Haplostats

Find unique haplotypes, fields for recombination and subset sharing.

Installation

Haplostats is available on PyPI. You can install it through pip:

pip install itaxotools-haplostats

Usage

In Python, import and instantiate HaploStats:

from itaxotools.haplostats import HaploStats
stats = HaploStats()

Add your data one entry at a time. Each entry is represented by its subset tag, plus a list of associated sequences. These are usually different alleles of the same specimen:

# Two specimens of different species, with two alleles each.
# There are three haplotypes in total. There is a single field
# for recombination (FFR), as the specimens are connected through
# a common sequence: 'ACT'.

stats.add('mysteriosa', ['ACT', 'ACC'])
stats.add('enigmatica', ['ACT', 'ATT'])

After adding all entries, you are ready to analyze the dataset:

haplotypes = stats.get_haplotypes()
fors = stats.get_fields_for_recombination()

common_haplotypes = stats.get_haplotypes_shared_between_subsets()
common_fors = stats.get_fields_for_recombination_shared_between_subsets()

For a more detailed look at the available methods, please have a look at the example script.