diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json new file mode 100644 index 0000000..bde618a --- /dev/null +++ b/.devcontainer/devcontainer.json @@ -0,0 +1,18 @@ +{ + "image": "mcr.microsoft.com/devcontainers/base:ubuntu", + "features": { + "ghcr.io/devcontainers/features/github-cli:1": {}, + "ghcr.io/devcontainers/features/common-utils:2": {} + }, + "customizations": { + "vscode": { + "extensions": [ + "github.vscode-github-actions", + "ms-toolsai.jupyter", + "tamasfe.even-better-toml", + "julialang.language-julia" + ] + } + }, + "onCreateCommand": "bash .devcontainer/onCreate.sh" +} diff --git a/.devcontainer/julia_startup.jl b/.devcontainer/julia_startup.jl new file mode 100644 index 0000000..06be6e3 --- /dev/null +++ b/.devcontainer/julia_startup.jl @@ -0,0 +1,2 @@ +ENV["JULIA_PKG_USE_CLI_GIT"] = true +ENV["JULIA_PKG_SERVER_REGISTRY_PREFERENCE"] = "eager" diff --git a/.devcontainer/onCreate.jl b/.devcontainer/onCreate.jl new file mode 100644 index 0000000..14b6116 --- /dev/null +++ b/.devcontainer/onCreate.jl @@ -0,0 +1,10 @@ +import Pkg + +Pkg.Registry.add(Pkg.RegistrySpec(url="https://github.com/cossio/CossioJuliaRegistry.git")) +Pkg.Registry.add("General") + +Pkg.add([ + "Revise", + "Makie", + "CairoMakie" +]) diff --git a/.devcontainer/onCreate.sh b/.devcontainer/onCreate.sh new file mode 100644 index 0000000..0aa34bb --- /dev/null +++ b/.devcontainer/onCreate.sh @@ -0,0 +1,9 @@ +# install Julia +curl -fsSL https://install.julialang.org | sh -s -- --yes + +# Julia startup file +mkdir -p ~/.julia/config +cp .devcontainer/julia_startup.jl ~/.julia/config/startup.jl + +# Install Julia packages, registries, ... +/home/vscode/.juliaup/bin/julia .devcontainer/onCreate.jl \ No newline at end of file diff --git a/.gitignore b/.gitignore index dba49bf..07f647d 100644 --- a/.gitignore +++ b/.gitignore @@ -1,27 +1,13 @@ -# Files generated by invoking Julia with --code-coverage -*.jl.cov +.DS_Store +.vscode/ +.CondaPkg/ *.jl.*.cov - -# Files generated by invoking Julia with --track-allocation +*.jl.cov *.jl.mem - -# System-specific files and directories generated by the BinaryProvider and BinDeps packages -# They contain absolute paths specific to the host computer, and so should not be committed -deps/deps.jl deps/build.log +deps/deps.jl deps/downloads/ -deps/usr/ deps/src/ - -# Build artifacts for creating documentation generated by the Documenter package +deps/usr/ docs/build/ -docs/site/ - -# File generated by Pkg, the package manager, based on a corresponding Project.toml -# It records a fixed state of all packages used by the project. As such, it should not be -# committed for packages, but should be committed for applications that require a static -# environment. -Manifest.toml - -.DS_Store -.vscode/ \ No newline at end of file +docs/site/ \ No newline at end of file diff --git a/Manifest.toml b/Manifest.toml new file mode 100644 index 0000000..8b0cf0c --- /dev/null +++ b/Manifest.toml @@ -0,0 +1,1526 @@ +# This file is machine-generated - editing it directly is not advised + +julia_version = "1.9.3" +manifest_format = "2.0" +project_hash = "62699c27949cff480232055628f2fd8321bfeda8" + +[[deps.AbstractFFTs]] +deps = ["LinearAlgebra"] +git-tree-sha1 = "d92ad398961a3ed262d8bf04a1a2b8340f915fef" +uuid = "621f4979-c628-5d54-868e-fcf4e3e8185c" +version = "1.5.0" +weakdeps = ["ChainRulesCore", "Test"] + + [deps.AbstractFFTs.extensions] + AbstractFFTsChainRulesCoreExt = "ChainRulesCore" + AbstractFFTsTestExt = "Test" + +[[deps.AbstractLattices]] +git-tree-sha1 = "f35684b7349da49fcc8a9e520e30e45dbb077166" +uuid = 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0000000..1f7250a --- /dev/null +++ b/repl/logo.jl @@ -0,0 +1,42 @@ +import CairoMakie +import FASTX +import Makie +using Base: front +using LogExpFunctions: xlogx +using SequenceLogos: __example_fasta, makie_sequence_logo! +using Statistics: mean + +records = collect(FASTX.FASTA.Reader(open(__example_fasta()))) +seqs = FASTX.sequence.(records) + +NTs = "ACGU⊟" + +function onehot(s::AbstractString) + return reshape(collect(s), 1, length(s)) .== collect(NTs) +end +X = reshape(reduce(hcat, onehot.(seqs)), length(NTs), :, length(seqs)) + +p = reshape(mean(X; dims=3), size(X, 1), size(X, 2)) +H = sum(-xlogx.(p) / log(2); dims=1) +weights = p .* (log2(5) .- H) + +#weights .= mean(weights) +letters = collect(NTs) +colors = [:red, :blue, :orange, :green, :black] + + +weights = [ + 1.0 1.0; + 2.0 3.0 +] +letters = ['A'; 'C'] +colors = [:red; :blue] + +let fig = Makie.Figure() + ax = Makie.Axis(fig[1,1]; width=1000, height=200) + tmp = makie_sequence_logo!(ax, weights, letters, colors) + Makie.resize_to_layout!(fig) + fig +end + +Makie.Vec2f.(weights) diff --git a/test/aqua.jl b/test/aqua.jl new file mode 100644 index 0000000..bb3853e --- /dev/null +++ b/test/aqua.jl @@ -0,0 +1,7 @@ +import Aqua +import SequenceLogos +using Test: @testset + +@testset verbose = true "aqua" begin + Aqua.test_all(SequenceLogos; ambiguities = false) +end diff --git a/test/runtests.jl b/test/runtests.jl index 11038f7..824efeb 100644 --- a/test/runtests.jl +++ b/test/runtests.jl @@ -1,39 +1 @@ -using Test: @test -using SequenceLogos: __example_fasta, makie_sequence_logo! -using Statistics: mean -using LogExpFunctions: xlogx -import FASTX -using Base: front -import Makie -import CairoMakie - -records = collect(FASTX.FASTA.Reader(open(__example_fasta()))) -seqs = FASTX.sequence.(records) - -NTs = "ACGU⊟" - -function onehot(s::AbstractString) - return reshape(collect(s), 1, length(s)) .== collect(NTs) -end -X = reshape(reduce(hcat, onehot.(seqs)), length(NTs), :, length(seqs)) - -p = reshape(mean(X; dims=3), size(X, 1), size(X, 2)) -H = sum(-xlogx.(p) / log(2); dims=1) -weights = p .* (log2(5) .- H) - -weights .= mean(weights) - -weights = [ - 1.0 1.0; - 2.0 3.0 -] -letters = ['A'; 'C'] -colors = [:red; :blue] - -fig = Makie.Figure() -ax = Makie.Axis(fig[1,1]; width=1000, height=200) -tmp = makie_sequence_logo!(ax, weights, letters, colors) -Makie.resize_to_layout!(fig) -fig - -Makie.Vec2f.(weights) +module aqua_tests include("aqua.jl") end