func (s *S) TestWriteFastq(c *check.C) {
for i, t := range fqTests {
if !t.verbatim {
continue
}
for j := 0; j < 2; j++ {
var n int
b := &bytes.Buffer{}
w := NewWriter(b)
w.QID = j == 0
seq := linear.NewQSeq("", nil, alphabet.DNA, alphabet.Sanger)
for i := range expectedIds {
seq.ID = t.ids[i]
seq.Seq = t.seqs[i]
_n, err := w.Write(seq)
c.Assert(err, check.Equals, nil, check.Commentf("Failed to write to buffer: %s", err))
n += _n
}
c.Check(n, check.Equals, b.Len())
if w.QID {
c.Check(string(b.Bytes()), check.Equals, t.fq, check.Commentf("Write test %d", i))
}
}
}
}
func (s *S) TestReadFastq(c *check.C) {
r := fastq.NewReader(strings.NewReader(fq), linear.NewQSeq("", nil, alphabet.DNA, alphabet.Sanger))
m, _ := multi.NewMulti("", nil, seq.DefaultQConsensus)
a, err := NewReader(r, m).Read()
c.Check(err, check.Equals, nil)
c.Check(a.Rows(), check.Equals, 25)
}
func (s *S) TestReadFastq(c *check.C) {
var (
obtainNfq []string
obtainQL [][]alphabet.QLetter
)
sc := seqio.NewScanner(
fastq.NewReader(
bytes.NewBufferString(fq0),
linear.NewQSeq("", nil, alphabet.DNA, alphabet.Sanger),
),
)
for sc.Next() {
t := sc.Seq().(*linear.QSeq)
header := t.Name()
if desc := t.Description(); len(desc) > 0 {
header += " " + desc
}
obtainNfq = append(obtainNfq, header)
obtainQL = append(obtainQL, (t.Slice().(alphabet.QLetters)))
}
c.Check(sc.Error(), check.Equals, nil)
c.Check(obtainNfq, check.DeepEquals, expectNfq)
c.Check(obtainQL, check.DeepEquals, expectQL)
}
func (r QRow) Clone() seq.Sequence {
b := make([]alphabet.QLetter, r.Len())
for i, c := range r.Align.Seq {
b[i] = c[r.Row]
}
return linear.NewQSeq(r.Name(), b, r.Alphabet(), r.Align.Encoding())
}
func ExampleSeq_Add() {
fmt.Printf("%v %-s\n", m.Rows(), m.Consensus(false))
m.Add(linear.NewQSeq("example DNA",
[]alphabet.QLetter{{'a', 40}, {'c', 39}, {'g', 40}, {'C', 38}, {'t', 35}, {'g', 20}},
alphabet.DNA, alphabet.Sanger))
fmt.Printf("%v %-s\n", m.Rows(), m.Consensus(false))
// Output:
// 3 acgntgacntggcgcncat
// 4 acgctgacntggcgcncat
}
// Consensus returns a quality sequence reflecting the consensus of the receiver determined by the
// ColumnConsense field.
func (m *Multi) Consensus(includeMissing bool) *linear.QSeq {
cm := make([]alphabet.QLetter, 0, m.Len())
alpha := m.Alphabet()
for i := m.Start(); i < m.End(); i++ {
cm = append(cm, m.ColumnConsense(m, alpha, i, includeMissing))
}
c := linear.NewQSeq("Consensus:"+m.ID, cm, m.Alpha, m.Encode)
c.SetOffset(m.Offset)
return c
}
// Consensus returns a quality sequence reflecting the consensus of the receiver determined by the
// ColumnConsense field.
func (s *Seq) Consensus(_ bool) *linear.QSeq {
cs := make([]alphabet.QLetter, 0, s.Len())
alpha := s.Alphabet()
for i := range s.Seq {
cs = append(cs, s.ColumnConsense(s, alpha, i, false))
}
qs := linear.NewQSeq("Consensus:"+s.ID, cs, s.Alpha, alphabet.Sanger)
qs.Strand = s.Strand
qs.SetOffset(s.Offset)
qs.Conform = s.Conform
return qs
}
func ExampleMulti_Add() {
var err error
fmt.Printf("%v %-s\n", m.Rows(), m.Consensus(false))
err = m.Add(linear.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 %-s\n", m.Rows(), m.Consensus(false))
err = m.Add(linear.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
// multi: inconsistent alphabets
}
func (s *S) TestReadFastq(c *check.C) {
for _, t := range fqTests {
r := NewReader(bytes.NewBufferString(t.fq), linear.NewQSeq("", nil, alphabet.DNA, alphabet.Sanger))
var n int
for n = 0; ; n++ {
if s, err := r.Read(); err != nil {
if err == io.EOF {
break
} else {
c.Fatalf("Failed to read %s in %q: %s", expectedIds[n], t.fq, err)
}
} else {
l := s.(*linear.QSeq)
header := l.Name()
if desc := l.Description(); len(desc) > 0 {
header += " " + desc
}
c.Check(header, check.Equals, t.ids[n])
c.Check(l.Slice(), check.DeepEquals, t.seqs[n])
}
}
c.Check(n, check.Equals, len(t.ids))
}
}
