Ejemplo n.º 1
0
func (s *S) TestKmerKmerUtilities(c *check.C) {
	for k := MinKmerLen; k <= 8; k++ { // again not testing all exhaustively
		for kmer := Kmer(0); uint(kmer) <= util.Pow4(k)-1; kmer++ {
			// Interconversion between string and Kmer
			if rk, err := KmerOf(k, Stringify(k, kmer)); err != nil {
				c.Fatalf("Failed Kmer conversion: %v", err)
			} else {
				c.Check(rk, check.Equals, kmer)
			}

			// Complementation
			dc := ComplementOf(k, ComplementOf(k, kmer))
			if dc != kmer {
				c.Logf("kmer: %s\ndouble complement: %s\n", Stringify(k, kmer), Stringify(k, dc))
			}
			c.Check(dc, check.Equals, kmer)

			// GC content
			ks := Stringify(k, kmer)
			gc := 0
			for _, b := range ks {
				if b == 'G' || b == 'C' {
					gc++
				}
			}
			c.Check(GCof(k, kmer), check.Equals, float64(gc)/float64(k))
		}
	}
}
Ejemplo n.º 2
0
Archivo: pals.go Proyecto: frogs/biogo
// Return an estimate of the amount of memory required for the filter.
func (p *PALS) filterMemRequired(filterParams *filter.Params) uintptr {
	words := util.Pow4(filterParams.WordSize)
	tubeWidth := filterParams.TubeOffset + filterParams.MaxError
	maxActiveTubes := (p.target.Len()+tubeWidth-1)/filterParams.TubeOffset + 1
	tubes := uintptr(maxActiveTubes) * unsafe.Sizeof(tubeState{})
	finger := unsafe.Sizeof(uint32(0)) * uintptr(words)
	pos := unsafe.Sizeof(0) * uintptr(p.target.Len())

	return finger + pos + tubes
}
Ejemplo n.º 3
0
// Render the rainbow based on block of sequence in the index with the given size.
// Vary specifies which color values change in response to kmer frequency. Setting desch to true
// specifies using the ordering described in Deschavanne (1999).
func (self *CGR) Paint(vary int, desch bool, block, size int) (i *image.RGBA, err error) {
	k := self.Index.GetK()

	kmask := util.Pow4(k)
	kmers := make([]uint, kmask)
	f := func(index *kmerindex.Index, _, kmer int) {
		kmers[kmer]++
	}
	self.Index.ForEachKmerOf(self.Index.Seq, block*size, (block+1)*size-1, f)

	c := &color.HSVA{}
	max := util.UMax(kmers...)
	scale := 1 / float64(max)

	for kmer, v := range kmers {
		x, y := 0, 0
		if desch {
			xdiff := 0
			for i, km := k-1, kmer; i >= 0; i, km = i-1, km>>2 {
				xdiff = ((km & 2) >> 1)
				x += xdiff << uint(i)
				y += ((km & 1) ^ (xdiff ^ 1)) << uint(i)
			}
		} else {
			for i, km := k-1, kmer; i >= 0; i, km = i-1, km>>2 {
				x += (km & 1) << uint(i)
				y += (((km & 1) ^ ((km & 2) >> 1)) ^ 1) << uint(i)
			}
		}
		val := float64(v) * scale
		if vary&H != 0 {
			c.H = val * 240
		} else {
			c.H = self.BackGround.H
		}
		if vary&S != 0 {
			c.S = val
		} else {
			c.S = self.BackGround.S
		}
		if vary&V != 0 {
			c.V = val
		} else {
			c.V = self.BackGround.V
		}
		if vary&A != 0 {
			c.A = val
		} else {
			c.A = self.BackGround.A
		}
		self.Set(x, y, c)
	}

	return self.RGBA, nil
}
Ejemplo n.º 4
0
// Create a new Kmer Index with a word size k based on sequence
func New(k int, sequence *seq.Seq) (i *Index, err error) {
	switch {
	case k > MaxKmerLen:
		return nil, bio.NewError("k greater than MaxKmerLen", 0, k, MaxKmerLen)
	case k < MinKmerLen:
		return nil, bio.NewError("k less than MinKmerLen", 0, k, MinKmerLen)
	case k+1 > sequence.Len():
		return nil, bio.NewError("sequence shorter than k+1-mer length", 0, k+1, sequence.Len())
	}

	i = &Index{
		finger:  make([]Kmer, util.Pow4(k)+1), // Need a Tn+1 finger position so that Tn can be recognised
		k:       k,
		kMask:   Kmer(util.Pow4(k) - 1),
		Seq:     sequence,
		indexed: false,
	}

	i.buildKmerTable()

	return
}
Ejemplo n.º 5
0
// Render the rainbow based on block of sequence in the index with the given size. Left and right define the extent of the rendering.
// Vary specifies which color values change in response to kmer frequency.
func (self *KmerRainbow) Paint(vary int, block, size, left, right int) (i *image.RGBA, err error) {
	right = util.Min(right, self.Rect.Dx())
	kmers := make([]uint32, self.RGBA.Rect.Dy())
	kmask := util.Pow4(self.Index.GetK())
	kmaskf := float64(kmask)
	f := func(index *kmerindex.Index, _, kmer int) {
		kmers[int(float64(kmer)*float64(self.RGBA.Rect.Dy())/kmaskf)]++
	}
	self.Index.ForEachKmerOf(self.Index.Seq, block*size, (block+1)*size-1, f)
	c := color.HSVA{}
	lf := float64(len(kmers)) / 360
	var val float64
	scale := 1 / float64(self.Max)
	for y, v := range kmers {
		val = float64(v) / scale
		c.H = float64(y) / lf
		if vary&S != 0 {
			c.S = val
		} else {
			c.S = self.BackGround.S
		}
		if vary&V != 0 {
			c.V = val
		} else {
			c.V = self.BackGround.V
		}
		if vary&A != 0 {
			c.A = val
		} else {
			c.A = self.BackGround.A
		}
		if left >= 0 && right > left {
			for x := left; x < right; x++ {
				self.Set(x, y, c)
			}
		} else {
			println(left, right)
			for x := 0; x < self.Rect.Dx(); x++ {
				self.Set(x, y, c)
			}
		}
	}

	return self.RGBA, nil
}
Ejemplo n.º 6
0
// Create a new KmerRainbow defined by the rectangle r, kmerindex index and background color.
func NewKmerRainbow(r image.Rectangle, index *kmerindex.Index, background color.HSVA) *KmerRainbow { // should generalise the BG color
	h := r.Dy()
	kmers := make([]int, h)
	kmask := util.Pow4(index.GetK())
	kmaskf := float64(kmask)
	f := func(index *kmerindex.Index, _, kmer int) {
		kmers[int(float64(kmer)*float64(h)/kmaskf)]++
	}
	index.ForEachKmerOf(index.Seq, 0, index.Seq.Len(), f)
	max := util.Max(kmers...)

	return &KmerRainbow{
		RGBA:       image.NewRGBA(r),
		Index:      index,
		Max:        max,
		BackGround: background,
	}
}
Ejemplo n.º 7
0
// Make a new KmerColor initialising the Kmer length to k.
func New(k int) (c *KmerColor) {
	return &KmerColor{
		kmask: kmerindex.Kmer(util.Pow4(k) - 1),
	}
}