Update findorfstest.jl and runtests.jl

test/data/out-seq03.faa

@@ -0,0 +1,64 @@
+>ORF01 id=01 start=5 stop=22 strand=- frame=2
+MKQND*
+>ORF02 id=02 start=37 stop=156 strand=+ frame=1
+MYFSCISGGIVPSSIASRYPLIEVRGERKSWDTLATNFF*
+>ORF03 id=03 start=107 stop=136 strand=- frame=2
+MYPTISVPL*
+>ORF04 id=04 start=140 stop=160 strand=- frame=2
+MIRKSL*
+>ORF05 id=05 start=194 stop=223 strand=- frame=2
+MKSVIWLPV*
+>ORF06 id=06 start=194 stop=247 strand=- frame=2
+MNFRSIVRMKSVIWLPV*
+>ORF07 id=07 start=194 stop=268 strand=- frame=2
+MLPVICIMNFRSIVRMKSVIWLPV*
+>ORF08 id=08 start=194 stop=283 strand=- frame=2
+MPQSSMLPVICIMNFRSIVRMKSVIWLPV*
+>ORF09 id=09 start=249 stop=347 strand=+ frame=3
+MHITGSILLCGMSDLPQRNIYDLSEKDQNDQG*
+>ORF10 id=10 start=282 stop=347 strand=+ frame=3
+MSDLPQRNIYDLSEKDQNDQG*
+>ORF11 id=11 start=334 stop=375 strand=+ frame=1
+MIRDSRNRIARVI*
+>ORF12 id=12 start=383 stop=415 strand=- frame=2
+MIFRNPVTTC*
+>ORF13 id=13 start=426 stop=590 strand=+ frame=3
+MDDYIAFYLVVGGNGSKYSKYIRIKITEEITNNVIGAAGYGRIKILNDNHILHI*
+>ORF14 id=14 start=430 stop=441 strand=+ frame=1
+MTT*
+>ORF15 id=15 start=434 stop=439 strand=- frame=2
+M*
+>ORF16 id=16 start=446 stop=490 strand=- frame=2
+MYLLYLLPLPPTTR*
+>ORF17 id=17 start=466 stop=528 strand=+ frame=1
+MGANTVSTSESKLPKKSPTM*
+>ORF18 id=18 start=523 stop=528 strand=+ frame=1
+M*
+>ORF19 id=19 start=542 stop=577 strand=- frame=2
+MWLSLRILIRP*
+>ORF20 id=20 start=542 stop=586 strand=- frame=2
+MWRMWLSLRILIRP*
+>ORF21 id=21 start=565 stop=657 strand=+ frame=1
+MTTTFSTSKGLLVSSTSRPEGLMMRISEFR*
+>ORF22 id=22 start=631 stop=657 strand=+ frame=1
+MMRISEFR*
+>ORF23 id=23 start=634 stop=657 strand=+ frame=1
+MRISEFR*
+>ORF24 id=24 start=650 stop=727 strand=- frame=2
+MPADCTPVKQLWRPLKCSWTPWRST*
+>ORF25 id=25 start=786 stop=872 strand=+ frame=3
+MFFGHIGNKSCNNDETKYTKNKICEYKF*
+>ORF26 id=26 start=823 stop=876 strand=+ frame=1
+MMKPNTPKIKYASINFR*
+>ORF27 id=27 start=826 stop=876 strand=+ frame=1
+MKPNTPKIKYASINFR*
+>ORF28 id=28 start=854 stop=865 strand=+ frame=2
+MRV*
+>ORF29 id=29 start=887 stop=976 strand=- frame=2
+MPTGRSAPSGASAINSKYVIKSYQKQDLL*
+>ORF30 id=30 start=910 stop=918 strand=+ frame=1
+MT*
+>ORF31 id=31 start=943 stop=978 strand=+ frame=1
+MPQMVLIFQLA*
+>ORF32 id=32 start=952 stop=978 strand=+ frame=1
+MVLIFQLA*

test/data/out-seq03.fna

@@ -0,0 +1,64 @@
+>ORF01 id=01 start=5 stop=22 strand=- frame=2
+ATGAAACAGAACGACTGA
+>ORF02 id=02 start=37 stop=156 strand=+ frame=1
+ATGTATTTTTCGTGCATTTCCGGTGGAATCGTGCCGTCCAGCATAGCCTCCAGATATCCCCTTATAGAGGTCAGAGGGGAACGGAAATCGTGGGATACATTGGCTACAAACTTTTTCTGA
+>ORF03 id=03 start=107 stop=136 strand=- frame=2
+ATGTATCCCACGATTTCCGTTCCCCTCTGA
+>ORF04 id=04 start=140 stop=160 strand=- frame=2
+ATGATCAGAAAAAGTTTGTAG
+>ORF05 id=05 start=194 stop=223 strand=- frame=2
+ATGAAATCGGTTATCTGGCTTCCTGTCTGA
+>ORF06 id=06 start=194 stop=247 strand=- frame=2
+ATGAATTTCAGGTCGATAGTGAGGATGAAATCGGTTATCTGGCTTCCTGTCTGA
+>ORF07 id=07 start=194 stop=268 strand=- frame=2
+ATGCTGCCGGTAATATGCATTATGAATTTCAGGTCGATAGTGAGGATGAAATCGGTTATCTGGCTTCCTGTCTGA
+>ORF08 id=08 start=194 stop=283 strand=- frame=2
+ATGCCACAGAGCAGTATGCTGCCGGTAATATGCATTATGAATTTCAGGTCGATAGTGAGGATGAAATCGGTTATCTGGCTTCCTGTCTGA
+>ORF09 id=09 start=249 stop=347 strand=+ frame=3
+ATGCATATTACCGGCAGCATACTGCTCTGTGGCATGAGTGATCTTCCTCAGAGGAATATATACGATCTCAGTGAAAAAGATCAGAATGATCAGGGATAG
+>ORF10 id=10 start=282 stop=347 strand=+ frame=3
+ATGAGTGATCTTCCTCAGAGGAATATATACGATCTCAGTGAAAAAGATCAGAATGATCAGGGATAG
+>ORF11 id=11 start=334 stop=375 strand=+ frame=1
+ATGATCAGGGATAGCAGGAACAGGATTGCCAGGGTGATATAG
+>ORF12 id=12 start=383 stop=415 strand=- frame=2
+ATGATATTCAGAAATCCTGTAACAACCTGCTGA
+>ORF13 id=13 start=426 stop=590 strand=+ frame=3
+ATGGATGACTACATAGCCTTTTACCTTGTAGTTGGAGGTAATGGGAGCAAATACAGTAAGTACATCCGAATCAAAATTACCGAAGAAATCACCAACAATGTAATAGGAGCCGCTGGTTACGGTCGAATCAAAATTCTCAATGACAACCACATTCTCCACATCTAA
+>ORF14 id=14 start=430 stop=441 strand=+ frame=1
+ATGACTACATAG
+>ORF15 id=15 start=434 stop=439 strand=- frame=2
+ATGTAG
+>ORF16 id=16 start=446 stop=490 strand=- frame=2
+ATGTACTTACTGTATTTGCTCCCATTACCTCCAACTACAAGGTAA
+>ORF17 id=17 start=466 stop=528 strand=+ frame=1
+ATGGGAGCAAATACAGTAAGTACATCCGAATCAAAATTACCGAAGAAATCACCAACAATGTAA
+>ORF18 id=18 start=523 stop=528 strand=+ frame=1
+ATGTAA
+>ORF19 id=19 start=542 stop=577 strand=- frame=2
+ATGTGGTTGTCATTGAGAATTTTGATTCGACCGTAA
+>ORF20 id=20 start=542 stop=586 strand=- frame=2
+ATGTGGAGAATGTGGTTGTCATTGAGAATTTTGATTCGACCGTAA
+>ORF21 id=21 start=565 stop=657 strand=+ frame=1
+ATGACAACCACATTCTCCACATCTAAGGGACTATTGGTATCCAGTACCAGTCGTCCGGAGGGATTGATGATGCGAATCTCGGAATTCAGGTAG
+>ORF22 id=22 start=631 stop=657 strand=+ frame=1
+ATGATGCGAATCTCGGAATTCAGGTAG
+>ORF23 id=23 start=634 stop=657 strand=+ frame=1
+ATGCGAATCTCGGAATTCAGGTAG
+>ORF24 id=24 start=650 stop=727 strand=- frame=2
+ATGCCGGCGGATTGTACACCAGTGAAACAACTTTGGAGACCGTTAAAATGCAGCTGGACTCCCTGGCGGTCTACCTGA
+>ORF25 id=25 start=786 stop=872 strand=+ frame=3
+ATGTTCTTTGGTCATATTGGGAACAAAAGTTGTAACAATGATGAAACCAAATACACCAAAAATAAAATATGCGAGTATAAATTTTAG
+>ORF26 id=26 start=823 stop=876 strand=+ frame=1
+ATGATGAAACCAAATACACCAAAAATAAAATATGCGAGTATAAATTTTAGATAA
+>ORF27 id=27 start=826 stop=876 strand=+ frame=1
+ATGAAACCAAATACACCAAAAATAAAATATGCGAGTATAAATTTTAGATAA
+>ORF28 id=28 start=854 stop=865 strand=+ frame=2
+ATGCGAGTATAA
+>ORF29 id=29 start=887 stop=976 strand=- frame=2
+ATGCCAACTGGAAGATCAGCACCATCTGGGGCATCGGCTATAAATTCGAAGTACGTAATTAAGTCATACCAAAAGCAGGATTTGTTATGA
+>ORF30 id=30 start=910 stop=918 strand=+ frame=1
+ATGACTTAA
+>ORF31 id=31 start=943 stop=978 strand=+ frame=1
+ATGCCCCAGATGGTGCTGATCTTCCAGTTGGCATGA
+>ORF32 id=32 start=952 stop=978 strand=+ frame=1
+ATGGTGCTGATCTTCCAGTTGGCATGA

test/findorfstest.jl

@@ -33,7 +33,6 @@
     # findorfs (GeneFinder.jl) --> 885
     # NCBI ORFfinder --> 375 ORFs
     # orfipy --> 375 (`orfipy NC_001416.1.fasta --start ATG --include-stop --min 75`)
-    # NC_001416 = fasta_to_dna("../../test/data/NC_001416.1.fasta")[1]
     NC_001416 = fasta_to_dna("data/NC_001416.1.fasta")[1]
     NC_001416_orfs = findorfs(NC_001416, min_len=75)
     @test length(NC_001416_orfs) == 885
@@ -42,7 +41,6 @@ end
 @testset "get_orfs_dna" begin
 
     seq01 = dna"ATGATGCATGCATGCATGCTAGTAACTAGCTAGCTAGCTAGTAA"
-    sseq01 = "ATGATGCATGCATGCATGCTAGTAACTAGCTAGCTAGCTAGTAA"
     orfseqs = get_orfs_dna(seq01)
 
     @test length(orfseqs) == 5

test/iotest.jl

@@ -0,0 +1,48 @@
+# Test the write_orfs_* methods
+@testset "write_orfs_f* " begin
+
+    # seq01 = dna"ATGATGCATGCATGCATGCTAGTAACTAGCTAGCTAGCTAGTAA"
+    # seq02 = dna"AACCAGGGCAATATCAGTACCGCGGGCAATGCAACCCTGACTGCCGGCGGTAACCTGAACAGCACTGGCAATCTGACTGTGGGCGGTGTTACCAACGGCACTGCTACTACTGGCAACATCGCACTGACCGGTAACAATGCGCTGAGCGGTCCGGTCAATCTGAATGCGTCGAATGGCACGGTGACCTTGAACACGACCGGCAATACCACGCTCGGTAACGTGACGGCACAAGGCAATGTGACGACCAATGTGTCCAACGGCAGTCTGACGGTTACCGGCAATACGACAGGTGCCAACACCAACCTCAGTGCCAGCGGCAACCTGACCGTGGGTAACCAGGGCAATATCAGTACCGCAGGCAATGCAACCCTGACGGCCGGCGACAACCTGACGAGCACTGGCAATCTGACTGTGGGCGGCGTCACCAACGGCACGGCCACCACCGGCAACATCGCGCTGACCGGTAACAATGCACTGGCTGGTCCTGTCAATCTGAACGCGCCGAACGGCACCGTGACCCTGAACACAACCGGCAATACCACGCTGGGTAATGTCACCGCACAAGGCAATGTGACGACTAATGTGTCCAACGGCAGCCTGACAGTCGCTGGCAATACCACAGGTGCCAACACCAACCTGAGTGCCAGCGGCAATCTGACCGTGGGCAACCAGGGCAATATCAGTACCGCGGGCAATGCAACCCTGACTGCCGGCGGTAACCTGAGC"
+
+    # Test case 1
+
+    # 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:
+    # 1) An alternative start codon (GTG) sequence at 48:347
+    # 2) A common start codon sequence at 426:590
+    # On the other hand, the NCBI ORFfinder program predicts 9 ORFs whose length is greater than 75 nt, from which one has an "outbound" stop
+    seq03 = dna"TTCGTCAGTCGTTCTGTTTCATTCAATACGATAGTAATGTATTTTTCGTGCATTTCCGGTGGAATCGTGCCGTCCAGCATAGCCTCCAGATATCCCCTTATAGAGGTCAGAGGGGAACGGAAATCGTGGGATACATTGGCTACAAACTTTTTCTGATCATCCTCGGAACGGGCAATTTCGCTTGCCATATAATTCAGACAGGAAGCCAGATAACCGATTTCATCCTCACTATCGACCTGAAATTCATAATGCATATTACCGGCAGCATACTGCTCTGTGGCATGAGTGATCTTCCTCAGAGGAATATATACGATCTCAGTGAAAAAGATCAGAATGATCAGGGATAGCAGGAACAGGATTGCCAGGGTGATATAGGAAATATTCAGCAGGTTGTTACAGGATTTCTGAATATCATTCATATCAGTATGGATGACTACATAGCCTTTTACCTTGTAGTTGGAGGTAATGGGAGCAAATACAGTAAGTACATCCGAATCAAAATTACCGAAGAAATCACCAACAATGTAATAGGAGCCGCTGGTTACGGTCGAATCAAAATTCTCAATGACAACCACATTCTCCACATCTAAGGGACTATTGGTATCCAGTACCAGTCGTCCGGAGGGATTGATGATGCGAATCTCGGAATTCAGGTAGACCGCCAGGGAGTCCAGCTGCATTTTAACGGTCTCCAAAGTTGTTTCACTGGTGTACAATCCGCCGGCATAGGTTCCGGCGATCAGGGTTGCTTCGGAATAGAGACTTTCTGCCTTTTCCCGGATCAGATGTTCTTTGGTCATATTGGGAACAAAAGTTGTAACAATGATGAAACCAAATACACCAAAAATAAAATATGCGAGTATAAATTTTAGATAAAGTGTTTTTTTCATAACAAATCCTGCTTTTGGTATGACTTAATTACGTACTTCGAATTTATAGCCGATGCCCCAGATGGTGCTGATCTTCCAGTTGGCATGATCCTTGATCTTCTC"
+
+    seq03fna = "data/out-seq03.fna"
+    open(seq03fna, "w") do io
+        write_orfs_fna(seq03, io)
+    end
+
+    seq03fnarecords = open(collect, FASTAReader, "data/out-seq03.fna")
+
+    @test seq03fnarecords[1] == FASTX.FASTA.Record("ORF01 id=01 start=5 stop=22 strand=- frame=2", "ATGAAACAGAACGACTGA")
+    @test length(seq03fnarecords) == 32
+    @test identifier(seq03fnarecords[1]) == "ORF01"
+    @test description(seq03fnarecords[1]) == "ORF01 id=01 start=5 stop=22 strand=- frame=2"
+    @test sequence(seq03fnarecords[1]) == "ATGAAACAGAACGACTGA"
+
+    # Test case 2
+
+    seq03faa = "data/out-seq03.faa"
+    open(seq03faa, "w") do io
+        write_orfs_faa(seq03, io)
+    end
+
+    seq03faarecords = open(collect, FASTAReader, "data/out-seq03.faa")
+
+    @test seq03faarecords[2] == FASTX.FASTA.Record("ORF02 id=02 start=37 stop=156 strand=+ frame=1", "MYFSCISGGIVPSSIASRYPLIEVRGERKSWDTLATNFF*")
+    @test length(seq03faarecords) == 32
+    @test identifier(seq03faarecords[2]) == "ORF02"
+    @test description(seq03faarecords[2]) == "ORF02 id=02 start=37 stop=156 strand=+ frame=1"
+    @test sequence(seq03faarecords[2]) == "MYFSCISGGIVPSSIASRYPLIEVRGERKSWDTLATNFF*"
+
+    # Test case 3 
+
+    @test seq03faarecords[3] == FASTX.FASTA.Record("ORF03 id=03 start=107 stop=136 strand=- frame=2", "MYPTISVPL*")
+
+end

test/runtests.jl

@@ -7,6 +7,7 @@ using GeneFinder
 using Aqua
 
 include("findorfstest.jl")
+include("iotest.jl")
 include("aquatest.jl")
 
 end