mafViper 0.1

A Python package for processing, analyzing and visualizing MAF files.

mafViper Documentation

A python package for reading, analyzing and visualizing mutation annotation files

Features

• Load and validate MAF files as pandas DataFrames.

• MAF processsing and classification tools (i.e synonymous vs. non-synonymous)

• Merge multiple MAF files into a single DF.

• Generate mutation summary plots, and Ti/Tv analyses.

Current Functions

• read_maf:

  • Loads a maf file into the env as a pandas df and validates columns
  • allows for somatic vs. non-somatic selection with useAll parameter

• classify_variants:

  • Seperates variants into synonymous and non-synonmous categories
  • discard_synonymous (default True) allows you to drop synonymous mutations from dataframe

• merge_mafs:

  • merges a list of maf files into one maf
  • discard_synonymous parameter allows you to drop synonymous mutations after merge

• get_titv:

  • Classifies SNVs into Ti/Tv and returns a summary df for plotting and analyses
  • Summary df contains SNV class, Raw counts by class, and fractional proportions of each class

• get_maf_summary:

  • creates a set of maf summary analysis plots and pdf per user input
  • Top Mutated Genes plot (default 10)
  • Stacked Bar chart for Variants Per Sample (add stat line- default median)
  • Variant Classifaction Summary Plot
  • Boxplot of variant classes
  • SNV Class summary plot(Ti/Tv data visualization)
  • Variant Type summary plot (SNP, INS, DEL, etc)

Installation

'''bash

pip install mafViper