PonyTools

Tools for analyzing Variant (VCF) data and the MNEc Affymetrix SNP Chip

Inlcudes python classes for:

• VCFs
• Axiom Genotype Calls
• FASTA files
• VCF style variants

Includes command line tools to:

• Convert AxiomCalls to VCFs
• Calculate Concordance between VCF Files
• Calculate Precision and Recall using different scores between a test VCF and a reference VCF
• Plot various summary statistics from VCF files
• Calculate the Di statistic using VCF files

Installation

Ponytool was developed using python 3.4

Ponytools is available using the populat python package manager pip Using pip, installing ponytools is as easy as:

pip install ponytools

We recommend installing ponytools in an virtual environement

We love virtualenvwrapper

Otherwise, requirements for ponytools include:

  matplotlib>=1.4.3                                                    
  pandas>=0.16                                                        
  ipython>=4.1.2                                                       
  scipy>=0.17.0                                                     
  ipdb>=0.8 

after these packages are installed, you should be able to:

$ git clone https://github.com/schae234/PonyTools.git
$ cd PonyTools
$ python3 setup.py install --user