lanctools 0.1.1

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lanctools

Tools for working with local ancestry data in the .lanc file format. This package contains two main components:

1. A function (and corresponding CLI) for converting FLARE and RFMix files to the .lanc format
2. A LancData class with methods for fast querying of local ancestry and local ancestry-masked genotypes

Installation

pip install lanctools

Quickstart

To load and query local ancestry data for a set of variants::

import numpy as np

from lanctools import LancData

ld = LancData(
    plink_prefix="chr1",
    lanc_file="chr1.lanc",
    ancestries=["YRI", "CEU"]
)

idx_var = np.arange(100, dtype=np.uint32)

lanc = ld.get_lanc(idx_var) # (N, 100, 2): phased local ancestry
geno = ld.get_geno(idx_var) # (N, 100, 2): phased genotypes
lanc_geno = ld.get_lanc_geno(idx_var) # (N, 100, len(ancestries))

To convert a FLARE (or RFMix) local ancestry file to .lanc:

from lanctools import convert_to_lanc

convert_to_lanc(
    file="chr1.anc.vcf.gz",
    file_fmt="FLARE",
    plink_prefix="chr1",
    output="chr1.lanc"
)

To perform the above conversion using the CLI tool:

lanctools convert-flare --file chr1.anc.vcf.gz --plink_prefix chr1 --output chr1.lanc