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) }