Metadata-Version: 1.2
Name: freqgen
Version: 0.1.0
Summary: Generate DNA sequences with specified amino acid, codon, and k-mer frequencies.
Home-page: https://github.com/Lab41/freqgen
Author: Benjamin Lee
Author-email: benjamindlee@me.com
License: MIT
Description: 
        # Freqgen
        
        <p align ="center">
        <img src='https://raw.githubusercontent.com/Lab41/freqgen/master/logo/Freqgen2-01_icon_only.png' height="150">
        </p>
        
        [![Build Status](https://travis-ci.org/Lab41/freqgen.svg?branch=master)](https://travis-ci.org/Lab41/freqgen) [![Documentation Status](https://readthedocs.org/projects/freqgen/badge/?version=latest)](https://freqgen.readthedocs.io/en/latest/?badge=latest) [![CodeFactor](https://www.codefactor.io/repository/github/lab41/freqgen/badge)](https://www.codefactor.io/repository/github/lab41/freqgen)
        
        
        Freqgen is a tool to generate coding DNA sequences with specified amino acid
        usage frequencies or sequence, GC content, codon usage bias, and/or *k*-mer
        usage bias. To accomplish this, Freqgen uses genetic algorithms to efficiently
        search the solution space of possible DNA sequences to find ones that most
        closely match the desired parameters.
        
        ## Features
        
        - CLI and Python API
        - Can simultaneously match multiple DNA statistics
        - Built-in visualization utility
        - Supports several fitness metrics (and you can bring your own!)
        
        ## 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:
        
        1. 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.fna -o new_sequence.faa -l LENGTH
        
        2. Create a YAML file containing *k*-mer frequencies for the amino acid
        sequence's DNA to have:
        
                $ freqgen featurize reference_sequences.fna -k INT -o reference_freqs.yaml
        
        3. Generate the DNA sequence coding for the amino acid sequence:
        
                $ freqgen -t reference_freqs.yaml -s new_sequence.faa -v -o optimized.fna
        
        4. Visualize the results of the optimization (*optional*):
        
                $ freqgen visualize --target reference_freqs.yaml --optimized optimized.fna
        
        ## Documentation
        
        Read the full docs over at
        [freqgen.readthedocs.io](http://freqgen.readthedocs.io).
        
        ## Citation
        
        To be determined!
        
Platform: UNKNOWN
Classifier: License :: OSI Approved :: Apache Software License
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: Implementation :: CPython
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Python: >=3.5.0
