lkirk/ts-two-locus-beta

Beta release of two-locus code for chris

installation

This script will install the tskit branch into a local virtual environment

./local-install.sh

To use:

source ve/bin/activate
python
>>> import tskit
>>> tskit.load('path/to/your/tree/sequence')
>>> ts.ld_matrix()

To specify row / column sites (this compares the sites 0, 1 against 2, 3 -- rows are 0, 1 and columns are 2, 3):

>>> ts.ld_matrix(sites=[[0, 1], [2, 3]])

To get sites within a genomic range (half open interval):

start_pos = 2
end_pos = 4
sites = [start_pos <= s.position < end_pos for s in ts.sites()]

To test the docker script:

source ve/bin/activate
python ./docker/analysis.py --input /path/to/your/tree/sequence