func (s *S) TestReadFastq(c *check.C) {
var (
obtainN []string
obtainQL [][]alphabet.QLetter
)
for _, fq := range fqs {
r := NewReader(bytes.NewBufferString(fq), nucleic.NewQSeq("", nil, alphabet.DNA, alphabet.Sanger))
for {
if s, err := r.Read(); err != nil {
if err == io.EOF {
break
} else {
c.Fatalf("Failed to read %q: %s", fq, err)
}
} else {
t := s.(*nucleic.QSeq)
header := *t.Name()
if desc := *t.Description(); len(desc) > 0 {
header += " " + desc
}
obtainN = append(obtainN, header)
obtainQL = append(obtainQL, *(t.Raw().(*[]alphabet.QLetter)))
}
}
c.Check(obtainN, check.DeepEquals, expectN)
obtainN = nil
c.Check(obtainQL, check.DeepEquals, expectQL)
obtainQL = nil
}
}
func (s *S) TestWriteFastq(c *check.C) {
fq := fqs[0]
names := 0
for _, n := range expectN {
names += len(n)
}
expectSize := []int{2722, 2722 - names}
var total int
for j := 0; j < 2; j++ {
b := &bytes.Buffer{}
w := NewWriter(b)
w.QID = j == 0
seq := nucleic.NewQSeq("", nil, alphabet.DNA, alphabet.Sanger)
for i := range expectN {
seq.ID = expectN[i]
seq.S = expectQL[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[j])
total = 0
if w.QID {
c.Check(string(b.Bytes()), check.Equals, fq)
}
}
}
func (self *QSeq) Extract(i int) nucleic.Sequence {
s := make([]alphabet.QLetter, 0, self.Len())
for _, c := range self.S {
s = append(s, c[i])
}
return nucleic.NewQSeq(self.SubIDs[i], s, self.alphabet, self.encoding)
}
func ExampleSeq_Add() {
fmt.Printf("%v %v\n", m.Count(), m)
m.Add(nucleic.NewQSeq("example DNA",
[]alphabet.QLetter{{'a', 40}, {'c', 39}, {'g', 40}, {'C', 38}, {'t', 35}, {'g', 20}},
alphabet.DNA, alphabet.Sanger))
fmt.Printf("%v %v\n", m.Count(), m)
// Output:
// 3 acgntgacntggcgcncat
// 4 acgctgacntggcgcncat
}
func (self *Multi) Consensus(includeMissing bool) (c *nucleic.QSeq) {
cs := make([]alphabet.QLetter, 0, self.Len())
for i := self.Start(); i < self.End(); i++ {
cs = append(cs, self.Consensify(self, i, includeMissing))
}
c = nucleic.NewQSeq("Consensus:"+self.ID, cs, self.alphabet, self.encoding)
c.Offset(self.offset)
return
}
func (self *QSeq) Consensus(_ bool) (qs *nucleic.QSeq) {
cs := make([]alphabet.QLetter, 0, self.Len())
for i := range self.S {
cs = append(cs, self.Consensify(self, i, false))
}
qs = nucleic.NewQSeq("Consensus:"+self.ID, cs, self.alphabet, alphabet.Sanger)
qs.Strand = self.Strand
qs.Offset(self.offset)
qs.Circular(self.circular)
return
}
func ExampleMulti_Add() {
var err error
fmt.Printf("%v %v\n", m.Count(), m)
err = m.Add(nucleic.NewQSeq("example DNA",
[]alphabet.QLetter{{'a', 40}, {'c', 39}, {'g', 40}, {'C', 38}, {'t', 35}, {'g', 20}},
alphabet.DNA, alphabet.Sanger))
if err != nil {
fmt.Println(err)
return
}
fmt.Printf("%v %v\n", m.Count(), m)
err = m.Add(nucleic.NewQSeq("example RNA",
[]alphabet.QLetter{{'a', 40}, {'c', 39}, {'g', 40}, {'C', 38}, {'t', 35}, {'g', 20}},
alphabet.RNA, alphabet.Sanger))
if err != nil {
fmt.Println(err)
return
}
// Output:
// 3 acgntgacntggcgcncat
// 4 acgctgacntggcgcncat
// Inconsistent alphabets
}