Metadata-Version: 2.1
Name: pinetree
Version: 0.3.0
Summary: stochastic simulation of gene expression with site-specific translation rates
Home-page: https://github.com/clauswilke/pinetree
Author: Benjamin Jack
Author-email: benjamin.r.jack@gmail.com
License: MIT
Download-URL: https://github.com/clauswilke/pinetree/archive/v0.3.0.tar.gz
Description: ![pinetree](https://github.com/clauswilke/pinetree/blob/master/docs/pinetree-logo.png?raw=true)
        
        # pinetree 
        [![Build Status](https://travis-ci.org/clauswilke/pinetree.svg?branch=master)](https://travis-ci.org/clauswilke/pinetree)
        [![Documentation Status](https://readthedocs.org/projects/pinetree/badge/?version=latest)](http://pinetree.readthedocs.io/en/latest/?badge=latest)
        
        A flexible gene expression simulator with codon-specific translation rates.
        
        ## Requirements
        
        Pinetree requires Python, CMake, and a modern C++ compiler. Python 3 is recommended.
        
        ## Installation
        
        To install the latest stable version of pinetree from PyPI, run the following:
        
        ```
        pip3 install cmake  # CMake must be installed before installing pinetree
        pip3 install pinetree 
        ```
        
        The latest development build may be installed from GitHub as follows:
        
        ```
        pip3 install cmake   
        git clone https://github.com/benjaminjack/pinetree.git
        cd pinetree
        pip3 install .
        ```
        
        ## Documentation
        
        Full documentation is available [here](http://pinetree.readthedocs.io/).
        
        You may also build the documentation from the source code. Building the documentation requires sphinx.
        
        ```
        pinetree/setup.py build_sphinx
        ```
        
        ## Reproducing plots from manuscript
        
        This repository contains scripts to reproduce the simulations and plots from the manuscript that describes Pinetree. R and the R packages `cowplot`, `readr`, `dplyr`, and `stringr` are required to generate plots. Run the following to reproduce the plots from the manuscript:
        
        ```
        python3 ./examples/three_genes.py
        python3 ./examples/three_genes_recoded.py
        Rscript plots.R
        ```
        
        To simulate a bacteriophage T7 infection, run the following script.
        
        ```
        # WARNING: This simulation takes approximately 2-3 hours to complete
        python3 ./examples/phage_model.py
        ```
        
        
        
        
Keywords: gene,codon,transcription,translation,biology,stochastic
Platform: UNKNOWN
Description-Content-Type: text/markdown
