Testing humann2.jl #53
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| @@ -8,6 +8,15 @@ using SparseArrays | |||
| using DelimitedFiles | |||
| using CSV | |||
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| @testset "Humann2" begin | |||
| df = CSV.read("files/humanntestfile.tsv", DataFrame, delim='\t', header=["#GeneFamily", "SRS014459-Stool_Abundance"], datarow = 2) | |||
| 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?
| @@ -8,6 +8,15 @@ using SparseArrays | |||
| using DelimitedFiles | |||
| using CSV | |||
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| @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
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@annelle-abatoni bump - can you wrap this up? |
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Closing, since we don't want to support |
I left the tests unanswered because I keep getting errors using these test files - I'm not sure why. I also don't fully understand
humann2_barplots's functionality.