func ExampleQSeq_RevComp() {
q := []alphabet.Qphred{
2, 13, 19, 22, 19, 18, 20, 23, 23, 20, 16, 21, 24, 22, 22, 18, 17, 18, 22, 23, 22, 24, 22, 24, 20, 15,
18, 18, 19, 19, 20, 12, 18, 17, 20, 20, 20, 18, 15, 18, 24, 21, 13, 8, 15, 20, 20, 19, 20, 20, 20, 18,
16, 16, 16, 10, 15, 18, 18, 18, 11, 2, 11, 20, 19, 18, 18, 16, 10, 12, 22, 0, 0, 0, 0}
l := []alphabet.Letter("NTTTCTTCTATATCCTTTTCATCTTTTAATCCATTCACCATTTTTTTCCCTCCACCTACCTNTCCTTCTCTTTCT")
if s, err := NewQSeq("example DNA", nil, alphabet.DNA, alphabet.Sanger); err == nil {
s.Stringify = func(p seq.Polymer) string {
s := p.(*QSeq)
lb, qb, b := []alphabet.Letter{}, []byte{}, []byte{}
for i, qp := range s.S {
ql := qp.Unpack(s.Alphabet().(alphabet.Nucleic))
if ql.Q > 2 {
ql.L &^= 0x20
} else {
ql.L = 'n'
}
lb = append(lb, ql.L)
qb = append(qb, s.QEncode(seq.Position{Pos: i}))
}
b = append(b, alphabet.LettersToBytes(lb)...)
b = append(b, '\n')
b = append(b, qb...)
return string(b)
}
for i := range l {
s.AppendQLetters(alphabet.QLetter{L: l[i], Q: q[i]})
}
fmt.Println("Forward:")
fmt.Println(s)
s.RevComp()
fmt.Println("Reverse:")
fmt.Println(s)
}
// Output:
// Forward:
// nTTTCTTCTATATCCTTTTCATCTTTTAATCCATTCACCATTTTTTTCCCTCCACCTACCTnTCCTTCTCTnnnn
// #.47435885169773237879795033445-3255530396.)05545553111+0333,#,54331+-7!!!!
// Reverse:
// nnnnAGAGAAGGAnAGGTAGGTGGAGGGAAAAAAATGGTGAATGGATTAAAAGATGAAAAGGATATAGAAGAAAn
// !!!!7-+13345,#,3330+11135554550).6930355523-54433059797873237796158853474.#
}
func ExampleQSeq_Append() {
q := []alphabet.Qphred{
2, 13, 19, 22, 19, 18, 20, 23, 23, 20, 16, 21, 24, 22, 22, 18, 17, 18, 22, 23, 22, 24, 22, 24, 20, 15,
18, 18, 19, 19, 20, 12, 18, 17, 20, 20, 20, 18, 15, 18, 24, 21, 13, 8, 15, 20, 20, 19, 20, 20, 20, 18,
16, 16, 16, 10, 15, 18, 18, 18, 11, 2, 11, 20, 19, 18, 18, 16, 10, 12, 22, 0, 0, 0, 0}
l := []alphabet.Letter("NTTTCTTCTATATCCTTTTCATCTTTTAATCCATTCACCATTTTTTTCCCTCCACCTACCTNTCCTTCTCTTTCT")
s := NewQSeq("example Protein", nil, alphabet.Protein, alphabet.Sanger)
s.Stringify = func(p seq.Polymer) string {
s := p.(*QSeq)
lb, qb, b := []alphabet.Letter{}, []byte{}, []byte{}
for i, ql := range s.S {
lb = append(lb, ql.L)
qb = append(qb, s.QEncode(seq.Position{Pos: i}))
}
b = append(b, alphabet.LettersToBytes(lb)...)
b = append(b, '\n')
b = append(b, qb...)
return string(b)
}
for i := range l {
s.AppendQLetters(alphabet.QLetter{L: l[i], Q: q[i]})
}
fmt.Println("Forward:")
fmt.Println(s)
s.Reverse()
fmt.Println("Reverse:")
fmt.Println(s)
// Output:
// Forward:
// NTTTCTTCTATATCCTTTTCATCTTTTAATCCATTCACCATTTTTTTCCCTCCACCTACCTNTCCTTCTCTTTCT
// #.47435885169773237879795033445-3255530396.)05545553111+0333,#,54331+-7!!!!
// Reverse:
// TCTTTCTCTTCCTNTCCATCCACCTCCCTTTTTTTACCACTTACCTAATTTTCTACTTTTCCTATATCTTCTTTN
// !!!!7-+13345,#,3330+11135554550).6930355523-54433059797873237796158853474.#
}