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|
package seq
import (
"fmt"
"testing"
)
func TestValidateSequence(t *testing.T) {
dna := []byte("acgt")
dna2 := []byte("ACGTRYMKSWHBVDN")
rna := []byte("acgu")
fake := []byte("acgturymkswhbvdnz")
ok := DNA.IsValid(dna) == nil &&
DNAredundant.IsValid(dna2) == nil &&
RNA.IsValid(rna) == nil &&
RNA.IsValid(fake) != nil
if !ok {
t.Error("validate sequence failed.")
return
}
}
func TestRevCom(t *testing.T) {
dna, _ := NewSeq(DNA, []byte("acgtccn-"))
if string(dna.RevCom().Seq) != "-nggacgt" {
t.Error("revcom sequence failed.")
return
}
rna, _ := NewSeq(RNA, []byte("auguccn-"))
if string(rna.RevCom().Seq) != "-nggacau" {
t.Error("revcom sequence failed.")
return
}
}
func TestBaseContent(t *testing.T) {
dna, _ := NewSeq(DNA, []byte("acgtACGT"))
content := dna.BaseContent("gc")
wanted := 0.5
if content != wanted {
t.Error(fmt.Printf("compution of base content failed: %f != %f", content, wanted))
return
}
}
func TestSubSeq(t *testing.T) {
s, _ := NewSeqWithoutValidation(DNA, []byte("ACGTNacgtn"))
ok := string(s.SubSeq(1, 1).Seq) == "A" &&
string(s.SubSeq(2, 4).Seq) == "CGT" &&
string(s.SubSeq(-4, -2).Seq) == "cgt" &&
string(s.SubSeq(-4, -1).Seq) == "cgtn" &&
string(s.SubSeq(-1, -1).Seq) == "n" &&
string(s.SubSeq(2, -2).Seq) == "CGTNacgt" &&
string(s.SubSeq(1, -1).Seq) == "ACGTNacgtn" &&
string(s.SubSeq(12, 14).Seq) == "" &&
string(s.SubSeq(-10, -1).Seq) == "ACGTNacgtn" &&
string(s.SubSeq(-10, -3).Seq) == "ACGTNacg" &&
string(s.SubSeq(1, 10).Seq) == "ACGTNacgtn" &&
string(s.SubSeq(3, 12).Seq) == "GTNacgtn" &&
string(s.SubSeq(3, 100).Seq) == "GTNacgtn"
if !ok {
t.Error(fmt.Printf("subseq error"))
}
ok = string(s.SubSeq(-4, 2).Seq) == "" &&
string(s.SubSeq(-3, -4).Seq) == ""
if !ok {
t.Error(fmt.Printf("subseq error"))
}
s, _ = NewSeqWithoutValidation(DNA, []byte(""))
ok = string(s.SubSeq(1, 4).Seq) == "" &&
string(s.SubSeq(2, 4).Seq) == "" &&
string(s.SubSeq(1, -1).Seq) == "" &&
string(s.SubSeq(-4, -1).Seq) == ""
if !ok {
t.Error(fmt.Printf("subseq error"))
}
}
func TestSubSeqInplace(t *testing.T) {
s, _ := NewSeqWithoutValidation(DNA, []byte("ACGTNacgtn"))
ok := string(s.Clone().SubSeqInplace(1, 1).Seq) == "A" &&
string(s.Clone().SubSeqInplace(2, 4).Seq) == "CGT" &&
string(s.Clone().SubSeqInplace(-4, -2).Seq) == "cgt" &&
string(s.Clone().SubSeqInplace(-4, -1).Seq) == "cgtn" &&
string(s.Clone().SubSeqInplace(-1, -1).Seq) == "n" &&
string(s.Clone().SubSeqInplace(2, -2).Seq) == "CGTNacgt" &&
string(s.Clone().SubSeqInplace(1, -1).Seq) == "ACGTNacgtn" &&
string(s.Clone().SubSeqInplace(-10, -1).Seq) == "ACGTNacgtn" &&
string(s.Clone().SubSeqInplace(-10, -3).Seq) == "ACGTNacg" &&
string(s.Clone().SubSeqInplace(1, 10).Seq) == "ACGTNacgtn" &&
string(s.Clone().SubSeqInplace(3, 10).Seq) == "GTNacgtn" &&
string(s.Clone().SubSeqInplace(3, 100).Seq) == "GTNacgtn"
if !ok {
t.Error(fmt.Printf("SubSeqInplace error"))
}
ok = string(s.Clone().SubSeqInplace(-4, 2).Seq) == "" &&
string(s.Clone().SubSeqInplace(-3, -4).Seq) == ""
if !ok {
t.Error(fmt.Printf("SubSeqInplace error"))
}
s, _ = NewSeqWithoutValidation(DNA, []byte(""))
ok = string(s.Clone().SubSeqInplace(1, 4).Seq) == "" &&
string(s.Clone().SubSeqInplace(2, 4).Seq) == "" &&
string(s.Clone().SubSeqInplace(1, -1).Seq) == "" &&
string(s.Clone().SubSeqInplace(-4, -1).Seq) == ""
if !ok {
t.Error(fmt.Printf("subseq error"))
}
}
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