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MutagenesisForge - A framework for modeling codon-level mutational biases and d_N/d_S selection

Overview

MutagenesisForge is a codon-level simulation software designed to calculate dN/dS null models built on user-inputed data for comparative genomic analyses. It allows for the construction of input data-built codon-specific null models of evolution designed to offer data complementary to d_N/d_Svalues produced from popular calculator tools. With MutagenesisForge, simulation functionality is brought to the user through one tool. The exhaust and context methods are available both through the MutagenesisForge Python package or as a command line interface.

Additionally, MutagenesisForge supports mutation modeling according to popular substitution models through the MutationModel object.

Installation

pip install MutagenesisForge

Exhaustive Codon Model

Example CLI Usage

MutagenesisForge exhaustive --flags

Example Python Usage

import MutagenesisForge as mf

exhaust_dNdS = mf.exhaustive(
  path='example.fa,
  bed_path='example.bed',
  model='K2P',
  alpha=2.0,
  beta=1.0,
  gamma=0.5
)

Context Codon Model

Example CLI Usage

MutagenesisForge context --flags

Example Python Usage

import MutagenesisForge as mf

context_dNdS = mf.context(
  vcf='example.vcf'
  fasta='example.fa',
  bed='example.bed',
  context_model='codon',
  model='JC69',
  gamma=0.5
)

MutationModel Object

Example Usage

import MutagenesisForge as mf

# Initialize the MutationModel object using K2P substitution model
K2P_model = mf.MutationModel(
  model_type='K2P',
  alpha=2.0
  gamma=1.0
  gamma=0.5
)

# See the probability for an adenine to mutation to a guanine according to the mutation model
mut_probs = K2P_model.get_mutation_probability(
  base='A',
  mutated_base='G'
)

# Simulate a mutation to an adenine according to the mutation model
mutated_base = K2P_model.mutate(
  base = 'A'
)