library-simulator

Python software package for simulating random mutagenesis experiments

Project description

Library simulator is a python package for generating random mutagenesis libraries given a nucleotide sequence and error-prone polymerase.

Examples

Create a library

from library_simulator import LibrarySimulator
lib = LibrarySimulator("example.fasta",mutation_spectrum="published")
lib.simulate(num_samples=10,mutation_rate=2)
lib.clones

aa: amino acid changes (*: new stop codon)
base: base changes (- and + are insertions and deletions)
num: total number of amino acid changes (could be a huge number if there is an early stop or indel)
indel: whether or not there is an indel
stop: whether or not there is new stop codon
start: whether or not the real start codon was messed up

Find the frequencies of classes of mutants versus mutation rate

from library_simulator import LibrarySimulator, util
lib = LibrarySimulator("example.fasta",mutation_spectrum="published")
f_v_r = util.freq_vs_mutation_rate(lib,num_samples=10000)
util.plot_freq_vs_mutation_rate(f_v_r)

See example/examples.ipynb for more functionality.

Installation

pip install library_simulator

Assumptions

The number of mutations per clone is determined by a Poisson process.
The sites mutated are independent within a clone and between clones
The probability of each possible mutation (A->T, G->C, etc.) is determined by the enzyme, not the sequence. The profiles for different enzymes are found in: library_simulator/mutation_spectra

Project details

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0.1

Jun 3, 2019

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