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Testing humann2.jl #53

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Testing humann2.jl #53

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f7e3f08
adding test cases for humann2.jl
annelle-abatoni Aug 31, 2021
3b5b93e
adding test files
annelle-abatoni Aug 31, 2021
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10 changes: 10 additions & 0 deletions test/files/humanntestfile.tsv
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Original file line number Diff line number Diff line change
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#GeneFamily SRS014459-Stool_Abundance
UniRef50_unknown|g__Parabacteroides|s__Parabacteroides_distasonis 24.94925526
UniRef50_unknown|g__Bacteroides|s__Bacteroides_cellulosilyticus 21.90659622
UniRef50_unknown|g__Bacteroides|s__Bacteroides_stercoris 14.12141848
UniRef50_unknown|g__Eubacterium|s__Eubacterium_rectale 8.044842004
UniRef50_B3C5F2 37.03703704
UNMAPPED 15961
UniRef50_A9FGD2: 50S ribosomal protein L36 111.1111111
UniRef50_A9FGD2: 50S ribosomal protein L36|g__Bacteroides.s__Bacteroides_cellulosilyticus 111.1111111
UniRef50_unknown 69.02211197
10 changes: 10 additions & 0 deletions test/files/metadata_test_humann.csv
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sampleID,ageYears,gender,collectionDate
sample1,0.2,male,2020-01-01
sample3,1.3,female,2020-02-01
sample4,2,female,2021-03-02
sample5,5,,2021-04-03
sample6,,male,2021-05-30
sample7,3.6,male,
sample8,2.14,female,2021-07-01
sample9,3.5,male,2021-08-01
sample10,1.4,female,2021-09-01
9 changes: 9 additions & 0 deletions test/runtests.jl
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Expand Up @@ -8,6 +8,15 @@ using SparseArrays
using DelimitedFiles
using CSV

@testset "Humann2" begin
df = CSV.read("files/humanntestfile.tsv", DataFrame, delim='\t', header=["#GeneFamily", "SRS014459-Stool_Abundance"], datarow = 2)
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This should probably have a function like metaphlan_table<s> but for humann instead of this at some point, but deal with that later #23

metadata = CSV.File("files/metadata_test_humann.csv") |> Tables.Array
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There aren't actually any tests here... should at least test the type and shape of the object created.

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I keep running into this error when I run humann2_regroup and humann2_rename

ERROR: IOError: could not spawn humann2_rename_table -i /var/folders/jm/_25dbvt53_793g7w_1975c5c0000gn/T/jl_ahMrMf -n ec -o /var/folders/jm/_25dbvt53_793g7w_1975c5c0000gn/T/jl_afnvCf: no such file or directory (ENOENT)

Do you know how I can resolve this?

# @test humann2_regroup(df) ==
# @test humann2_rename(df) ==
# @test humann2_barplots(df, metadata) ==
# @test humann2_barplot(df, metadata) ==
end

@testset "Metaphlan" begin
taxstring = "k__Archaea|p__Euryarchaeota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter|s__Methanobrevibacter_smithii"
taxa = parsetaxa(taxstring)
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