func (s *S) TestKmerFrequencies(c *check.C) {
for k := MinKmerLen; k <= MaxKmerLen; k++ {
if i, err := New(k, s.Seq); err != nil {
c.Fatalf("New KmerIndex failed: %v", err)
} else {
freqs, ok := i.KmerFrequencies()
c.Check(ok, check.Equals, true)
hashFreqs := make(map[string]int)
for i := 0; i+k <= s.Seq.Len(); i++ {
hashFreqs[strings.ToLower(string(alphabet.LettersToBytes(s.Seq.Seq[i:i+k])))]++
}
for key := range freqs {
c.Check(freqs[key], check.Equals, hashFreqs[i.Format(key)],
check.Commentf("key %x, string of %q\n", key, i.Format(key)))
}
for key := range hashFreqs {
if keyKmer, err := i.KmerOf(key); err != nil {
c.Fatal(err)
} else {
c.Check(freqs[keyKmer], check.Equals, hashFreqs[key],
check.Commentf("keyKmer %x, string of %q, key %q\n", keyKmer, i.Format(keyKmer), key))
}
}
}
}
}
func (s *S) TestKmerPositions(c *check.C) {
for k := MinKmerLen; k < MaxKmerLen; k++ { // don't test full range to time's sake
if i, err := New(k, s.Seq); err != nil {
c.Fatalf("New KmerIndex failed: %v", err)
} else {
i.Build()
hashPos := make(map[string][]int)
for i := 0; i+k <= s.Seq.Len(); i++ {
p := strings.ToLower(string(alphabet.LettersToBytes(s.Seq.Seq[i : i+k])))
hashPos[p] = append(hashPos[p], i)
}
pos, ok := i.KmerIndex()
c.Check(ok, check.Equals, true)
for p := range pos {
c.Check(pos[p], check.DeepEquals, hashPos[i.Format(p)])
}
}
}
}
