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package seq
import (
"regexp"
"testing"
)
type codonTableTest struct {
table int
nt string
aa string
frame int
trim bool
clean bool
allowUnknownCodon bool
markInitCodonAsM bool
}
var codonTableTests []codonTableTest
func init() {
re := regexp.MustCompile(`\r?\n|\s`)
codonTableTests = make([]codonTableTest, 0, 10)
// https://www.ncbi.nlm.nih.gov/nuccore/AB021961.1
codonTableTests = append(codonTableTests,
codonTableTest{
table: 1,
nt: re.ReplaceAllString(`atgactgccatggaggagtcacagtcggatatcagcctcgagctccctctgagccaggag
acattttcaggcttatggaaactacttcctccagaagatatcctgccatcacctcactgc
atggacgatctgttgctgccccaggatgttgaggagttttttgaaggcccaagtgaagcc
ctccgagtgtcaggagctcctgcagcacaggaccctgtcaccgagacccctgggccagtg
gcccctgccccagccactccatggcccctgtcatcttttgtcccttctcaaaaaacttac
cagggcaactatggcttccacctgggcttcctgcagtctgggacagccaagtctgttatg
tgcacgtactctcctcccctcaataagctattctgccagctggcgaagacgtgccctgtg
cagttgtgggtcagcgccacacctccagctgggagccgtgtccgcgccatggccatctac
aagaagtcacagcacatgacggaggtcgtgagacgctgcccccaccatgagcgctgctcc
gatggtgatggcctggctcctccccagcatcgtatccgggtggaaggaaatttgtatccc
gagtatctggaagacaggcagacttttcgccacagcgtggtggtaccttatgagccaccc
gaggccggctctgagtataccaccatccactacaagtacatgtgtaatagctcctgcatg
gggggcatgaaccgccgacctatccttaccatcatcacactggaagactccagtgggaac
cttctgggacgggacagctttgaggttcgtgtttgtgcctgccctgggagagaccgccgt
acagaagaagaaaatttccgcaaaaaggaagtcctttgccctgaactgcccccagggagc
gcaaagagagcgctgcccacctgcacaagcgcctctcccccgcaaaagaaaaaaccactt
gatggagagtatttcaccctcaagatccgcgggcgtaaacgcttcgagatgttccgggag
ctgaatgaggccttagagttaaaggatgcccatgctacagaggagtctggagacagcagg
gctcactccagctacctgaagaccaagaagggccagtctacttcccgccataaaaaaaca
atggtcaagaaagtggggcctgactcagactga`, ""),
aa: re.ReplaceAllString(`MTAMEESQSDISLELPLSQETFSGLWKLLPPEDILPSPHCMDDL
LLPQDVEEFFEGPSEALRVSGAPAAQDPVTETPGPVAPAPATPWPLSSFVPSQKTYQG
NYGFHLGFLQSGTAKSVMCTYSPPLNKLFCQLAKTCPVQLWVSATPPAGSRVRAMAIY
KKSQHMTEVVRRCPHHERCSDGDGLAPPQHRIRVEGNLYPEYLEDRQTFRHSVVVPYE
PPEAGSEYTTIHYKYMCNSSCMGGMNRRPILTIITLEDSSGNLLGRDSFEVRVCACPG
RDRRTEEENFRKKEVLCPELPPGSAKRALPTCTSASPPQKKKPLDGEYFTLKIRGRKR
FEMFRELNEALELKDAHATEESGDSRAHSSYLKTKKGQSTSRHKKTMVKKVGPDSD`, ""),
frame: 1,
trim: true,
clean: false,
})
// ORF25 from https://www.ncbi.nlm.nih.gov/nuccore/AJ245616.1
codonTableTests = append(codonTableTests,
codonTableTest{
table: 11,
nt: re.ReplaceAllString(`atggaggaacaagcatggcgagaagtcctcgaacgtttagctcga
attgaaacaaagttagataactatgaaacagttcgagataaagcagaacgagcgctccta
atagctcaatcaaatgcgaaacttatagaaaaaatggaagctaataataagtgggcttgg
ggctttatgcttactcttgccgtaactgttattggttatttattcactaaaattagattc
tga`, ""),
aa: re.ReplaceAllString(`MEEQAWREVLERLARIETKLDNYETVRDKAERALLIAQSNAKLI
EKMEANNKWAWGFMLTLAVTVIGYLFTKIRF`, ""),
frame: 1,
trim: true,
clean: false,
})
codonTableTests = append(codonTableTests,
codonTableTest{
table: 11,
nt: re.ReplaceAllString(`tcagaatctaattttagtgaataaataaccaataacagttacggcaagagtaagcataaa
gccccaagcccacttattattagcttccattttttctataagtttcgcatttgattgagc
tattaggagcgctcgttctgctttatctcgaactgtttcatagttatctaactttgtttc
aattcgagctaaacgttcgaggacttctcgccatgcttgttcctccat`, ""),
aa: re.ReplaceAllString(`MEEQAWREVLERLARIETKLDNYETVRDKAERALLIAQSNAKLI
EKMEANNKWAWGFMLTLAVTVIGYLFTKIRF`, ""),
frame: -1,
trim: true,
clean: false,
})
codonTableTests = append(codonTableTests,
codonTableTest{
table: 11,
nt: re.ReplaceAllString(`tcagaatctaattttagtgaataaataaccaataacagttacggcaagagtaagcataaa
gccccaagcccacttattattagcttccattttttctataagtttcgcatttgattgagc
tattaggagcgctcgttctgctttatctcgaactgtttcatagttatctaactttgtttc
aattcgagctaaacgttcgaggacttctcgccatgcttgttcctccatc`, ""),
aa: re.ReplaceAllString(`MEEQAWREVLERLARIETKLDNYETVRDKAERALLIAQSNAKLI
EKMEANNKWAWGFMLTLAVTVIGYLFTKIRF`, ""),
frame: -2,
trim: true,
clean: false,
})
codonTableTests = append(codonTableTests,
codonTableTest{
table: 11,
nt: re.ReplaceAllString(`tcagaatctaattttagtgaataaataaccaataacagttacggcaagagtaagcataaa
gccccaagcccacttattattagcttccattttttctataagtttcgcatttgattgagc
tattaggagcgctcgttctgctttatctcgaactgtttcatagttatctaactttgtttc
aattcgagctaaacgttcgaggacttctcgccatgcttgttcctccatcc`, ""),
aa: re.ReplaceAllString(`MEEQAWREVLERLARIETKLDNYETVRDKAERALLIAQSNAKLI
EKMEANNKWAWGFMLTLAVTVIGYLFTKIRF`, ""),
frame: -3,
trim: true,
clean: false,
})
codonTableTests = append(codonTableTests,
codonTableTest{
table: 11,
nt: re.ReplaceAllString(`atNgaggaacaagcatggcgagaagtcctcgaacgtttagctcga
attgaaacaaagttagataactatgaaacagttcgagataaagcagaacgagcgctccta
atagctcaatcaaatgcgaaacttatagaaaaaatggaagctaataataagtgggcttgg
ggctttatgcttactcttgccgtaactgttattggttatttattcactaaaattagattc
tga`, ""),
aa: re.ReplaceAllString(`XEEQAWREVLERLARIETKLDNYETVRDKAERALLIAQSNAKLI
EKMEANNKWAWGFMLTLAVTVIGYLFTKIRF*`, ""),
frame: 1,
trim: false,
clean: false,
allowUnknownCodon: true,
})
}
func TestCodonTableStranslation(t *testing.T) {
var aa []byte
var err error
for i, test := range codonTableTests {
aa, err = CodonTables[test.table].Translate([]byte(test.nt), test.frame, test.trim, test.clean, test.allowUnknownCodon, test.markInitCodonAsM)
if err != nil {
t.Errorf("test %d err: %s", i, err)
}
if len(aa) != len(test.aa) {
t.Errorf("test %d err: len unequal, answer: %d, result: %d", i, len(aa), len(test.aa))
}
if string(aa) != test.aa {
t.Errorf("test %d err: result not right", i)
}
}
}
|
