项目作者: clauswilke

项目描述 :
🌲 a flexible gene expression simulator with codon-specific translation rates
高级语言: C++
项目地址: git://github.com/clauswilke/pinetree.git
创建时间: 2017-01-25T17:36:36Z
项目社区:https://github.com/clauswilke/pinetree

开源协议:MIT License

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pinetree

pinetree

Build Status
Documentation Status

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:

  1. pip3 install cmake # CMake must be installed before installing pinetree
  2. pip3 install pinetree

The latest development build may be installed from GitHub as follows:

  1. pip3 install cmake
  2. git clone https://github.com/benjaminjack/pinetree.git
  3. cd pinetree
  4. pip3 install .

Documentation

Full documentation is available here.

You may also build the documentation from the source code. Building the documentation requires sphinx.

  1. 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:

  1. python3 ./examples/three_genes.py
  2. python3 ./examples/three_genes_recoded.py
  3. Rscript plots.R

To simulate a bacteriophage T7 infection, run the following script.

  1. # WARNING: This simulation takes approximately 2-3 hours to complete
  2. python3 ./examples/phage_model.py