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    "info": {
        "author": "Daniel Standage",
        "author_email": "daniel.standage@nbacc.dhs.gov",
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        "classifiers": [
            "Environment :: Console",
            "Framework :: IPython",
            "Framework :: Jupyter",
            "Intended Audience :: Science/Research",
            "License :: OSI Approved :: BSD License",
            "Programming Language :: Python :: 3",
            "Topic :: Scientific/Engineering :: Bio-Informatics"
        ],
        "description": "# happer\n\nDaniel Standage, 2018  \nhttps://github.com/bioforensics/happer\n\n**happer** is a minimal Python library for generating complete haplotype sequences.\nGiven a reference sequence and haplotype alleles annotated in BED format, happer will mutate the reference and produce sequences to match the specified haplotypes.\n\n\n## Installation\n\nTo install:\n\n```bash\npip3 install happer\n```\n\nTo make sure the package installed correctly:\n\n```bash\npip3 install pytest\npy.test --pyargs happer\n```\n\nhapper requires Python version 3.\n\n\n## Usage\n\nReference sequences must be provided in Fasta format, and haplotype alleles must be specified in BED format as follows.\nAlleles corresponding to different haplotypes at the locus are separated by a `|` character, so for example a diploid individual should have 2 `|`-separated alleles annotated at each locus, while a tetraploid would have 4 alleles.\nIn the example below, the `CCGA` alleles are phased and represent one haplotype, while the `TATG` alleles are phased and represent another haplotype.\n\n```txt\n#SeqID    Start  End     Alleles\nchr1     38827  38828   C|T\nchr1     59288  59289   C|A\nchr2     24771  24772   G|T\nchr4     201191 201192  A|G\n```\n\nTo invoke happer from the command line:\n\n```\n[standage@lappy ~]$ happer --out haploseqs.fasta refr.fasta alleles.bed\n```\n\nTo invoke happer directly in Python:\n\n```python\n>>> import happer\n>>> seqfile = open('refr.fasta', 'r')\n>>> alleles = open('alleles.bed', 'r')\n>>> for label, haploseq in happer.mutate.mutate(seqfile, alleles):\n...     # do whatever you'd like with the sequences\n```",
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        "summary": "Library for applying haplotypes to reference DNA sequences",
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