Metadata-Version: 1.2
Name: freqgen
Version: 0.1
Summary: Generate sequences
Home-page: https://github.com/Benjamin-Lee/seqgen
Author: Benjamin Lee
Author-email: benjamindlee@me.com
License: MIT
Description: 
        Freqgen
        =======
        
        |Build Status| |Cov| |CodeFactor| |Docs|
        
        Freqgen is a tool to generate coding DNA sequences with specified GC content,
        amino acid usage, codon usage bias, and *k*-mer usage bias. Freqgen uses genetic
        algorithms to efficiently search the solution space of possible DNA sequences to
        find sequences that most closely match the desired parameters.
        
        Features
        --------
        
        - Supports both CLI and Python module usage
        - Thoroughly documented with examples
        - Leverages NumPy for C optimized number crunching
        - Can simultaneously match multiple DNA statistics
        
        Installation
        ------------
        
        Simply run::
        
        $ pip install freqgen
        
        Or, to get the latest (but not necessarily stable) development version::
        
        $ pip install git+https://github.com/Lab41/freqgen.git
        
        Five-second CLI tutorial
        ------------------------
        
        The basic flow of Freqgen can be summarized in three steps.
        
        #. Generate a new amino acid sequence based on the amino acid usage profile of reference sequences. If you already have a specific amino acid sequence in mind (*i.e* for synthetic biology uses), skip this step::
        
            $ freqgen aa reference_sequences.fasta -o new_sequence.fasta -l LENGTH
        
        #. Create a YAML file containing *k*-mer frequencies for the amino acid sequence's DNA to have::
        
            $ freqgen featurize reference_sequences.fasta -k INT -o reference_sequences.yaml
        
        #. Generate the DNA sequence coding for the amino acid sequence::
        
            $ freqgen -f reference_sequences.yaml -s new_sequence.fasta -v
        
        Documentation
        -------------
        
        Read the docs over at `freqgen.readthedocs.io <http://freqgen.readthedocs.io>`_.
        
        Citation
        --------
        
        To be determined.
        
        
        .. |Build Status| image:: https://travis-ci.org/Lab41/freqgen.svg?branch=master
           :target: https://travis-ci.org/Lab41/freqgen
        
        .. |Cov| image:: https://codecov.io/gh/Lab41/freqgen/branch/master/graph/badge.svg
           :target: https://codecov.io/gh/Lab41/freqgen
        
        .. |Docs| image:: http://readthedocs.org/projects/freqgen/badge/?version=latest
           :target: http://freqgen.readthedocs.io/en/latest/?badge=latest
        
        .. |CodeFactor| image:: https://www.codefactor.io/repository/github/Lab41/freqgen/badge
           :target: https://www.codefactor.io/repository/github/Lab41/freqgen/
        
Platform: UNKNOWN
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: Implementation :: CPython
Classifier: Programming Language :: Python :: Implementation :: PyPy
Requires-Python: >=3.4.0
