func init() {
var err error
m, err = NewMulti("example multi",
[]protein.Sequence{
protein.NewSeq("example protein 1", []alphabet.Letter("ACGCTGACTTGGTGCACGT"), alphabet.Protein),
protein.NewSeq("example protein 2", []alphabet.Letter("ACGGTGACCTGGCGCGCAT"), alphabet.Protein),
protein.NewSeq("example protein 3", []alphabet.Letter("ACGATGACGTGGCGCTCAT"), alphabet.Protein),
},
protein.Consensify)
if err != nil {
panic(err)
}
}
func (s *S) TestReadFasta(c *check.C) {
var (
obtainN []string
obtainS [][]alphabet.Letter
)
for _, fa := range fas {
r := NewReader(bytes.NewBufferString(fa), protein.NewSeq("", nil, alphabet.Protein))
for {
if s, err := r.Read(); err != nil {
if err == io.EOF {
break
} else {
c.Fatalf("Failed to read %q: %s", fa, err)
}
} else {
t := s.(*protein.Seq)
header := *t.Name()
if desc := *t.Description(); len(desc) > 0 {
header += " " + desc
}
obtainN = append(obtainN, header)
obtainS = append(obtainS, *(t.Raw().(*[]alphabet.Letter)))
}
}
c.Check(obtainN, check.DeepEquals, expectN)
obtainN = nil
for i := range obtainS {
c.Check(len(obtainS[i]), check.Equals, len(expectS[i]))
c.Check(obtainS[i], check.DeepEquals, expectS[i])
}
obtainS = nil
}
}
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] = protein.NewSeq(fmt.Sprintf("example DNA %d", i), ss[i], alphabet.Protein)
}
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) protein.Sequence {
s := make([]alphabet.Letter, 0, self.Len())
for _, c := range self.S {
s = append(s, c[i])
}
return protein.NewSeq(self.SubIDs[i], s, self.alphabet)
}
func ExampleNewMulti() {
m, err := NewMulti("example multi",
[]protein.Sequence{
protein.NewSeq("example protein 1", []alphabet.Letter("ACGCTGACTTGGTGCACGT"), alphabet.Protein),
protein.NewSeq("example protein 2", []alphabet.Letter("ACGGTGACCTGGCGCGCAT"), alphabet.Protein),
protein.NewSeq("example protein 3", []alphabet.Letter("ACGATGACGTGGCGCTCAT"), alphabet.Protein),
},
protein.Consensify)
if err != nil {
return
}
aligned(m)
// Output:
// ACGCTGACTTGGTGCACGT
// ACGGTGACCTGGCGCGCAT
// ACGATGACGTGGCGCTCAT
//
// acgxtgacxtggcgcxcat
}
func (s *S) TestWriteFasta(c *check.C) {
fa := fas[0]
expectSize := 4649
var total int
b := &bytes.Buffer{}
w := NewWriter(b, 60)
seq := protein.NewSeq("", nil, alphabet.Protein)
for i := range expectN {
seq.ID = expectN[i]
seq.S = expectS[i]
if n, err := w.Write(seq); err != nil {
c.Fatalf("Failed to write to buffer: %s", err)
} else {
total += n
}
}
c.Check(total, check.Equals, expectSize)
c.Check(string(b.Bytes()), check.Equals, fa)
}