Metadata-Version: 1.1
Name: gsalib
Version: 1.0.6
Summary: Python version of R gsalib to read GATK Report tables into pandas DataFrames
Home-page: https://github.com/myourshaw/gsalib
Author: Michael Yourshaw
Author-email: myourshaw@gmail.com
License: MIT License
Project-URL: Bug Reports, https://github.com/myourshaw/gsalib/issues
Project-URL: Funding, https://donate.pypi.org
Project-URL: Say Thanks!, https://cran.r-project.org/web/packages/gsalib/index.html
Project-URL: Source, https://github.com/myourshaw/gsalib/
Project-URL: Documentation, https://gsalib.readthedocs.io/en/latest/
Description: gsalib: Python/pandas package of utility functions for GATK
        =============================================================
        
        ``gsalib`` makes it easy for Python users to analyze metrics reports created by the Broad Institute's Genome Analysis Toolkit (GATK). The Broad provides an R library called gsalib that allows you to load GATKReport files into R for further analysis (https://gatkforums.broadinstitute.org/gatk/discussion/1244/what-is-the-gatkreport-file-format). Python ``gsalib`` is an adaptation of the R libray that allows you to load GATKReport files into Python/pandas DataFrames.
        
        Neither the R nor Python versions of ``gsalib`` support the samtools.metrics reports created by `Picard Tools <https://broadinstitute.github.io/picard/picard-metric-definitions.html>`_. To analyze Picard reports with Python, consider using the ``picard.parse`` function in the `Crimson <https://pypi.python.org/pypi/Crimson>`_ module.
        
        Features
        --------
        
        - Enables analysis of GATK reports with powerful pandas DataFrames and plotting
        - Reads GATKReport versions 0.x and 1.x
        - Compatible with Python >=2.7 and >=3.4
        
        Installation
        ------------
        
        Install ``gsalib`` by running ::
        
            pip install gsalib
        
        Example
        -------
        
        Read a report and get a table's DataFrame::
        
            from gsalib import GatkReport
        
            report = GatkReport('/path/to/gsalib/test/test_v1.0_gatkreport.table')
            table = report.tables['ExampleTable']
        
        Documentation
        -------------
        
        https://gsalib.readthedocs.io/en/latest/
        
        Contribute
        ----------
        
        - Issue Tracker: https://github.com/myourshaw/gsalib/issues
        - Source Code: https://github.com/myourshaw/gsalib
        
        License
        -------
        
        The project is licensed under the MIT license.
        
Keywords: gsalib GATK report table R pandas DataFrame
Platform: UNKNOWN
Classifier: Development Status :: 5 - Production/Stable
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 2
Classifier: Programming Language :: Python :: 2.7
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.4
Classifier: Programming Language :: Python :: 3.5
Classifier: Programming Language :: Python :: 3.6
