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Disabled cgMLST section of tests, added calling tests for pubMLST C. …
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…jejuni
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@dfornika
dfornika committed May 11, 2018
1 parent 3abb959 commit 90262cd
Showing 1 changed file with 111 additions and 53 deletions.
164 changes: 111 additions & 53 deletions test/runtests.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -10,43 +10,28 @@ TEST_DIR = (dirname(@__FILE__))
TMPDIR = mktempdir()
VERSION = "testing"

c_jejuni_pubmlst_dir = string(TMPDIR, "/", "c_jejuni_pubmlst")
l_pneumophila_cgmlst_dir = string(TMPDIR, "/", "l_pneumophila_cgmlst")
s_enterica_enterobase_cgmlst_dir = string(TMPDIR, "/", "s_enterica_enterobase_cgmlst")
s_enterica_enterobase_cgmlst_db_file = string(TMPDIR,"/", "s_enterica_enterobase_cgmlst_31.db")
@testset "mentalist_tests" begin
c_jejuni_pubmlst_dir = string(TMPDIR, "/", "c_jejuni_pubmlst")
c_jejuni_pubmlst_db_file = string(TMPDIR, "/", "c_jejuni_pubmlst_31.db")
c_jejuni_fastq_file = string("../data/SRR5824107_small.fastq.gz")
l_pneumophila_cgmlst_dir = string(TMPDIR, "/", "l_pneumophila_cgmlst")
s_enterica_enterobase_cgmlst_dir = string(TMPDIR, "/", "s_enterica_enterobase_cgmlst")
s_enterica_enterobase_cgmlst_db_file = string(TMPDIR,"/", "s_enterica_enterobase_cgmlst_31.db")

@testset "download_pubmlst_scheme" begin
mkdir(c_jejuni_pubmlst_dir)
download_pubmlst_scheme("Campylobacter jejuni", c_jejuni_pubmlst_dir)
c_jejuni_allele_filenames = open(string(TEST_DIR, "/", "test_data", "/", "c_jejuni_pubmlst_allele_filenames.txt"))
for c_jejuni_allele_filename in eachline(c_jejuni_allele_filenames)
@test isfile(string(c_jejuni_pubmlst_dir, "/", chomp(c_jejuni_allele_filename)))
c_jejuni_pubmlst_loci_files = ""
@testset "download_pubmlst_scheme" begin
mkdir(c_jejuni_pubmlst_dir)
c_jejuni_pubmlst_loci_files, c_jejuni_profile_file = download_pubmlst_scheme("Campylobacter jejuni", c_jejuni_pubmlst_dir)
c_jejuni_allele_filenames = open(string(TEST_DIR, "/", "test_data", "/", "c_jejuni_pubmlst_allele_filenames.txt"))
for c_jejuni_allele_filename in eachline(c_jejuni_allele_filenames)
@test isfile(string(c_jejuni_pubmlst_dir, "/", chomp(c_jejuni_allele_filename)))
end
end
end

@testset "download_cgmlst_scheme" begin
mkdir(l_pneumophila_cgmlst_dir)
download_cgmlst_scheme("Legionella pneumophila", l_pneumophila_cgmlst_dir)
l_pneumophila_allele_filenames = open(string(TEST_DIR, "/", "test_data", "/", "l_pneumophila_cgmlst_allele_filenames.txt"))
for l_pneumophila_allele_filename in eachline(l_pneumophila_allele_filenames)
@test isfile(string(l_pneumophila_cgmlst_dir, "/", chomp(l_pneumophila_allele_filename)))
end
end

s_enterica_enterobase_cgmlst_locus_files = ""
@testset "download_s_enterica_enterobase_cgmlst_scheme" begin
mkdir(s_enterica_enterobase_cgmlst_dir)
s_enterica_enterobase_cgmlst_locus_files = download_enterobase_scheme("S", "cg", s_enterica_enterobase_cgmlst_dir)
s_enterica_enterobase_cgmlst_allele_filenames = open(string(TEST_DIR, "/", "test_data", "/", "s_enterica_enterobase_cgmlst_allele_filenames.txt"))
for s_enterica_enterobase_cgmlst_allele_filename in eachline(s_enterica_enterobase_cgmlst_allele_filenames)
@test isfile(string(s_enterica_enterobase_cgmlst_dir, "/", chomp(s_enterica_enterobase_cgmlst_allele_filename)))
end
end

@testset "build_s_enterica_enterobase_cgmlst_db" begin
@testset "build_c_jejuni_db" begin
K::Int8 = 31
results, loci = kmer_class_for_each_locus(K, s_enterica_enterobase_cgmlst_locus_files, true)
@test typeof(results) == Array{Any,1}
results, loci = kmer_class_for_each_locus(K, c_jejuni_pubmlst_loci_files, true)
@test typeof(results) == Vector{Any}
@test typeof(loci) == Vector{String}

kmer_classification = combine_loci_classification(K, results, loci)
Expand All @@ -61,29 +46,102 @@ end
@test all([length(kmer) == K for kmer in kmer_list])

profile = nothing
args = Dict("k" => K, "fasta_files" => s_enterica_enterobase_cgmlst_locus_files)
save_db(K, kmer_classification, loci, s_enterica_enterobase_cgmlst_db_file, profile, VERSION)
@test isfile(s_enterica_enterobase_cgmlst_db_file)
args = Dict("k" => K, "fasta_files" => c_jejuni_pubmlst_loci_files)
save_db(K, kmer_classification, loci, c_jejuni_pubmlst_db_file, profile, args)
@test isfile(c_jejuni_pubmlst_db_file)
end

@testset "call_c_jejuni" begin
# open the db:
kmer_classification, loci, loci2alleles, k, profile = open_db(c_jejuni_pubmlst_db_file)
# @test typeof(kmer_classification) == DataStructures.DefaultDict{Bio.Seq.Kmer{Bio.Seq.DNANucleotide,31},Vector{Tuple{Int16,Int16,Vector{Int16}}}}
@test typeof(loci) == Vector{String}
@test typeof(loci2alleles) == Dict{Int16,Vector{Int16}}

# count kmers:
votes, loci_votes = count_kmers_and_vote(DNAKmer{k}, [c_jejuni_fastq_file], kmer_classification, loci2alleles)

@test typeof(loci_votes) == DataStructures.DefaultDict{Int16,Int64,Int64}
@test loci_votes[29] == 0
@test loci_votes[306] == 0
@test loci_votes[1090] == 0
@test loci_votes[1316] == 0
@test loci_votes[1333] == 0


@test typeof(votes) == Dict{Int16,Dict{Int16,Int64}}
@test votes[7][288] == 482
@test votes[7][306] == 437
@test votes[7][520] == 516
@test votes[4][306] == 1533
@test votes[4][29] == 484
@test votes[4][413] == -775

end

@testset "complement_alleles" begin
@test complement_alleles([], 0) == Int16[]
@test complement_alleles([], 1) == [Int16(1)]
@test complement_alleles([-1], 0) == Int16[]
@test complement_alleles([-1], 1) == [Int16(1)]
@test complement_alleles([0], 0) == Int16[]
@test complement_alleles([0], 1) == [Int16(1)]
@test complement_alleles([1], 0) == Int16[]
@test complement_alleles([1], 1) == Int16[]
@test complement_alleles([], 0) == Int16[]
end

@testset "twin" begin
@test twin(DNAKmer{0}, DNAKmer("")) == DNAKmer("")
@test twin(DNAKmer{1}, DNAKmer("A")) == DNAKmer("T")
@test twin(DNAKmer{1}, DNAKmer("C")) == DNAKmer("G")
@test twin(DNAKmer{1}, DNAKmer("G")) == DNAKmer("C")
@test twin(DNAKmer{1}, DNAKmer("T")) == DNAKmer("A")
# @testset "download_cgmlst_scheme" begin
# mkdir(l_pneumophila_cgmlst_dir)
# download_cgmlst_scheme("Legionella pneumophila", l_pneumophila_cgmlst_dir)
# l_pneumophila_allele_filenames = open(string(TEST_DIR, "/", "test_data", "/", "l_pneumophila_cgmlst_allele_filenames.txt"))
# for l_pneumophila_allele_filename in eachline(l_pneumophila_allele_filenames)
# @test isfile(string(l_pneumophila_cgmlst_dir, "/", chomp(l_pneumophila_allele_filename)))
# end
# end

# s_enterica_enterobase_cgmlst_locus_files = ""
# @testset "download_s_enterica_enterobase_cgmlst_scheme" begin
# mkdir(s_enterica_enterobase_cgmlst_dir)
# s_enterica_enterobase_cgmlst_locus_files = download_enterobase_scheme("S", "cg", s_enterica_enterobase_cgmlst_dir)
# s_enterica_enterobase_cgmlst_allele_filenames = open(string(TEST_DIR, "/", "test_data", "/", "s_enterica_enterobase_cgmlst_allele_filenames.txt"))
# for s_enterica_enterobase_cgmlst_allele_filename in eachline(s_enterica_enterobase_cgmlst_allele_filenames)
# @test isfile(string(s_enterica_enterobase_cgmlst_dir, "/", chomp(s_enterica_enterobase_cgmlst_allele_filename)))
# end
# end

# @testset "build_s_enterica_enterobase_cgmlst_db" begin
# K::Int8 = 31
# results, loci = kmer_class_for_each_locus(K, s_enterica_enterobase_cgmlst_locus_files, true)
# @test typeof(results) == Array{Any,1}
# @test typeof(loci) == Vector{String}
#
# kmer_classification = combine_loci_classification(K, results, loci)
# loci_list, weight_list, alleles_list, kmer_list, allele_ids_per_locus = kmer_classification
# @test typeof(loci_list) == Vector{Int32}
# @test typeof(weight_list) == Vector{Int16}
# @test typeof(alleles_list) == Vector{Int16}
# @test typeof(kmer_list) == Vector{String}
# @test typeof(allele_ids_per_locus) == Vector{Int64}
# @test length(weight_list) == length(kmer_list)
# @test all([x != 0 for x in weight_list])
# @test all([length(kmer) == K for kmer in kmer_list])
#
# profile = nothing
# args = Dict("k" => K, "fasta_files" => s_enterica_enterobase_cgmlst_locus_files)
# save_db(K, kmer_classification, loci, s_enterica_enterobase_cgmlst_db_file, profile, VERSION)
# @test isfile(s_enterica_enterobase_cgmlst_db_file)
# end

@testset "complement_alleles" begin
@test complement_alleles([], 0) == Int16[]
@test complement_alleles([], 1) == [Int16(1)]
@test complement_alleles([-1], 0) == Int16[]
@test complement_alleles([-1], 1) == [Int16(1)]
@test complement_alleles([0], 0) == Int16[]
@test complement_alleles([0], 1) == [Int16(1)]
@test complement_alleles([1], 0) == Int16[]
@test complement_alleles([1], 1) == Int16[]
@test complement_alleles([], 0) == Int16[]
end

@testset "twin" begin
@test twin(DNAKmer{0}, DNAKmer("")) == DNAKmer("")
@test twin(DNAKmer{1}, DNAKmer("A")) == DNAKmer("T")
@test twin(DNAKmer{1}, DNAKmer("C")) == DNAKmer("G")
@test twin(DNAKmer{1}, DNAKmer("G")) == DNAKmer("C")
@test twin(DNAKmer{1}, DNAKmer("T")) == DNAKmer("A")
end

end

# rm(TMPDIR, recursive=true)

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