haplopy 0.0.2

Haplotype reconstruction from unphased genotypes

HaploPy – Haplotype estimation and phasing in Python

This package contains tools for estimating haplotype (or allele list) frequencies in a population using measurements of unphased genotype data, that is, phenotypes.

Introduction

In layman terms, a phenotype is defined as an observation of two-allele sets over multiple gene loci:

    Aa ––––––– Bb ––––––– Cc
    |          |          |
  locus 1    locus 2    locus 3

Note that the above datum doesn't reveal what are the exact haplotype (allele sequence) pair behind the phenotype. Possible parent haplotype pairs that could result into the above phenotype are given by

(ABC, abc), (aBC, Abc), (AbC, aBc), (abC, ABc)

In other words, the mapping that maps a haplotype pair to a phenotype is defined by the example

(Abc, aBC) => (Aa, Bb, Cc)

and so on. Note that each item in the phenotype is a set of two alleles where the order doesn't matter.

Problem: Suppose that we have a set of phenotype observations from a large population of N individuals. For each individual phenotype we would like to estimate what are the most probable haplotype pair that resulted into the phenotype. The main ingredient of solution is the estimation of individual haplotype frequencies in the population

Installation

The package is found in PyPi.

pip install haplopy

Examples

Estimate haplotype frequencies

Simulate dataset using a prescribed haplotype probabilities and a multinomial distribution model.

import haplopy as hp


p_haplotypes = {
    ("A", "B", "C"): 0.34,
    ("a", "B", "c"): 0.20,
    ("a", "B", "C"): 0.13,
    ("a", "b", "c"): 0.23,
    ("A", "b", "C"): 0.10
}

phenotypes = hp.multinomial.Model(p_haplotypes).random(100)

fig = hp.plot.plot_haplotypes(p_haplotypes)
fig = hp.plot.plot_phenotypes(phenotypes)

Pretend that we don't know the underlying haplotype distribution and let's try to estimate it.

model = hp.multinomial.Model().fit(phenotypes)
fig = hp.plot.plot_haplotypes(
    model.p_haplotypes,
    thres=1.0e-6  # Hide probabilities smaller than this
)

To-be-added features

• TODO Phasing of unphased phenotypes given a haplotype frequency model
• TODO Imputation of missing locus measurements