README_Danpos3.md

DANPOS3

For questions on this code, please feel free to checkout the DANPOS project forum at: https://groups.google.com/forum/#!forum/danpos

Background

This repo contains updated code from DANPOS2.

• This package was originally forked from code from danpos-2.2.2 (Jun 15 10:20) which is dependent on python 2.7
• https://sites.google.com/site/danposdoc/download/danpos-2.2.2.tgz
• For information on how to use Danpos3 commands please see the Danpos2 manual at : https://sites.google.com/site/danposdoc/ where this code originated from.

Summary

This code was written to update umap to work with Python3 and fix other bugs.

Installation

To download the repository

git clone https://github.com/sklasfeld/DANPOS3.git

To install the exact versions of the dependencies use type:

cd DANPOS3
pip install -r requirements.txt

To be able to execute these scripts from other directories easily, please set your current working directory to your $PATH variable.

Package and Library versions

• Python 3.7.6
• R version 4.0.1
• samtools 1.7 using htslib 1.7
• Python Libraries
  • rpy2 3.3.3
  • argparse 1.1
  • numpy 1.18.5
  • pysam 0.16.0.1
  • scipy 1.5.4

To test your environment for these packages, use the script print_versions.py