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        "author": "LUMC, Jeroen F.J. Laros",
        "author_email": "J.F.J.Laros@lumc.nl",
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            "Development Status :: 3 - Alpha",
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            "License :: OSI Approved :: MIT License",
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            "Programming Language :: Python",
            "Programming Language :: Python :: 2",
            "Programming Language :: Python :: 2.7",
            "Programming Language :: Python :: 3",
            "Programming Language :: Python :: 3.3",
            "Programming Language :: Python :: 3.4",
            "Topic :: Scientific/Engineering :: Bio-Informatics"
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        "description": "# Back translation\nThis library provides functions for back translation from amino acids to\nnucleotides.\n\n    from __future__ import unicode_literals\n\n    from backtranslate.backtranslate import BackTranslate\n\n    # Create a class instance, optionally giving the translation table id.\n    bt = BackTranslate()\n    # Find all substitutions that transform the codon 'TTG' into a stop codon.\n    substitutions = bt.with_dna('TGG', '*')\n\n\nSometimes we do not have access to the DNA sequence so we have to find\npossible substitutions from the amino acids directly.\n\n    # Find all substitutions that transform a Tryptophan into a stop codon.\n    substitutions = bt.without_dna('W', '*')\n\nTo find out which substitution predictions can be improved by adding codon\ninformation, use the following function.\n\n    bt.improvable()\n\nTo get substitutions in a readable format, we can use the following:\n\n    from backtranslate.util import subst_to_cds\n\n    # Transform the substitutions to CDS coordinates.\n    variants = subst_to_cds(substitutions, 12)\n\n## Command line interface\nUse the command `backtranslate` to find substitutions that explain an amino\nacid change:\n\n    $ backtranslate with_dna -o 210 data/mhv.fa - 1 Leu\n    1       A       C\n    1       A       T\n\n\nIf no reference is available, use the `without_dna` subcommand:\n\n    $ backtranslate without_dna - Asp 92 Tyr\n    274     G       T\n\n\nThe command `find_stops` finds a list of positions and substitutions that lead\nto stop codons. This list of destructive substitutions are useful when\nanalysing a pool of viral transcripts. Counting the appropriate nucleotides at\nthe given positions gives insight into how many transcripts are active.\n\n    $ backtranslate find_stops -o 210 data/mhv.fa -\n    216     A       T\n    225     A       T\n    230     C       A\n    230     C       G\n    243     A       T\n    ...",
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        "license": "MIT License",
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        "name": "backtranslate",
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