Metadata-Version: 2.1
Name: haplotype_plot
Version: 1.1.1
Summary: Generates haplotype plots from VCF files.
Home-page: https://github.com/neobernad/haplotype_plot
Author: José Antonio Bernabé-Díaz
Author-email: joseantonio.bernabe1@um.com
License: MIT
Description: # Haplotype plot
        
        Generates haplotype plots for VCF files.
        **Requires Python 3 to run**.
        
        [![Build Status](https://travis-ci.org/neobernad/haplotype_plot.svg?branch=master)](https://travis-ci.org/neobernad/haplotype_plot)
        [![codecov](https://codecov.io/gh/neobernad/haplotype_plot/branch/master/graph/badge.svg)](https://codecov.io/gh/neobernad/haplotype_plot)
        
        # Pypi
        
        You may install haplotype plot from pip:
        
        ```bash
        pip install haplotype-plot
        ```
        
        # Usage
        
        ```bash
        usage: main.py [-h] -v VCF [-o OUTPUT] -c CHR -p PARENTAL [--phase]
                       [--version] [-z {HOM,HET}] [--conf KEY=VALUE [KEY=VALUE ...]]
        
        Creates a haplotype plot from a VCF file
        
        optional arguments:
          -h, --help            show this help message and exit
          -v VCF, --vcf VCF     path to the input sorted VCF file
          -o OUTPUT, --output OUTPUT
                                path to the output PNG haplotype plot file
          -c CHR, --chr CHR     chromosome to plot from the VCF
          -p PARENTAL, --parental PARENTAL
                                sample name from the VCF used as parental haplotype
          --phase               if specified, it will phase the genotypes. An output
                                VCF with the phased genotypes is created
          --version             show program's version number and exit
          -z {HOM,HET}, --zygosis {HOM,HET}
                                zygosis of the input VCF file
          --conf KEY=VALUE [KEY=VALUE ...]
                                set a number of key-value pairs to modify the default
                                plot configuration (do not put spaces before or after
                                the = sign). If a value contains spaces, you should
                                define it with double quotes: foo="this is a
                                sentence". Possible values are: 'start=integer',
                                'end=integer', 'show=boolean', 'xtickslabels=boolean',
                                'size_y=float'
        ```
        
        For examples of use please go to the [documentation](https://neobernad.github.io/haplotype_plot/#/).
        
        ---
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Software Development :: Build Tools
Classifier: Topic :: Scientific/Engineering
Classifier: Operating System :: Microsoft :: Windows
Classifier: Operating System :: Unix
Classifier: Operating System :: MacOS
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3.6
Requires-Python: >=3
Description-Content-Type: text/markdown
