func init() {
var err error
m, err = NewMulti("example multi",
[]nucleic.Sequence{
nucleic.NewSeq("example DNA 1", []alphabet.Letter("ACGCTGACTTGGTGCACGT"), alphabet.DNA),
nucleic.NewSeq("example DNA 2", []alphabet.Letter("ACGGTGACCTGGCGCGCAT"), alphabet.DNA),
nucleic.NewSeq("example DNA 3", []alphabet.Letter("ACGATGACGTGGCGCTCAT"), alphabet.DNA),
},
nucleic.Consensify)
if err != nil {
panic(err)
}
}
// Return an unpacked sequence.
func (self *Seq) Unpack() (n *nucleic.Seq) {
n = nucleic.NewSeq(self.ID, alphabet.BytesToLetters([]byte(self.String())), self.alphabet)
n.Circular(self.circular)
n.Offset(self.offset)
return
}
func ExampleSet_AppendEach() {
ss := [][]alphabet.Letter{
[]alphabet.Letter("ACGCTGACTTGGTGCACGT"),
[]alphabet.Letter("ACGACTGGGACGT"),
[]alphabet.Letter("ACGCTGACTGGCCGT"),
[]alphabet.Letter("GCCTTTGCACGT"),
}
set = make(Set, 4)
for i := range set {
set[i] = nucleic.NewSeq(fmt.Sprintf("example DNA %d", i), ss[i], alphabet.DNA)
}
as := [][]alphabet.QLetter{
alphabet.QLetter{L: 'A'}.Repeat(2),
alphabet.QLetter{L: 'C'}.Repeat(2),
alphabet.QLetter{L: 'G'}.Repeat(2),
alphabet.QLetter{L: 'T'}.Repeat(2),
}
set.AppendEach(as)
for _, s := range set {
fmt.Println(s)
}
// Output:
// ACGCTGACTTGGTGCACGTAA
// ACGACTGGGACGTCC
// ACGCTGACTGGCCGTGG
// GCCTTTGCACGTTT
}
func (self *Seq) Extract(i int) nucleic.Sequence {
s := make([]alphabet.Letter, 0, self.Len())
for _, c := range self.S {
s = append(s, c[i])
}
return nucleic.NewSeq(self.SubIDs[i], s, self.alphabet)
}
func ExampleNewMulti() {
m, err := NewMulti("example multi",
[]nucleic.Sequence{
nucleic.NewSeq("example DNA 1", []alphabet.Letter("ACGCTGACTTGGTGCACGT"), alphabet.DNA),
nucleic.NewSeq("example DNA 2", []alphabet.Letter("ACGGTGACCTGGCGCGCAT"), alphabet.DNA),
nucleic.NewSeq("example DNA 3", []alphabet.Letter("ACGATGACGTGGCGCTCAT"), alphabet.DNA),
},
nucleic.Consensify)
if err != nil {
return
}
aligned(m)
// Output:
// ACGCTGACTTGGTGCACGT
// ACGGTGACCTGGCGCGCAT
// ACGATGACGTGGCGCTCAT
//
// acgntgacntggcgcncat
}
// Return an unpacked sequence and quality.
func (self *QSeq) Unpack() (n *nucleic.Seq, q *quality.Phred) {
n = nucleic.NewSeq(self.ID, alphabet.BytesToLetters([]byte(self.String())), self.alphabet)
n.Circular(self.circular)
n.Offset(self.offset)
qb := make([]alphabet.Qphred, self.Len())
for i, v := range self.S {
qb[i] = alphabet.Qphred(v >> 2)
}
q = quality.NewPhred(self.ID, qb, self.encoding)
q.Circular(self.circular)
q.Offset(self.offset)
return
}