{
    "info": {
        "author": "Milovan Suvakov, Abyzov Lab, Mayo Clinic",
        "author_email": "suvakov@gmail.com",
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        "classifiers": [
            "Development Status :: 3 - Alpha",
            "License :: OSI Approved :: MIT License",
            "Operating System :: OS Independent",
            "Programming Language :: Python :: 2",
            "Programming Language :: Python :: 2.7",
            "Programming Language :: Python :: 3",
            "Programming Language :: Python :: 3.5",
            "Programming Language :: Python :: 3.6",
            "Programming Language :: Python :: 3.7"
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        "description": "![CNVpytor Logo](cnvpytor/imgs/cnvpytor_w_640.png)\n\n# CNVpytor - a python extension of CNVnator\n\nCNVpytor is a Python package and command line tool for CNV analysis from depth-of-coverage by mapped reads developed in Abyzov Lab, Mayo Clinic.\n\n**CNVpytor project is in early development stage.**\n\nFor more details check [API Documentation](https://abyzovlab.github.io/CNVpytor/)\n\n\nSource::\n    https://github.com/abyzovlab/CNVpytor\n\nBug reports::\n    https://github.com/abyzovlab/CNVpytor/issues\n\n## Install\n```\n> git clone https://github.com/abyzovlab/CNVpytor.git\n> cd CNVpytor\n> python setup.py install\n```\nFor single user (without admin privileges) use:\n```\n> python setup.py install --user\n```\n\n## Simple example\n\nCall CNV using read depth:\n```\n> cnvpytor -root file.pytor -rd file.bam\n> cnvpytor -root file.pytor -his 1000 10000 100000\n> TODO: cnvpytor -root file.pytor -partition 1000 10000 100000\n> TODO: cnvpytor -root file.pytor -call 1000 10000 100000\n```\n\nCall CNV using single nucleotide polymorphism::\n```\n> cnvpytor -root file.pytor -snp file.vcf\n> cnvpytor -root file.pytor -pileup file.bam\n> cnvpytor -root file.pytor -baf 10000 100000\n> TODO: cnvpytor -root file.pytor -call baf 10000 100000\n```\n\nPlot - command line\n```\n> cnvpytor -root file.pytor -plot stat\n> cnvpytor -root file.pytor -plot 10000 100000\n> cnvpytor -root file.pytor -plot stat manhattan 100000 -o file.pdf\n> cnvpytor -root file.pytor -plot baf -chrom 1 2 3 4\n> cnvpytor -root file.pytor -plot regions 1:10M-20M,2:20M-43M 3:10M-20M 10000\n> TODO: cnvpytor -root file.pytor -plot circular\n```\n\nPlot - interactive mode\n```\n> cnvpytor -root file.pytor -view 10000\ncnvpytor> chr1:1M-50M\ncnvpytor> rd\ncnvpytor> set panels rd likelihood\ncnvpytor> show\n    Parameters\n        * bin_size: 10000\n        * panels: ['rd','likelihood']\n        * use_mask_rd: False\n        * plot_files: [('file1.pytor', True),('file2.pytor', True)]\n        * plot_file: 0\n        * grid: auto\n    Available plot styles: classic, seaborn, ...\ncnvpytor> set bin_size 100000    \ncnvpytor> chr1:1M-50M chr2:60M-65M > filename.png\n```\n\n\n## Bugs\n\nPlease report any bugs that you find on GitHub:\nhttps://github.com/abyzovlab/CNVpytor/issues\n\nOr, even better, fork the repository on GitHub and create a pull request.\n\n## License\n\nReleased under MIT licence.\n\n\n",
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