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package seq
import (
"regexp"
"strings"
"testing"
)
func TestAlphabet(t *testing.T) {
dna := []byte("acgtACGT")
dna2 := []byte("ACGTRYSWKMBDHV")
rna := []byte("AUGCUUCCGGCCUGUUCCCUGAGACCUCAAGUGUGAGUGUACUAU" +
"UGAUGCUUCACACCUGGGCUCUCCGGGUACCAGGACGGUUUGAGCAGAU")
rna2 := []byte("ACGURYSWKMBDHV")
protein := []byte(regexp.MustCompile(`\r?\n|\s`).ReplaceAllString(
`MGLNRFMRAMMVVFITANCITINPDIIFAATDSEDSSLNTDEWEEEKTEEQPSEVNTGPR
YETAREVSSRDIKELEKSNKVRNTNKADLIAMLKEKAEKGPNINNNNSEQTENAAINEEA
SGADRPAIQVERRHPGLPSDSAAEIKKRRKAIASSDSELESLTYPDKPTKVNKKKVAKES
VADASESDLDSSMQSADESSPQPLKANQQPFFPKVFKKIKDAGKWVRDKIDENPEVKKAI
VDKSAGLIDQLLTKKKSEEVNASDFPPPPTDEELRLALPETPMLLGFNAPATSEPSSFEF
PPPPTDEELRLALPETPMLLGFNAPATSEPSSFEFPPPPTEDELEIIRETASSLDSSFTR
GDLASLRNAINRHSQNFSDFPPIPTEEELNGRGGRPTSEEFSSLNSGDFTDDENSETTEE
EIDRLADLRDRGTGKHSRNAGFLPLNPFASSPVPSLSPKVSKISAPALISDITKKTPFKN
PSQPLNVFNKKTTTKTVTKKPTPVKTAPKLAELPATKPQETVLRENKTPFIEKQAETNKQ
SINMPSLPVIQKEATESDKEEMKPQTEEKMVEESESANNANGKNRSAGIEEGKLIAKSAE
DEKAKEEPGNHTTLILAMLAIGVFSLGAFIKIIQLRKNN`, ""))
ok := DNA.IsValid(dna) == nil &&
DNAredundant.IsValid(dna2) == nil &&
RNA.IsValid(rna) == nil &&
RNAredundant.IsValid(rna2) == nil &&
Protein.IsValid(protein) == nil
if !ok {
t.Error("validating sequence failed.")
return
}
// fmt.Println("protein", GuessAlphabet(protein))
// fmt.Println("dna2", GuessAlphabet(dna2))
// fmt.Println("dna", GuessAlphabet(dna))
// fmt.Println("rna2", GuessAlphabet(rna2))
// fmt.Println("rna", GuessAlphabet(rna))
ok = GuessAlphabet(dna) == DNA && GuessAlphabet(dna2) == DNAredundant && GuessAlphabet(rna) == RNA && GuessAlphabet(rna2) == RNAredundant && GuessAlphabet(protein) == Protein
if !ok {
t.Error("guessing alphabet error")
return
}
}
func TestAlphabet2(t *testing.T) {
s := regexp.MustCompile(`\r?\n|\s`).ReplaceAllString(
`MGLNRFMRAMMVVFITANCITINPDIIFAATDSEDSSLNTDEWEEEKTEEQPSEVNTGPR
YETAREVSSRDIKELEKSNKVRNTNKADLIAMLKEKAEKGPNINNNNSEQTENAAINEEA
SGADRPAIQVERRHPGLPSDSAAEIKKRRKAIASSDSELESLTYPDKPTKVNKKKVAKES
VADASESDLDSSMQSADESSPQPLKANQQPFFPKVFKKIKDAGKWVRDKIDENPEVKKAI
VDKSAGLIDQLLTKKKSEEVNASDFPPPPTDEELRLALPETPMLLGFNAPATSEPSSFEF
PPPPTDEELRLALPETPMLLGFNAPATSEPSSFEFPPPPTEDELEIIRETASSLDSSFTR
GDLASLRNAINRHSQNFSDFPPIPTEEELNGRGGRPTSEEFSSLNSGDFTDDENSETTEE
EIDRLADLRDRGTGKHSRNAGFLPLNPFASSPVPSLSPKVSKISAPALISDITKKTPFKN
PSQPLNVFNKKTTTKTVTKKPTPVKTAPKLAELPATKPQETVLRENKTPFIEKQAETNKQ
SINMPSLPVIQKEATESDKEEMKPQTEEKMVEESESANNANGKNRSAGIEEGKLIAKSAE
DEKAKEEPGNHTTLILAMLAIGVFSLGAFIKIIQLRKNN>`, "")
protein := []byte(strings.Repeat(s, 1000))
ok := Protein.IsValid(protein) == nil
if ok {
t.Error("validating sequence failed.")
return
}
}
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