Metadata-Version: 1.1
Name: library-simulator
Version: 0.1
Summary: Python software package for simulating random mutagenesis experiments
Home-page: https://github.com/harmslab/library_simulator
Author: Michael J. Harms
Author-email: harmsm@gmail.com
License: UNKNOWN
Download-URL: https://github.com/harmslab/library_simulator/tarball/0.1
Description: =================
        Library Simulator
        =================
        
        Library simulator is a python package for generating random mutagenesis
        libraries given a nucleotide sequence and error-prone polymerase. 
        
        Examples
        ========
        
        Create a library
        ----------------
        
        .. code:: python
        
            from library_simulator import LibrarySimulator
            lib = LibrarySimulator("example.fasta",mutation_spectrum="published")
            lib.simulate(num_samples=10,mutation_rate=2)
            lib.clones
        
        .. image:: example/output-table.png
        
        - **aa**: amino acid changes (:code:`*`: new stop codon)
        - **base**: base changes (:code:`-` and :code:`+` are insertions and deletions)
        - **num**: total number of amino acid changes (could be a huge number if there is
          an early stop or indel)
        - **indel**: whether or not there is an indel
        - **stop**: whether or not there is new stop codon
        - **start**: whether or not the real start codon was messed up
        
        Find the frequencies of classes of mutants versus mutation rate
        ---------------------------------------------------------------
        
        .. code:: python
        
            from library_simulator import LibrarySimulator, util
            lib = LibrarySimulator("example.fasta",mutation_spectrum="published")
            f_v_r = util.freq_vs_mutation_rate(lib,num_samples=10000)
            util.plot_freq_vs_mutation_rate(f_v_r)
        
        .. image:: example/mutation-rate.png
        
        See :code:`example/examples.ipynb` for more functionality.
        
        Installation
        ============
        
        .. code:: python
        
            pip install library_simulator
        
        
        Assumptions
        ===========
        
        - The number of mutations per clone is determined by a Poisson process.
        - The sites mutated are independent within a clone and between clones
        - The probability of each possible mutation (A->T, G->C, etc.) is determined
          by the enzyme, not the sequence.  The profiles for different enzymes
          are found in: :code:`library_simulator/mutation_spectra`
        
Platform: UNKNOWN
Classifier: Programming Language :: Python
