Bring more tests to life

camilogarciabotero · Jul 3, 2024 · cb861c9 · cb861c9
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commit cb861c9
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Showing 2 changed files with 41 additions and 50 deletions.
diff --git a/test/data/NC_001884-orfs.faa b/test/data/NC_001884-orfs.faa
diff --git a/test/findorfstest.jl b/test/findorfstest.jl
@@ -1,43 +1,57 @@
 
-@testitem "findorfs tests" begin
+@testitem "findorfs tests" default_imports=false begin
     # cd(@__DIR__)
     # using GeneFinder: findorfs, NaiveFinder, ORF
     # A random seq to start
-
-    using BioSequences: @dna_str
-    using GeneFinder: findorfs, NaiveFinder, ORF, source
-    # using GeneFinder: findorfs, NaiveFinder, ORF, Features, STRAND_POS, STRAND_NEG, source, sequence, groupname
+    using Test, BioSequences, GeneFinder
 
     seq01 = dna"ATGATGCATGCATGCATGCTAGTAACTAGCTAGCTAGCTAGTAA"
 
-    orf01 = ORF{4,NaiveFinder}("seq01", 1, 33, STRAND_POS, 1, Features((score = 0.0,)), nothing) # ORF{4,NaiveFinder}("phi", 7, 15, '+', 1, Features((score = 0,)), nothing)
+    orf01 = ORF{4,NaiveFinder}("seq01", 1, 33, STRAND_POS, 1, Features((score = 0.0,)), nothing) # ORF{4,NaiveFinder}("phi", 7, 15, STRAND_POS, 1, Features((score = 0,)))
     # source(orf01)
     # GeneFinder.source(orf01)
-    orfs = findorfs(seq01)
-    @view(seq01[begin:end])
-    seq01
+    orfs01 = findorfs(seq01)
+    # @view(seq01[begin:end])
+    getindex(seq01, orf01.first:orf01.last)
+
+    orfs01test = [
+        ORF{4,NaiveFinder}("seq01", 1, 33, STRAND_POS, 1, Features((score = 0.0,)), nothing),
+        ORF{4,NaiveFinder}("seq01", 4, 33, STRAND_POS, 1, Features((score = 0.0,)), nothing),
+        ORF{4,NaiveFinder}("seq01", 8, 22, STRAND_POS, 2, Features((score = 0.0,)), nothing),
+        ORF{4,NaiveFinder}("seq01", 12,29, STRAND_POS, 3, Features((score = 0.0,)), nothing),
+        ORF{4,NaiveFinder}("seq01", 16,33, STRAND_POS, 1, Features((score = 0.0,)), nothing)
+    ]
+
+    @test println(orfs01) == println(orfs01test)
+    @test length(orfs01) == 5
+
+    # known failures
     # seq01[orf01]
     # sequence(orf01) == dna"ATGATGCATGCATGCATGCTAGTAACTAGCTAG"
-
     # groupname(orf01) == "seq01"
 
-    # @test orfs01 == [
-    #     ORF{4,NaiveFinder}("seq01", 1, 33, '+', 1, seq01[1:33], Dict(:score => 0.0), nothing),
-    #     ORF{4,NaiveFinder}("seq01", 4, 33, '+', 1, seq01[4:33], Dict(:score => 0.0), nothing),
-    #     ORF{4,NaiveFinder}("seq01", 8, 22, '+', 2, seq01[8:22], Dict(:score => 0.0), nothing),
-    #     ORF{4,NaiveFinder}("seq01", 12, 29, '+', 3, seq01[12:29], Dict(:score => 0.0), nothing),
-    #     ORF{4,NaiveFinder}("seq01", 16, 33, '+', 1, seq01[16:33], Dict(:score => 0.0), nothing)
-    # ]
-
-    # @test length(orfs01) == 5
-end
-
     # > 180195.SAMN03785337.LFLS01000089 -> finds only 1 gene in Prodigal (from Pyrodigal tests)
-    # seq02 = dna"AACCAGGGCAATATCAGTACCGCGGGCAATGCAACCCTGACTGCCGGCGGTAACCTGAACAGCACTGGCAATCTGACTGTGGGCGGTGTTACCAACGGCACTGCTACTACTGGCAACATCGCACTGACCGGTAACAATGCGCTGAGCGGTCCGGTCAATCTGAATGCGTCGAATGGCACGGTGACCTTGAACACGACCGGCAATACCACGCTCGGTAACGTGACGGCACAAGGCAATGTGACGACCAATGTGTCCAACGGCAGTCTGACGGTTACCGGCAATACGACAGGTGCCAACACCAACCTCAGTGCCAGCGGCAACCTGACCGTGGGTAACCAGGGCAATATCAGTACCGCAGGCAATGCAACCCTGACGGCCGGCGACAACCTGACGAGCACTGGCAATCTGACTGTGGGCGGCGTCACCAACGGCACGGCCACCACCGGCAACATCGCGCTGACCGGTAACAATGCACTGGCTGGTCCTGTCAATCTGAACGCGCCGAACGGCACCGTGACCCTGAACACAACCGGCAATACCACGCTGGGTAATGTCACCGCACAAGGCAATGTGACGACTAATGTGTCCAACGGCAGCCTGACAGTCGCTGGCAATACCACAGGTGCCAACACCAACCTGAGTGCCAGCGGCAATCTGACCGTGGGCAACCAGGGCAATATCAGTACCGCGGGCAATGCAACCCTGACTGCCGGCGGTAACCTGAGC"
-    # orfs02 = findorfs(seq02, NaiveFinder())
+    seq02 = dna"AACCAGGGCAATATCAGTACCGCGGGCAATGCAACCCTGACTGCCGGCGGTAACCTGAACAGCACTGGCAATCTGACTGTGGGCGGTGTTACCAACGGCACTGCTACTACTGGCAACATCGCACTGACCGGTAACAATGCGCTGAGCGGTCCGGTCAATCTGAATGCGTCGAATGGCACGGTGACCTTGAACACGACCGGCAATACCACGCTCGGTAACGTGACGGCACAAGGCAATGTGACGACCAATGTGTCCAACGGCAGTCTGACGGTTACCGGCAATACGACAGGTGCCAACACCAACCTCAGTGCCAGCGGCAACCTGACCGTGGGTAACCAGGGCAATATCAGTACCGCAGGCAATGCAACCCTGACGGCCGGCGACAACCTGACGAGCACTGGCAATCTGACTGTGGGCGGCGTCACCAACGGCACGGCCACCACCGGCAACATCGCGCTGACCGGTAACAATGCACTGGCTGGTCCTGTCAATCTGAACGCGCCGAACGGCACCGTGACCCTGAACACAACCGGCAATACCACGCTGGGTAATGTCACCGCACAAGGCAATGTGACGACTAATGTGTCCAACGGCAGCCTGACAGTCGCTGGCAATACCACAGGTGCCAACACCAACCTGAGTGCCAGCGGCAATCTGACCGTGGGCAACCAGGGCAATATCAGTACCGCGGGCAATGCAACCCTGACTGCCGGCGGTAACCTGAGC"
+    orfs02 = findorfs(seq02, finder=NaiveFinder)
+
+    @test length(orfs02) == 12
 
-    # @test length(orfs02) == 12
-    # @test orfs02 == [ORF{NaiveFinder}(29:40, '+', 2, nothing), ORF{NaiveFinder}(137:145, '+', 2, nothing), ORF{NaiveFinder}(164:184, '+', 2, nothing), ORF{NaiveFinder}(173:184, '+', 2, nothing), ORF{NaiveFinder}(236:241, '+', 2, nothing), ORF{NaiveFinder}(248:268, '+', 2, nothing), ORF{NaiveFinder}(362:373, '+', 2, nothing), ORF{NaiveFinder}(470:496, '+', 2, nothing), ORF{NaiveFinder}(551:574, '+', 2, nothing), ORF{NaiveFinder}(569:574, '+', 2, nothing), ORF{NaiveFinder}(581:601, '+', 2, nothing), ORF{NaiveFinder}(695:706, '+', 2, nothing)]
+    orfs02test = [
+        ORF{4,NaiveFinder}("seq02", 29, 40, STRAND_POS, 2 , Features((score = 0.0,)), nothing), 
+        ORF{4,NaiveFinder}("seq02", 137,145, STRAND_POS, 2, Features((score = 0.0,)), nothing), 
+        ORF{4,NaiveFinder}("seq02", 164,184, STRAND_POS, 2, Features((score = 0.0,)), nothing), 
+        ORF{4,NaiveFinder}("seq02", 173,184, STRAND_POS, 2, Features((score = 0.0,)), nothing), 
+        ORF{4,NaiveFinder}("seq02", 236,241, STRAND_POS, 2, Features((score = 0.0,)), nothing), 
+        ORF{4,NaiveFinder}("seq02", 248,268, STRAND_POS, 2, Features((score = 0.0,)), nothing), 
+        ORF{4,NaiveFinder}("seq02", 362,373, STRAND_POS, 2, Features((score = 0.0,)), nothing), 
+        ORF{4,NaiveFinder}("seq02", 470,496, STRAND_POS, 2, Features((score = 0.0,)), nothing), 
+        ORF{4,NaiveFinder}("seq02", 551,574, STRAND_POS, 2, Features((score = 0.0,)), nothing), 
+        ORF{4,NaiveFinder}("seq02", 569,574, STRAND_POS, 2, Features((score = 0.0,)), nothing), 
+        ORF{4,NaiveFinder}("seq02", 581,601, STRAND_POS, 2, Features((score = 0.0,)), nothing), 
+        ORF{4,NaiveFinder}("seq02", 695,706, STRAND_POS, 2, Features((score = 0.0,)), nothing)
+    ]
+
+    @test println(orfs02) == println(orfs02test)
 
     # From pyrodigal issue #13 link: https://github.com/althonos/pyrodigal/blob/1f939b0913b48dbaa55d574b20e124f1b8323825/pyrodigal/tests/test_orf_finder.py#L271
     # Pyrodigal predicts 2 genes from this sequence:
@@ -47,7 +61,7 @@ end
     # seq03 = dna"TTCGTCAGTCGTTCTGTTTCATTCAATACGATAGTAATGTATTTTTCGTGCATTTCCGGTGGAATCGTGCCGTCCAGCATAGCCTCCAGATATCCCCTTATAGAGGTCAGAGGGGAACGGAAATCGTGGGATACATTGGCTACAAACTTTTTCTGATCATCCTCGGAACGGGCAATTTCGCTTGCCATATAATTCAGACAGGAAGCCAGATAACCGATTTCATCCTCACTATCGACCTGAAATTCATAATGCATATTACCGGCAGCATACTGCTCTGTGGCATGAGTGATCTTCCTCAGAGGAATATATACGATCTCAGTGAAAAAGATCAGAATGATCAGGGATAGCAGGAACAGGATTGCCAGGGTGATATAGGAAATATTCAGCAGGTTGTTACAGGATTTCTGAATATCATTCATATCAGTATGGATGACTACATAGCCTTTTACCTTGTAGTTGGAGGTAATGGGAGCAAATACAGTAAGTACATCCGAATCAAAATTACCGAAGAAATCACCAACAATGTAATAGGAGCCGCTGGTTACGGTCGAATCAAAATTCTCAATGACAACCACATTCTCCACATCTAAGGGACTATTGGTATCCAGTACCAGTCGTCCGGAGGGATTGATGATGCGAATCTCGGAATTCAGGTAGACCGCCAGGGAGTCCAGCTGCATTTTAACGGTCTCCAAAGTTGTTTCACTGGTGTACAATCCGCCGGCATAGGTTCCGGCGATCAGGGTTGCTTCGGAATAGAGACTTTCTGCCTTTTCCCGGATCAGATGTTCTTTGGTCATATTGGGAACAAAAGTTGTAACAATGATGAAACCAAATACACCAAAAATAAAATATGCGAGTATAAATTTTAGATAAAGTGTTTTTTTCATAACAAATCCTGCTTTTGGTATGACTTAATTACGTACTTCGAATTTATAGCCGATGCCCCAGATGGTGCTGATCTTCCAGTTGGCATGATCCTTGATCTTCTC"
     # orfs03 = findorfs(seq03, NaiveFinder(), minlen=75)
     # @test length(orfs03) == 9
-    # @test orfs03 == [ORF{NaiveFinder}(37:156, '+', 1, nothing), ORF{NaiveFinder}(194:268, '-', 2, nothing), ORF{NaiveFinder}(194:283, '-', 2, nothing), ORF{NaiveFinder}(249:347, '+', 3, nothing), ORF{NaiveFinder}(426:590, '+', 3, nothing), ORF{NaiveFinder}(565:657, '+', 1, nothing), ORF{NaiveFinder}(650:727, '-', 2, nothing), ORF{NaiveFinder}(786:872, '+', 3, nothing), ORF{NaiveFinder}(887:976, '-', 2, nothing)]
+    # @test orfs03 == [ORF{NaiveFinder}(37:156, STRAND_POS, 1), ORF{NaiveFinder}(194:268, '-', 2), ORF{NaiveFinder}(194:283, '-', 2), ORF{NaiveFinder}(249:347, STRAND_POS, 3), ORF{NaiveFinder}(426:590, STRAND_POS, 3), ORF{NaiveFinder}(565:657, STRAND_POS, 1), ORF{NaiveFinder}(650:727, '-', 2), ORF{NaiveFinder}(786:872, STRAND_POS, 3), ORF{NaiveFinder}(887:976, '-', 2)]
                                                                                                            #|->  This occured in Pyrodigal
     # Lambda phage tests
     # Compare to https://github.com/jonas-fuchs/viral_orf_finder/blob/master/orf_finder.py 
@@ -60,27 +74,4 @@ end
     # NC_001416 = fasta2bioseq("data/NC_001416.1.fasta")[1]
     # NC_001416_orfs = findorfs(NC_001416, NaiveFinder(), minlen=75)
     # @test length(NC_001416_orfs) == 885
-# end
-
-# @testitem "getorfs dna" default_imports=false begin
-
-#     using BioSequences: @dna_str, DNAAlphabet
-#     using GeneFinder: NaiveFinder, getorfs, findorfs, ORF
-#     using Test: @test
-
-#     seq01 = dna"ATGATGCATGCATGCATGCTAGTAACTAGCTAGCTAGCTAGTAA"
-#     orfseqs = getorfs(seq01, DNAAlphabet{4}(), NaiveFinder())
-
-#     # @test length(orfseqs) == 5
-#     # @test orfseqs[1] == dna"ATGATGCATGCATGCATGCTAGTAACTAGCTAG"
-# end
-
-# @testitem "getorfs proteins" begin
-#     using BioSequences, GeneFinder, Test
-
-#     seq01 = dna"ATGATGCATGCATGCATGCTAGTAACTAGCTAGCTAGCTAGTAA"
-#     aas = getorfs(seq01, AminoAcidAlphabet(), NaiveFinder())
-
-#     @test length(aas) == 5
-#     @test aas[1] == aa"MMHACMLVTS*"
-# end
+end