tbvcfreport [OPTIONS] COMMAND [ARGS]...
        
          Generate an HTML-based VCF report from SnpEff annotated VCF file(s).
        
        Options:
          --help  Show this message and exit.
        
        Commands:
          generate  Generate an interactive HTML-based VCF report.
        
        ```
        
        ```sh
        $ tbvcfreport generate --help
        Usage: tbvcfreport generate [OPTIONS] VCF_DIR
        
          Generate an interactive HTML-based VCF report.
        
        Options:
          -t, --tbprofiler-report FILENAME
                                          TBProfiler json report.
          -f, --filter-udi / -nf, --no-filter-udi
                                          Filter upstream, downstream and intergenic
                                          variants.  [default: True]
          --help                          Show this message and exit.
        
        ```
        
        ```sh
        $ tbvcfreport generate VCF_DIR/
        Processing...
        ```
        
        This will generate a `{vcf-file-name}.html` file in the current working directory (`pwd`).
        
        ## In Galaxy
        
        :construction:
        
        We have also added `tbvcfreport` to the [Galaxy](https://github.com/galaxyproject) [Test Tool Shed](https://testtoolshed.g2.bx.psu.edu/repository?repository_id=0f42e4f01e64b182).
        
        Kindly see [`this repository`](https://testtoolshed.g2.bx.psu.edu/repository?repository_id=0f42e4f01e64b182) for the latest revision.
        
        ![Galaxy-tbvcfreport](img/tbvcfreport.png)
        
Keywords: neo4j,vcf,tuberculosis,h37rv,snpeff
Platform: UNKNOWN
Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
Classifier: Intended Audience :: Science/Research
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Requires-Python: ~=3.6
Description-Content-Type: text/markdown
