openmendel/admixture.jl

Julia wrapper of the ADMIXTURE program for estimating ancestry

ADMIXTURE.jl

Documentation	Build Status	Code Coverage

ADMIXTURE.jl is a Julia wrapper of the popular ADMIXTURE program for estimating ancestry in a model-based manner from large autosomal SNP genotype data sets.

The methodology is described in following papers:

1. D Alexander, J Novembre, and K Lange. (2009) Fast model-based estimation of ancestry in unrelated individuals, Genome Research, 19(9):1655–1664. https://dx.doi.org/10.1101/gr.094052.109

2. D Alexander and K Lange. (2011) Enhancements to the ADMIXTURE algorithm for individual ancestry estimation. BMC Bioinformatics, 12:246. https://doi.org/10.1186/1471-2105-12-246

3. S Shringarpure, C Bustamante, K Lange, and D Alexander. (2016) Efficient analysis of large datasets and sex bias with ADMIXTURE. BMC Bioinformatics 17:218. https://doi.org/10.1186/s12859-016-1082-x

ADMIXTURE.jl requires Julia v1.3 or later. See documentation for usage. It is not yet registered and can be installed, in the Julia Pkg mode, by

(@v1.5) Pkg> add https://github.com/OpenMendel/ADMIXTURE.jl

The original ADMIXTURE software thus ADMIXTURE.jl only support Linux and MacOS.

As a quick example, suppose a set of PLINK files hapmap3.bed, hapmap3.bim, hapmap3.fam are available in the current directory. Then

P, Q = admixture("hapmap3.bed", 3)

returns the P matrix (allele frequencies of the inferred ancestral populations) and the Q matrix (the ancestry fractions). The output files by ADMIXTURE are saved in the working directory.

For more details, check the documentation.

admixture.jl's Issues

Cannot install the package on my M1 laptop with macOS Ventura 13.2.1

I am trying to install the package on my M1 personal laptop with macOS Ventura 13.2.1, and I keep getting the following errors :

ERROR: LoadError: Cannot locate artifact 'ADMIXTURE' for aarch64-apple-darwin-libgfortran5-cxx11-julia_version+1.8.5 in '/Users/julienst-pierre/.julia/packages/ADMIXTURE/XL2Kg/Artifacts.toml'
Stacktrace:
[1] error(s::String)
@ Base ./error.jl:35
[2] artifact_slash_lookup(name::String, artifact_dict::Dict{String, Any}, artifacts_toml::String, platform::Base.BinaryPlatforms.Platform)
@ Artifacts /Applications/Julia-1.8.app/Contents/Resources/julia/share/julia/stdlib/v1.8/Artifacts/src/Artifacts.jl:609
[3] var"@artifact_str"(source::LineNumberNode, module::Module, name::Any, platform::Any)
@ Artifacts /Applications/Julia-1.8.app/Contents/Resources/julia/share/julia/stdlib/v1.8/Artifacts/src/Artifacts.jl:679
[4] var"@artifact_str"(source::LineNumberNode, module::Module, name::Any)
@ Artifacts /Applications/Julia-1.8.app/Contents/Resources/julia/share/julia/stdlib/v1.8/Artifacts/src/Artifacts.jl:642
[5] include
@ ./Base.jl:419 [inlined]
[6] include_package_for_output(pkg::Base.PkgId, input::String, depot_path::Vector{String}, dl_load_path::Vector{String}, load_path::Vector{String}, concrete_deps::Vector{Pair{Base.PkgId, UInt64}}, source::Nothing)
@ Base ./loading.jl:1554
[7] top-level scope
@ stdin:1
in expression starting at /Users/julienst-pierre/.julia/packages/ADMIXTURE/XL2Kg/src/ADMIXTURE.jl:9
in expression starting at /Users/julienst-pierre/.julia/packages/ADMIXTURE/XL2Kg/src/ADMIXTURE.jl:1
in expression starting at stdin:1

ERROR: Failed to precompile ADMIXTURE [354e233f-a9b1-4b8f-922c-9a29fc289231] to /Users/julienst-pierre/.julia/compiled/v1.8/ADMIXTURE/jl_W2ohS5.
Stacktrace:
[1] error(s::String)
@ Base ./error.jl:35
[2] compilecache(pkg::Base.PkgId, path::String, internal_stderr::IO, internal_stdout::IO, keep_loaded_modules::Bool)
@ Base ./loading.jl:1707
[3] compilecache
@ ./loading.jl:1651 [inlined]
[4] _require(pkg::Base.PkgId)
@ Base ./loading.jl:1337
[5] _require_prelocked(uuidkey::Base.PkgId)
@ Base ./loading.jl:1200
[6] macro expansion
@ ./loading.jl:1180 [inlined]
[7] macro expansion
@ ./lock.jl:223 [inlined]
[8] require(into::Module, mod::Symbol)
@ Base ./loading.jl:1144