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    "info": {
        "author": "Michael J. Harms",
        "author_email": "harmsm@gmail.com",
        "bugtrack_url": null,
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        "description": "=================\nLibrary Simulator\n=================\n\nLibrary simulator is a python package for generating random mutagenesis\nlibraries given a nucleotide sequence and error-prone polymerase. \n\nExamples\n========\n\nCreate a library\n----------------\n\n.. code:: python\n\n    from library_simulator import LibrarySimulator\n    lib = LibrarySimulator(\"example.fasta\",mutation_spectrum=\"published\")\n    lib.simulate(num_samples=10,mutation_rate=2)\n    lib.clones\n\n.. image:: example/output-table.png\n\n- **aa**: amino acid changes (:code:`*`: new stop codon)\n- **base**: base changes (:code:`-` and :code:`+` are insertions and deletions)\n- **num**: total number of amino acid changes (could be a huge number if there is\n  an early stop or indel)\n- **indel**: whether or not there is an indel\n- **stop**: whether or not there is new stop codon\n- **start**: whether or not the real start codon was messed up\n\nFind the frequencies of classes of mutants versus mutation rate\n---------------------------------------------------------------\n\n.. code:: python\n\n    from library_simulator import LibrarySimulator, util\n    lib = LibrarySimulator(\"example.fasta\",mutation_spectrum=\"published\")\n    f_v_r = util.freq_vs_mutation_rate(lib,num_samples=10000)\n    util.plot_freq_vs_mutation_rate(f_v_r)\n\n.. image:: example/mutation-rate.png\n\nSee :code:`example/examples.ipynb` for more functionality.\n\nInstallation\n============\n\n.. code:: python\n\n    pip install library_simulator\n\n\nAssumptions\n===========\n\n- The number of mutations per clone is determined by a Poisson process.\n- The sites mutated are independent within a clone and between clones\n- The probability of each possible mutation (A->T, G->C, etc.) is determined\n  by the enzyme, not the sequence.  The profiles for different enzymes\n  are found in: :code:`library_simulator/mutation_spectra`\n\n\n",
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        "name": "library-simulator",
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        "summary": "Python software package for simulating random mutagenesis experiments",
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