{
    "info": {
        "author": "Andrew Riha",
        "author_email": "apriha@gmail.com",
        "bugtrack_url": null,
        "classifiers": [
            "Development Status :: 5 - Production/Stable",
            "Intended Audience :: Developers",
            "Intended Audience :: End Users/Desktop",
            "Intended Audience :: Healthcare Industry",
            "Intended Audience :: Science/Research",
            "License :: OSI Approved :: BSD License",
            "Natural Language :: English",
            "Operating System :: OS Independent",
            "Programming Language :: Python :: 3.5",
            "Programming Language :: Python :: 3.6",
            "Programming Language :: Python :: 3.7",
            "Programming Language :: Python :: 3.8",
            "Topic :: Scientific/Engineering",
            "Topic :: Scientific/Engineering :: Bio-Informatics",
            "Topic :: Scientific/Engineering :: Information Analysis",
            "Topic :: Utilities"
        ],
        "description": ".. image:: https://raw.githubusercontent.com/apriha/snps/master/docs/images/snps_banner.png\n\n|build| |codecov| |docs| |pypi| |python| |downloads|\n\nsnps\n====\ntools for reading, writing, merging, and remapping SNPs \ud83e\uddec\n\nCapabilities\n------------\n- Read raw data (genotype) files from a variety of direct-to-consumer (DTC) DNA testing sources\n- Read and write VCF files for Builds 36, 37, and 38 (e.g., convert `23andMe <https://www.23andme.com>`_ to VCF)\n- Merge raw data files from different DNA tests, identifying discrepant SNPs in the process\n- Remap SNPs between assemblies / builds (e.g., convert SNPs from Build 36 to Build 37, etc.)\n\nSupported Genotype Files\n------------------------\n``snps`` supports `VCF <https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3137218/>`_ files and\ngenotype files from the following DNA testing sources:\n\n- `23andMe <https://www.23andme.com>`_\n- `Ancestry <https://www.ancestry.com>`_\n- `C\u00f3digo 46 <https://codigo46.com.mx>`_\n- `Family Tree DNA <https://www.familytreedna.com>`_\n- `Genes for Good <https://genesforgood.sph.umich.edu>`_\n- `LivingDNA <https://livingdna.com>`_\n- `Mapmygenome <https://mapmygenome.in>`_\n- `MyHeritage <https://www.myheritage.com>`_\n\nDependencies\n------------\n``snps`` requires `Python <https://www.python.org>`_ 3.5+ and the following Python packages:\n\n- `numpy <http://www.numpy.org>`_\n- `pandas <http://pandas.pydata.org>`_\n- `atomicwrites <https://github.com/untitaker/python-atomicwrites>`_\n- `PyVCF <https://github.com/jamescasbon/PyVCF>`_\n\nInstallation\n------------\n``snps`` is `available <https://pypi.org/project/snps/>`_ on the\n`Python Package Index <https://pypi.org>`_. Install ``snps`` (and its required\nPython dependencies) via ``pip``::\n\n    $ pip install snps\n\nExamples\n--------\nDownload Example Data\n`````````````````````\nLet's download some example data from `openSNP <https://opensnp.org>`_:\n\n>>> from snps.resources import Resources\n>>> r = Resources()\n>>> paths = r.download_example_datasets()\nDownloading resources/662.23andme.340.txt.gz\nDownloading resources/662.ftdna-illumina.341.csv.gz\n\nLoad Raw Data\n`````````````\nLoad a `23andMe <https://www.23andme.com>`_ raw data file:\n\n>>> from snps import SNPs\n>>> s = SNPs('resources/662.23andme.340.txt.gz')\n\nThe loaded SNPs are available via a ``pandas.DataFrame``:\n\n>>> df = s.snps\n>>> df.columns.values\narray(['chrom', 'pos', 'genotype'], dtype=object)\n>>> df.index.name\n'rsid'\n>>> len(df)\n991786\n\n``snps`` also attempts to detect the build / assembly of the data:\n\n>>> s.build\n37\n>>> s.build_detected\nTrue\n>>> s.assembly\n'GRCh37'\n\nRemap SNPs\n``````````\nLet's remap the SNPs to change the assembly / build:\n\n>>> s.snps.loc[\"rs3094315\"].pos\n752566\n>>> chromosomes_remapped, chromosomes_not_remapped = s.remap_snps(38)\nDownloading resources/GRCh37_GRCh38.tar.gz\n>>> s.build\n38\n>>> s.assembly\n'GRCh38'\n>>> s.snps.loc[\"rs3094315\"].pos\n817186\n\nSNPs can be remapped between Build 36 (``NCBI36``), Build 37 (``GRCh37``), and Build 38\n(``GRCh38``).\n\nMerge Raw Data Files\n````````````````````\nThe dataset consists of raw data files from two different DNA testing sources. Let's combine\nthese files using a ``SNPsCollection``.\n\n>>> from snps import SNPsCollection\n>>> sc = SNPsCollection(\"resources/662.ftdna-illumina.341.csv.gz\", name=\"User662\")\nLoading resources/662.ftdna-illumina.341.csv.gz\n>>> sc.build\n36\n>>> chromosomes_remapped, chromosomes_not_remapped = sc.remap_snps(37)\nDownloading resources/NCBI36_GRCh37.tar.gz\n>>> sc.snp_count\n708092\n\nAs the data gets added, it's compared to the existing data, and SNP position and genotype\ndiscrepancies are identified. (The discrepancy thresholds can be tuned via parameters.)\n\n>>> sc.load_snps([\"resources/662.23andme.340.txt.gz\"], discrepant_genotypes_threshold=300)\nLoading resources/662.23andme.340.txt.gz\n27 SNP positions were discrepant; keeping original positions\n151 SNP genotypes were discrepant; marking those as null\n>>> len(sc.discrepant_snps)  # SNPs with discrepant positions and genotypes, dropping dups\n169\n>>> sc.snp_count\n1006960\n\nSave SNPs\n`````````\nOk, so far we've remapped the SNPs to the same build and merged the SNPs from two files,\nidentifying discrepancies along the way. Let's save the merged dataset consisting of over 1M+\nSNPs to a CSV file:\n\n>>> saved_snps = sc.save_snps()\nSaving output/User662_GRCh37.csv\n\nMoreover, let's get the reference sequences for this assembly and save the SNPs as a VCF file:\n\n>>> saved_snps = sc.save_snps(vcf=True)\nDownloading resources/fasta/GRCh37/Homo_sapiens.GRCh37.dna.chromosome.1.fa.gz\nDownloading resources/fasta/GRCh37/Homo_sapiens.GRCh37.dna.chromosome.2.fa.gz\nDownloading resources/fasta/GRCh37/Homo_sapiens.GRCh37.dna.chromosome.3.fa.gz\nDownloading resources/fasta/GRCh37/Homo_sapiens.GRCh37.dna.chromosome.4.fa.gz\nDownloading resources/fasta/GRCh37/Homo_sapiens.GRCh37.dna.chromosome.5.fa.gz\nDownloading resources/fasta/GRCh37/Homo_sapiens.GRCh37.dna.chromosome.6.fa.gz\nDownloading resources/fasta/GRCh37/Homo_sapiens.GRCh37.dna.chromosome.7.fa.gz\nDownloading resources/fasta/GRCh37/Homo_sapiens.GRCh37.dna.chromosome.8.fa.gz\nDownloading resources/fasta/GRCh37/Homo_sapiens.GRCh37.dna.chromosome.9.fa.gz\nDownloading resources/fasta/GRCh37/Homo_sapiens.GRCh37.dna.chromosome.10.fa.gz\nDownloading resources/fasta/GRCh37/Homo_sapiens.GRCh37.dna.chromosome.11.fa.gz\nDownloading resources/fasta/GRCh37/Homo_sapiens.GRCh37.dna.chromosome.12.fa.gz\nDownloading resources/fasta/GRCh37/Homo_sapiens.GRCh37.dna.chromosome.13.fa.gz\nDownloading resources/fasta/GRCh37/Homo_sapiens.GRCh37.dna.chromosome.14.fa.gz\nDownloading resources/fasta/GRCh37/Homo_sapiens.GRCh37.dna.chromosome.15.fa.gz\nDownloading resources/fasta/GRCh37/Homo_sapiens.GRCh37.dna.chromosome.16.fa.gz\nDownloading resources/fasta/GRCh37/Homo_sapiens.GRCh37.dna.chromosome.17.fa.gz\nDownloading resources/fasta/GRCh37/Homo_sapiens.GRCh37.dna.chromosome.18.fa.gz\nDownloading resources/fasta/GRCh37/Homo_sapiens.GRCh37.dna.chromosome.19.fa.gz\nDownloading resources/fasta/GRCh37/Homo_sapiens.GRCh37.dna.chromosome.20.fa.gz\nDownloading resources/fasta/GRCh37/Homo_sapiens.GRCh37.dna.chromosome.21.fa.gz\nDownloading resources/fasta/GRCh37/Homo_sapiens.GRCh37.dna.chromosome.22.fa.gz\nDownloading resources/fasta/GRCh37/Homo_sapiens.GRCh37.dna.chromosome.X.fa.gz\nDownloading resources/fasta/GRCh37/Homo_sapiens.GRCh37.dna.chromosome.Y.fa.gz\nDownloading resources/fasta/GRCh37/Homo_sapiens.GRCh37.dna.chromosome.MT.fa.gz\nSaving output/User662_GRCh37.vcf\n\nAll `output files <https://snps.readthedocs.io/en/latest/output_files.html>`_ are saved to the\noutput directory.\n\nDocumentation\n-------------\nDocumentation is available `here <https://snps.readthedocs.io/>`_.\n\nAcknowledgements\n----------------\nThanks to Mike Agostino, Padma Reddy, Kevin Arvai, `openSNP <https://opensnp.org>`_,\n`Open Humans <https://www.openhumans.org>`_, and `Sano Genetics <https://sanogenetics.com>`_.\n\n.. https://github.com/rtfd/readthedocs.org/blob/master/docs/badges.rst\n.. |build| image:: https://travis-ci.org/apriha/snps.svg?branch=master\n   :target: https://travis-ci.org/apriha/snps\n.. |codecov| image:: https://codecov.io/gh/apriha/snps/branch/master/graph/badge.svg\n   :target: https://codecov.io/gh/apriha/snps\n.. |docs| image:: https://readthedocs.org/projects/snps/badge/?version=latest\n   :target: https://snps.readthedocs.io/\n.. |pypi| image:: https://img.shields.io/pypi/v/snps.svg\n   :target: https://pypi.python.org/pypi/snps\n.. |python| image:: https://img.shields.io/pypi/pyversions/snps.svg\n   :target: https://www.python.org\n.. |downloads| image:: https://pepy.tech/badge/snps\n   :target: https://pepy.tech/project/snps\n\n\n",
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