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Update for compatibility with Microbiome 0.9 (breaking) (#99)
* add Retest * bump version * fix indexing breaks * fix lack of inline tests
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@@ -4,20 +4,22 @@ keywords = ["microbiology", "microbiome", "biology", "metagenomics"] | |
| license = "MIT" | ||
| desc = "Convenience functions for working with the bioBakery" | ||
| authors = ["kescobo <[email protected]>", "annelle-abatoni <[email protected]>", "anikaluo <[email protected]>", "Vanja Klepac-Ceraj <[email protected]>"] | ||
| version = "0.5.6" | ||
| version = "0.6" | ||
|
|
||
| [deps] | ||
| CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b" | ||
| Conda = "8f4d0f93-b110-5947-807f-2305c1781a2d" | ||
| Microbiome = "3bd8f0ae-a0f2-5238-a5af-e1b399a4940c" | ||
| ReTest = "e0db7c4e-2690-44b9-bad6-7687da720f89" | ||
| Reexport = "189a3867-3050-52da-a836-e630ba90ab69" | ||
| SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" | ||
| Tables = "bd369af6-aec1-5ad0-b16a-f7cc5008161c" | ||
|
|
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| [compat] | ||
| CSV = "0.8, 0.9, 0.10" | ||
| Conda = "1.5" | ||
| Microbiome = "0.8, 0.9" | ||
| Microbiome = "0.9" | ||
| Reexport = "0.2, 1" | ||
| ReTest = "0.3" | ||
| Tables = "1.2.1" | ||
| julia = "1.6" | ||
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,117 @@ | ||
| module BiobakeryUtilsTests | ||
|
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||
| using Random | ||
| using ReTest | ||
| using BiobakeryUtils | ||
| using BiobakeryUtils.Conda | ||
| using SparseArrays | ||
| using DelimitedFiles | ||
| using CSV | ||
|
|
||
| isdir(Conda.bin_dir(:BiobakeryUtils)) || BiobakeryUtils.install_deps() | ||
| ENV["PATH"] = ENV["PATH"] * ":" * Conda.bin_dir(:BiobakeryUtils) | ||
|
|
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| @testset "CLI" begin | ||
| @testset "Utilities" begin | ||
| cmd = ["thing", "foo_bar"] | ||
| cmd2 = copy(cmd) | ||
|
|
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| BiobakeryUtils.add_cli_kwargs!(cmd, Dict(:some_thing=> "foo", :bool=> true)) | ||
| @test all(cmd .== ["thing", "foo_bar", "--some_thing", "foo", "--bool"]) | ||
| BiobakeryUtils.add_cli_kwargs!(cmd2, Dict(:some_thing=> "foo", :bool=> true); optunderscores=false) | ||
| @test all(cmd2 .== ["thing", "foo_bar", "--some-thing", "foo", "--bool"]) | ||
| end | ||
|
|
||
| @testset "Metaphlan" begin | ||
| @test BiobakeryUtils.check_for_install("metaphlan") |> isnothing | ||
| @test BiobakeryUtils.check_for_install("merge_metaphlan_tables.py") |> isnothing | ||
|
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| @test metaphlan("", ""; help=true).exitcode == 0 | ||
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| profiles = filter(f-> contains(f, "_profile.tsv"), readdir(joinpath(@__DIR__, "files/metaphlan"), join=true)) | ||
| @test metaphlan_merge(profiles, joinpath(@__DIR__, "files/metaphlan/merged_abundance_table.tsv")).exitcode == 0 | ||
| end | ||
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| @testset "Humann" begin | ||
| @test BiobakeryUtils.check_for_install("humann") |> isnothing | ||
| @test BiobakeryUtils.check_for_install("humann_rename_table") |> isnothing | ||
| @test BiobakeryUtils.check_for_install("humann_renorm_table") |> isnothing | ||
| @test BiobakeryUtils.check_for_install("humann_join_tables") |> isnothing | ||
| @test BiobakeryUtils.check_for_install("humann") |> isnothing | ||
| @test humann("", ""; help=true).exitcode == 0 | ||
|
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||
| end | ||
| end | ||
|
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||
| @testset "Metaphlan" begin | ||
| profile_1 = metaphlan_profile(joinpath(@__DIR__, "files/metaphlan/SRS014464-Anterior_nares_profile.tsv"); sample="SRS014464") | ||
| @test profile_1["k__Bacteria", "SRS014464"] == 100.0 | ||
| @test profile_1["o__Pseudomonadales", "SRS014464"] == 97.28734 | ||
| @test size(profile_1) == (13, 1) | ||
| profile_2 = metaphlan_profile(joinpath(@__DIR__, "files/metaphlan/SRS014459-Stool_profile.tsv"), 3) | ||
| @test size(profile_2) == (2, 1) | ||
| @test profile_2["p__Firmicutes", "SRS014459-Stool_profile"] == 68.90167 | ||
| profile_3 = metaphlan_profile(joinpath(@__DIR__, "files/metaphlan/SRS014464-Anterior_nares_profile.tsv"), :phylum) | ||
| @test size(profile_3) == (2, 1) | ||
| @test profile_3["p__Proteobacteria", 1] == 97.28734 | ||
|
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| merge_profile_1 = metaphlan_profiles(joinpath(@__DIR__, "files/metaphlan/merged_abundance_table.tsv"); samplestart=3) | ||
| @test size(merge_profile_1) == (62, 6) | ||
| @test merge_profile_1["g__Moraxella", 5] == 97.28734 | ||
| merge_profile_2 = metaphlan_profiles(joinpath(@__DIR__, "files/metaphlan/merged_abundance_table.tsv"), :family; samplestart=3) | ||
| @test size(merge_profile_2) == (13, 6) | ||
| @test merge_profile_2["f__Micrococcaceae", "SRS014464-Anterior_nares"] == 0.0 | ||
| merge_profile_3 = metaphlan_profiles(joinpath(@__DIR__, "files/metaphlan/merged_abundance_table.tsv"), 7; samplestart=3) | ||
| @test size(merge_profile_3) == (16, 6) | ||
| @test merge_profile_3["s__Haemophilus_haemolyticus", 3] == 1.35528 | ||
| CSV.write(joinpath(@__DIR__, "files/metaphlan/merged_abundance_table2.csv"), merge_profile_1) | ||
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| profiles = filter(f-> contains(f, "_profile.tsv"), readdir(joinpath(@__DIR__, "files/metaphlan"), join=true)) | ||
| @test_throws ArgumentError metaphlan_profiles(profiles; samples = ["sample1"]) | ||
| multi_profile_1 = metaphlan_profiles(profiles; samples=["sample$i" for i in 1:length(profiles)]) | ||
| @test abundances(multi_profile_1) == abundances(metaphlan_profiles(profiles)) | ||
| @test size(multi_profile_1) == (62, 6) | ||
| @test multi_profile_1["p__Firmicutes", "sample1"] == 68.90167 | ||
| multi_profile_2 = metaphlan_profiles(profiles, 3; samples=["sample$i" for i in 1:length(profiles)]) | ||
| @test abundances(multi_profile_2) == abundances(metaphlan_profiles(profiles, :class)) | ||
| @test size(multi_profile_2) == (6,6) | ||
| @test multi_profile_2["c__Bacteroidia", "sample1"] == 31.09833 | ||
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| taxstring = "k__Archaea|p__Euryarchaeota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter|s__Methanobrevibacter_smithii" | ||
| taxa = parsetaxa(taxstring) | ||
| @test length(taxa) == 7 | ||
| @test parsetaxon(taxstring, 1) == Taxon("Archaea", :kingdom) | ||
| @test parsetaxon(taxstring, :family) == Taxon("Methanobacteriaceae", :family) | ||
| @test parsetaxon(taxstring) == Taxon("Methanobrevibacter_smithii", :species) | ||
| @test_throws ArgumentError parsetaxon(taxstring, 8) | ||
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| @test parsetaxon("k__Archaea|p__Euryarchaeota|c__Methanobacteria", 2) == Taxon("Euryarchaeota", :phylum) | ||
| @test parsetaxon("k__Archaea|p__Euryarchaeota|c__Methanobacteria") == Taxon("Methanobacteria", :class) | ||
| end | ||
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| @testset "HUMAnN" begin | ||
| p1 = humann_profile(joinpath(@__DIR__, "files/humann/single_1.tsv")) | ||
| p2 = humann_profile(joinpath(@__DIR__, "files/humann/single_2.tsv")) | ||
| @test p1 isa CommunityProfile | ||
| @test size(p1) == (560, 1) | ||
| @test samplenames(p1) == ["single_1"] | ||
| @test samplenames(humann_profile(joinpath(@__DIR__, "files/humann/single_1.tsv"); sample = "sample1")) == ["sample1"] | ||
| @test samplenames(humann_profile(joinpath(@__DIR__, "files/humann/single_1.tsv"); sample = MicrobiomeSample("sample1"))) == ["sample1"] | ||
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| @test all(f-> !hastaxon(f), features(p1)) # unstratified | ||
| @test all(f-> !occursin('|', name(f)), features(p1)) | ||
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| pj = humann_profiles(joinpath(@__DIR__, "files/humann/joined.tsv")) | ||
| @test size(pj) == (560, 2) | ||
| @test isempty(setdiff(features(pj), features(commjoin(p1, p2)))) | ||
| @test samplenames(pj) == samplenames(commjoin(p1, p2)) | ||
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| pj_strat = humann_profiles(joinpath(@__DIR__, "files/humann/joined.tsv"); stratified = true) | ||
| @test size(pj_strat) == (1358, 2) | ||
| @test !isempty(setdiff(features(pj_strat), features(pj))) | ||
| @test isempty(setdiff(featurenames(pj_strat), featurenames(pj))) | ||
| @test isempty(setdiff(features(filter(!hastaxon, pj_strat)), features(pj))) | ||
| CSV.write(joinpath(@__DIR__, "files/humann/joined_roundtrip.tsv"), pj_strat; delim='\t') | ||
| end | ||
|
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||
| end # module |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,114 +1,6 @@ | ||
| using Random | ||
| using Test | ||
| using BiobakeryUtils | ||
| using BiobakeryUtils.Conda | ||
| using SparseArrays | ||
| using DelimitedFiles | ||
| using CSV | ||
|
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||
| isdir(Conda.bin_dir(:BiobakeryUtils)) || BiobakeryUtils.install_deps() | ||
| ENV["PATH"] = ENV["PATH"] * ":" * Conda.bin_dir(:BiobakeryUtils) | ||
|
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| @testset "CLI" begin | ||
| @testset "Utilities" begin | ||
| cmd = ["thing", "foo_bar"] | ||
| cmd2 = copy(cmd) | ||
|
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| BiobakeryUtils.add_cli_kwargs!(cmd, Dict(:some_thing=> "foo", :bool=> true)) | ||
| @test all(cmd .== ["thing", "foo_bar", "--some_thing", "foo", "--bool"]) | ||
| BiobakeryUtils.add_cli_kwargs!(cmd2, Dict(:some_thing=> "foo", :bool=> true); optunderscores=false) | ||
| @test all(cmd2 .== ["thing", "foo_bar", "--some-thing", "foo", "--bool"]) | ||
| end | ||
|
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| @testset "Metaphlan" begin | ||
| @test BiobakeryUtils.check_for_install("metaphlan") |> isnothing | ||
| @test BiobakeryUtils.check_for_install("merge_metaphlan_tables.py") |> isnothing | ||
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| @test metaphlan("", ""; help=true).exitcode == 0 | ||
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| profiles = filter(f-> contains(f, "_profile.tsv"), readdir("files/metaphlan", join=true)) | ||
| @test metaphlan_merge(profiles, "files/metaphlan/merged_abundance_table.tsv").exitcode == 0 | ||
| end | ||
|
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| @testset "Humann" begin | ||
| @test BiobakeryUtils.check_for_install("humann") |> isnothing | ||
| @test BiobakeryUtils.check_for_install("humann_rename_table") |> isnothing | ||
| @test BiobakeryUtils.check_for_install("humann_renorm_table") |> isnothing | ||
| @test BiobakeryUtils.check_for_install("humann_join_tables") |> isnothing | ||
| @test BiobakeryUtils.check_for_install("humann") |> isnothing | ||
| @test humann("", ""; help=true).exitcode == 0 | ||
|
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| end | ||
| end | ||
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| @testset "Metaphlan" begin | ||
| profile_1 = metaphlan_profile("files/metaphlan/SRS014464-Anterior_nares_profile.tsv"; sample="SRS014464") | ||
| @test first(abundances(profile_1["Bacteria", "SRS014464"])) == 100.0 | ||
| @test first(abundances(profile_1["Pseudomonadales", "SRS014464"])) == 97.28734 | ||
| @test size(profile_1) == (13, 1) | ||
| profile_2 = metaphlan_profile("files/metaphlan/SRS014459-Stool_profile.tsv", 3) | ||
| @test size(profile_2) == (2, 1) | ||
| @test first(abundances(profile_2["Firmicutes", "SRS014459-Stool_profile"])) == 68.90167 | ||
| profile_3 = metaphlan_profile("files/metaphlan/SRS014464-Anterior_nares_profile.tsv", :phylum) | ||
| @test size(profile_3) == (2, 1) | ||
| @test first(abundances(profile_3["Proteobacteria", 1])) == 97.28734 | ||
|
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| merge_profile_1 = metaphlan_profiles("files/metaphlan/merged_abundance_table.tsv"; samplestart=3) | ||
| @test size(merge_profile_1) == (62, 6) | ||
| @test first(abundances(merge_profile_1["Moraxella", 5])) == 97.28734 | ||
| merge_profile_2 = metaphlan_profiles("files/metaphlan/merged_abundance_table.tsv", :family; samplestart=3) | ||
| @test size(merge_profile_2) == (13, 6) | ||
| @test first(abundances(merge_profile_2["Micrococcaceae", "SRS014464-Anterior_nares"])) == 0.0 | ||
| merge_profile_3 = metaphlan_profiles("files/metaphlan/merged_abundance_table.tsv", 7; samplestart=3) | ||
| @test size(merge_profile_3) == (16, 6) | ||
| @test first(abundances(merge_profile_3["Haemophilus_haemolyticus", 3])) == 1.35528 | ||
| CSV.write("files/metaphlan/merged_abundance_table2.csv", merge_profile_1) | ||
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| profiles = filter(f-> contains(f, "_profile.tsv"), readdir("files/metaphlan", join=true)) | ||
| @test_throws ArgumentError metaphlan_profiles(profiles; samples = ["sample1"]) | ||
| multi_profile_1 = metaphlan_profiles(profiles; samples=["sample$i" for i in 1:length(profiles)]) | ||
| @test abundances(multi_profile_1) == abundances(metaphlan_profiles(profiles)) | ||
| @test size(multi_profile_1) == (62, 6) | ||
| @test first(abundances(multi_profile_1["Firmicutes", "sample1"])) == 68.90167 | ||
| multi_profile_2 = metaphlan_profiles(profiles, 3; samples=["sample$i" for i in 1:length(profiles)]) | ||
| @test abundances(multi_profile_2) == abundances(metaphlan_profiles(profiles, :class)) | ||
| @test size(multi_profile_2) == (6,6) | ||
| @test first(abundances(multi_profile_2["Bacteroidia", "sample1"])) == 31.09833 | ||
|
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| taxstring = "k__Archaea|p__Euryarchaeota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter|s__Methanobrevibacter_smithii" | ||
| taxa = parsetaxa(taxstring) | ||
| @test length(taxa) == 7 | ||
| @test parsetaxon(taxstring, 1) == Taxon("Archaea", :kingdom) | ||
| @test parsetaxon(taxstring, :family) == Taxon("Methanobacteriaceae", :family) | ||
| @test parsetaxon(taxstring) == Taxon("Methanobrevibacter_smithii", :species) | ||
| @test_throws ArgumentError parsetaxon(taxstring, 8) | ||
|
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| @test parsetaxon("k__Archaea|p__Euryarchaeota|c__Methanobacteria", 2) == Taxon("Euryarchaeota", :phylum) | ||
| @test parsetaxon("k__Archaea|p__Euryarchaeota|c__Methanobacteria") == Taxon("Methanobacteria", :class) | ||
| end | ||
|
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| @testset "HUMAnN" begin | ||
| p1 = humann_profile("files/humann/single_1.tsv") | ||
| p2 = humann_profile("files/humann/single_2.tsv") | ||
| @test p1 isa CommunityProfile | ||
| @test size(p1) == (560, 1) | ||
| @test samplenames(p1) == ["single_1"] | ||
| @test samplenames(humann_profile("files/humann/single_1.tsv"; sample = "sample1")) == ["sample1"] | ||
| @test samplenames(humann_profile("files/humann/single_1.tsv"; sample = MicrobiomeSample("sample1"))) == ["sample1"] | ||
|
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| @test all(f-> !hastaxon(f), features(p1)) # unstratified | ||
| @test all(f-> !occursin('|', name(f)), features(p1)) | ||
|
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| pj = humann_profiles("files/humann/joined.tsv") | ||
| @test size(pj) == (560, 2) | ||
| @test isempty(setdiff(features(pj), features(commjoin(p1, p2)))) | ||
| @test samplenames(pj) == samplenames(commjoin(p1, p2)) | ||
|
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| pj_strat = humann_profiles("files/humann/joined.tsv"; stratified = true) | ||
| @test size(pj_strat) == (1358, 2) | ||
| @test !isempty(setdiff(features(pj_strat), features(pj))) | ||
| @test isempty(setdiff(featurenames(pj_strat), featurenames(pj))) | ||
| @test isempty(setdiff(features(filter(!hastaxon, pj_strat)), features(pj))) | ||
| CSV.write("files/humann/joined_roundtrip.tsv", pj_strat; delim='\t') | ||
| end | ||
| include("BiobakeryUtilsTests.jl") | ||
| BiobakeryUtilsTests.runtests() | ||
|
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| # # uncomment if there are ever inline tests | ||
| # using BiobakeryUtils | ||
| # BiobakeryUtils.runtests() |
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@JuliaRegistrator register
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Registration pull request created: JuliaRegistries/General/55058
After the above pull request is merged, it is recommended that a tag is created on this repository for the registered package version.
This will be done automatically if the Julia TagBot GitHub Action is installed, or can be done manually through the github interface, or via: