{
    "info": {
        "author": "Roberto Preste",
        "author_email": "robertopreste@gmail.com",
        "bugtrack_url": null,
        "classifiers": [
            "Development Status :: 2 - Pre-Alpha",
            "Intended Audience :: Developers",
            "License :: OSI Approved :: MIT License",
            "Natural Language :: English",
            "Programming Language :: Python :: 3",
            "Programming Language :: Python :: 3.6",
            "Programming Language :: Python :: 3.7"
        ],
        "description": "========\nallfreqs\n========\n\n\n.. image:: https://img.shields.io/pypi/v/allfreqs.svg\n        :target: https://pypi.python.org/pypi/allfreqs\n\n.. image:: https://www.repostatus.org/badges/latest/wip.svg\n    :alt: Project Status: WIP \u2013 Initial development is in progress, but there has not yet been a stable, usable release suitable for the public.\n    :target: https://www.repostatus.org/#wip\n\n.. image:: https://travis-ci.com/robertopreste/allfreqs.svg?branch=master\n        :target: https://travis-ci.com/robertopreste/allfreqs\n\n.. image:: https://readthedocs.org/projects/allfreqs/badge/?version=latest\n        :target: https://allfreqs.readthedocs.io/en/latest/?badge=latest\n        :alt: Documentation Status\n\n.. image:: https://pyup.io/repos/github/robertopreste/allfreqs/python-3-shield.svg\n     :target: https://pyup.io/repos/github/robertopreste/allfreqs/\n     :alt: Python 3\n\n.. image:: https://img.shields.io/badge/Say%20Thanks-!-1EAEDB.svg\n   :target: https://saythanks.io/to/robertopreste\n\n\nCalculate allele frequencies from a sequence multialignment.\n\n\n* Free software: MIT license\n* Documentation: https://allfreqs.readthedocs.io\n* GitHub repo: https://github.com/robertopreste/allfreqs\n\n\nFeatures\n========\n\nCalculate allele frequencies from a nucleotide multialignment in fasta or csv format.\n\nAllele frequencies will be returned as a table in which each row is a nucleotide position (based on the provided reference sequence) and columns are A, C, G, T frequencies as well as gaps and other non-canonical nucleotides.\n\nFor example, given the following multialignment:\n\n+------+----------+\n| ID   | Sequence |\n+======+==========+\n| ref  | ACGTACGT |\n+------+----------+\n| seq1 | A-GTAGGN |\n+------+----------+\n| seq2 | ACCAGCGT |\n+------+----------+\n\nthe resulting allele frequencies will be:\n\n+----------+-----+-----+-----+-----+-----+-----+\n| position | A   | C   | G   | T   | gap | oth |\n+==========+=====+=====+=====+=====+=====+=====+\n| 1.0_A    | 1.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 |\n+----------+-----+-----+-----+-----+-----+-----+\n| 2.0_C    | 0.0 | 0.5 | 0.0 | 0.0 | 0.5 | 0.0 |\n+----------+-----+-----+-----+-----+-----+-----+\n| 3.0_G    | 0.0 | 0.5 | 0.5 | 0.0 | 0.0 | 0.0 |\n+----------+-----+-----+-----+-----+-----+-----+\n| 4.0_T    | 0.5 | 0.0 | 0.0 | 0.5 | 0.0 | 0.0 |\n+----------+-----+-----+-----+-----+-----+-----+\n| 5.0_A    | 0.5 | 0.0 | 0.5 | 0.0 | 0.0 | 0.0 |\n+----------+-----+-----+-----+-----+-----+-----+\n| 6.0_C    | 0.0 | 0.5 | 0.5 | 0.0 | 0.0 | 0.0 |\n+----------+-----+-----+-----+-----+-----+-----+\n| 7.0_G    | 0.0 | 0.0 | 1.0 | 0.0 | 0.0 | 0.0 |\n+----------+-----+-----+-----+-----+-----+-----+\n| 8.0_T    | 0.0 | 0.0 | 0.0 | 0.5 | 0.0 | 0.5 |\n+----------+-----+-----+-----+-----+-----+-----+\n\nallfreqs can be used either as a command line tool or through its Python API.\n\nFor more information, please refer to the Usage_ section of the documentation.\n\nInstallation\n============\n\n**PLEASE NOTE: allfreqs only supports Python >= 3.6!**\n\nThe preferred installation method for allfreqs is using ``pip``::\n\n    $ pip install allfreqs\n\nFor more information, please refer to the Installation_ section of the documentation.\n\nCredits\n=======\n\nThis package was created with Cookiecutter_ and the `cc-pypackage`_ project template.\n\n.. _Usage: https://allfreqs.readthedocs.io/en/latest/usage.html\n.. _Installation: https://allfreqs.readthedocs.io/en/latest/installation.html\n.. _Cookiecutter: https://github.com/audreyr/cookiecutter\n.. _`cc-pypackage`: https://github.com/robertopreste/cc-pypackage\n\n\n=======\nHistory\n=======\n\n0.1.0 (2019-07-08)\n==================\n\n* First release.\n\n0.1.1 (2019-08-08)\n------------------\n\n* Read and process multialignments from fasta and csv files (Python module only).\n\n0.1.2 (2019-10-17)\n------------------\n\n* Add tests with and without reference included in multialignments;\n* Add tests with real datasets (coming from haplogroup-specific multialignments).\n\n0.1.3 (2019-10-18)\n------------------\n\n* Add more detailed tests for real datasets;\n* Implement more efficient frequency calculation;\n* Add dunder methods and sanity checks;\n* Fix requirements and testing framework;\n* Clean code.\n\n\n",
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