Metadata-Version: 1.1
Name: g2gtools
Version: 0.2.0
Summary: A suite of tools for the reconstruction of personal diploid genomes and better coordinate conversion
Home-page: http://churchill-lab.github.io/g2gtools/
Author: Matthew J. Vincent and Kwangbom "KB" Choi, The Jackson Laboratory
Author-email: kb.choi@jax.org
License: MIT
Description: ===============================
        g2gtools
        ===============================
        
        .. image:: https://badge.fury.io/py/g2gtools.png
            :target: http://badge.fury.io/py/g2gtools
        
        .. image:: https://travis-ci.org/churchill-lab/g2gtools.png?branch=master
            :target: https://travis-ci.org/churchill-lab/g2gtools
        
        .. image:: https://anaconda.org/kbchoi/g2gtools/badges/version.svg
            :target: https://anaconda.org/kbchoi/g2gtools
        
        .. image:: https://readthedocs.org/projects/g2gtools/badge/?version=latest
            :target: http://g2gtools.readthedocs.org/en/latest/?badge=latest
            :alt: Documentation Status
        
        .. image:: https://zenodo.org/badge/39776319.svg
            :target: https://zenodo.org/badge/latestdoi/39776319
        
        **g2gtools** creates custom genomes by incorporating SNPs and indels into reference genome, extracts regions of interest, e.g., exons or transcripts, , and converts coordinates of files (bam, gtf, bed) between two genomes. Unlike other liftover tools, g2gtools does not throw away alignments that land on indel regions. Release Version 0.2 can now create personal **diploid** genomes. The new version still lifts over diploid alignments on personal genome coordinates back to that of reference so we can compare alignments from among samples in a population.
        
        * Free software: MIT License
        * Documentation for Release Ver. 0.2.XX: http://churchill-lab.github.io/g2gtools/.
        * Documentation for Release Ver. 0.1.XX: https://g2gtools.readthedocs.org.
        
        
        Reference
        ~~~~~~~~~
        
        Manuscript in preparation (expected in 2018)
        
        
        
        History
        -------
        
        0.2.0 (05/09/2018)
        ~~~~~~~~~~~~~~~~~~
        
        * Support for diploid VCF
        * Reimplemented to support G2G VCI (Variant Call Information)
        * Support python3
        
        0.1.31 (02/17/2017)
        ~~~~~~~~~~~~~~~~~~~
        
        * Final release for custom haploid reconstruction
        
        0.1.29 (05/17/2016)
        ~~~~~~~~~~~~~~~~~~~
        
        * Fixed parsing issue with GATK-generated VCF files
        
        0.1.27 (05/04/2016)
        ~~~~~~~~~~~~~~~~~~~
        
        * Uploaded the package to Anaconda Cloud
        * Fixed Travis CI fail
        
        0.1.23 (02/15/2016)
        ~~~~~~~~~~~~~~~~~~~
        
        * Setup Travis CI for automated building
        
        0.1.22 (02/15/2016)
        ~~~~~~~~~~~~~~~~~~~
        
        * Updated documentation
        
        0.1.20 (02/03/2016)
        ~~~~~~~~~~~~~~~~~~~
        
        * Released to public with documentation at g2gtools.readthedocs.org
        
        0.1.0 (02/09/2015)
        ~~~~~~~~~~~~~~~~~~
        
        * Started github repository
        
Keywords: g2gtools,personal genomes,liftover
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Natural Language :: English
Classifier: Programming Language :: Python :: 2
Classifier: Programming Language :: Python :: 2.7
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.5
Classifier: Programming Language :: Python :: 3.6
