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        "author": "Brian D. Weitzner",
        "author_email": "bweitzner@lyellbio.com",
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            "Development Status :: 5 - Production/Stable",
            "Intended Audience :: Developers",
            "Intended Audience :: Science/Research",
            "License :: OSI Approved :: MIT License",
            "Natural Language :: English",
            "Programming Language :: Python :: 3",
            "Programming Language :: Python :: 3.6",
            "Programming Language :: Python :: 3.7",
            "Topic :: Scientific/Engineering",
            "Topic :: Scientific/Engineering :: Bio-Informatics"
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        "description": "=============\nCodon Harmony\n=============\n\n\n.. image:: https://img.shields.io/pypi/v/codon_harmony.svg\n        :target: https://pypi.python.org/pypi/codon_harmony\n        \n.. image:: https://img.shields.io/badge/License-MIT-yellow.svg\n        :target: https://opensource.org/licenses/MIT\n        :alt: MIT License\n\n.. image:: https://img.shields.io/travis/weitzner/codon_harmony.svg\n        :target: https://travis-ci.org/weitzner/codon_harmony\n\n.. image:: https://readthedocs.org/projects/codon-harmony/badge/?version=latest\n        :target: https://codon-harmony.readthedocs.io/en/latest/?badge=latest\n        :alt: Documentation status\n\n.. image:: https://codecov.io/gh/weitzner/codon_harmony/branch/master/graph/badge.svg\n        :target: https://codecov.io/gh/weitzner/codon_harmony\n        :alt: Coverage report\n\n.. image:: https://pyup.io/repos/github/weitzner/codon_harmony/shield.svg\n     :target: https://pyup.io/repos/github/weitzner/codon_harmony/\n     :alt: Updates\n\n.. image:: https://img.shields.io/badge/code%20style-black-000000.svg\n     :target: https://github.com/ambv/black\n     :alt: Code style: black\n\n\nAmino acid reverse translation and DNA optimization tool based on species-specific codon-use distributions.\nSpecies-specifc data can be found on the `Codon Usage Database`_ using the `NCBI Taxonomy database`_ id (e.g. 413997) or the organism's Latin name (e.g. *Escherichia coli* B). Mapping species names to Taxonomy IDs can be done here_.\n\n.. _`Codon Usage Database`: http://www.kazusa.or.jp/codon\n.. _`NCBI Taxonomy database`: http://www.ncbi.nlm.nih.gov/taxonomy\n.. _here: https://www.ncbi.nlm.nih.gov/Taxonomy/TaxIdentifier/tax_identifier.cgi\n\n* Documentation: https://codon-harmony.readthedocs.io\n\n\nFeatures\n--------\n\n1. Reverse translates input amino acid sequence to DNA.\n2. Calculates the host's per-AA codon usage profile \u2013 codons used less than a specified threshold (defaults to 10%) are dropped.\n3. Compares the reverse-translated DNA sequence to the host profile, determines which codons are overused/underused.\n4. Stochastically mutates codons according to host profile.\n5. Ranks sequences by codon adaptation index relative to host\n6. Processes DNA to remove unwanted features:\n\n   * high GC content within a sliding window and across the entire sequence\n   * unwanted restriction sites\n   * alternate start positions (GA-rich regions 18 bp upstream of ATG/GTG/TTG)\n   * 3-consecutive identical codons and 9-mer repeat chunks\n   * areas with more than 4 (variable) consecutive identical bps (\"local homopolymers\")\n   * RNA hairpins, detected by looking for 10-mers with reverse complements (including wobble bases) in the sequence\n   * RNA splice sites, detected by similarity to consensus donor and acceptor site sequences\n   \nThe process is repeated from step 3 for a specified number of cycles (defaults to 1000) OR until the per-AA codon profile of current DNA and host profile matches (within tolerance).\n\nFuture work\n-----------\n\n- More advanced RNA-structure removal\n\n  * CONTRAfold_ \u2013 overkill for now\n  * nupack_ \u2013 overkill for now\n\n.. _CONTRAfold: http://contra.stanford.edu/contrafold/\n.. _nupack: http://nupack.org\n\n\n=======\nHistory\n=======\n\n0.9.2 (2019-02-06)\n------------------\n\n* First release on PyPI.\n\n\n0.9.4 (2019-02-20)\n------------------\n\n* Full suite of tests added, bugs uncovered and fixed\n* Adjustments to the packaging setup -- actaully installable now\n\n\n0.9.5 (2019-02-25)\n------------------\n\n* Adding support for RNA splice site detection and removal\n\n\n0.9.6 (2019-02-28)\n------------------\n\n* Updating the way optimization failures are reported and displayed\n* Parallelizing via a process pool\n\n\n1.0.0 (2019-03-06)\n------------------\n\n* Added ability to use offline tables in addition to fetching from the internet\n* Full suite of tests and documentation\n* Tested on real-world sequences to",
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