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// Copyright ©2011-2012 The bíogo Authors. All rights reserved.
// Use of this source code is governed by a BSD-style
// license that can be found in the LICENSE file.
package pals
import (
"github.com/biogo/biogo/align/pals/dp"
"github.com/biogo/biogo/align/pals/filter"
"github.com/biogo/biogo/alphabet"
"github.com/biogo/biogo/seq"
"github.com/biogo/biogo/seq/linear"
"github.com/biogo/biogo/util"
"bytes"
"fmt"
"math"
"testing"
"gopkg.in/check.v1"
)
const (
Q = 4
)
var (
maxk byte = 8
l [Q]byte = [Q]byte{'A', 'C', 'G', 'T'}
ps *Packed
)
// Helpers
type B struct {
*bytes.Buffer
}
func (b *B) Close() error { return nil }
// Checkers
type floatApproxChecker struct {
*check.CheckerInfo
}
var floatApprox check.Checker = &floatApproxChecker{
&check.CheckerInfo{Name: "Approximately", Params: []string{"obtained", "expected", "epsilon"}},
}
func (checker *floatApproxChecker) Check(params []interface{}, names []string) (result bool, error string) {
return math.Abs(params[0].(float64)-params[1].(float64))/params[0].(float64) < params[2].(float64), ""
}
// Tests
func Test(t *testing.T) { check.TestingT(t) }
type ft struct {
start, end int
result *Feature
}
// 1: deBruijn1 4 0-0
// 2: deBruijn2 16 1-1
// 3: deBruijn3 64 2-2
// 4: deBruijn4 256 3-3
// 5: deBruijn5 1024 4-5
// 6: deBruijn6 4096 6-10
// 7: deBruijn7 16384 11-27
// 8: deBruijn8 65536 28-92
var T []ft = []ft{
{1020, 1030, &Feature{"deBruijn2", 0, 6, Contig("deBruijn2"), nil}},
{1025, 1030, &Feature{"deBruijn2", 1, 6, Contig("deBruijn2"), nil}},
{1010, 1060, &Feature{"deBruijn2", 0, 16, Contig("deBruijn2"), nil}},
{0, 1060, &Feature{"deBruijn1", 0, 4, Contig("deBruijn1"), nil}},
{4 * binSize, 4*binSize + 904, &Feature{"deBruijn5", 0, 904, Contig("deBruijn5"), nil}},
{29 * binSize, 32*binSize - 1, &Feature{"deBruijn8", 1024, 4095, Contig("deBruijn8"), nil}},
}
type pt struct {
l int
id float64
k, s, d, t int
list float64
}
var P []pt = []pt{
{l: 50, id: 0.1, k: 6, s: 6, d: 0, t: 32, list: 7.3},
{l: 60, id: 0.1, k: 7, s: 7, d: 0, t: 32, list: 1.8},
{l: 70, id: 0.1, k: 8, s: 8, d: 0, t: 32, list: 0.46},
{l: 80, id: 0.1, k: 10, s: 10, d: 0, t: 32, list: 0.029},
{l: 90, id: 0.1, k: 11, s: 11, d: 0, t: 32, list: 0.0071},
{l: 100, id: 0.1, k: 6, s: 12, d: 1, t: 33, list: 7.3},
{l: 200, id: 0.5, k: 6, s: 25, d: 3, t: 35, list: 7.3},
{l: 200, id: 0.9, k: 10, s: 200, d: 19, t: 51, list: 0.029},
{l: 400, id: 0.8, k: 6, s: 50, d: 7, t: 39, list: 7.3},
{l: 400, id: 0.9, k: 10, s: 400, d: 39, t: 71, list: 0.029},
{l: 400, id: 0.99, k: 15, s: 400, d: 4, t: 36, list: 2.8e-05},
}
type S struct{}
var _ = check.Suite(&S{})
func (s *S) SetUpSuite(c *check.C) {
p := NewPacker("")
for k := byte(1); k <= maxk; k++ {
a := &linear.Seq{
Annotation: seq.Annotation{
ID: fmt.Sprintf("deBruijn%d", k),
},
Seq: make(alphabet.Letters, 0, util.Pow(Q, k)),
}
for _, i := range util.DeBruijn(byte(Q), k) {
a.Seq = append(a.Seq, alphabet.Letter(l[i]))
}
a.Loc = Contig(a.ID)
p.Pack(a)
}
ps = p.FinalisePack()
}
func (s *S) TestOptimise(c *check.C) {
// minHitLen int, minId float64, target, query *seq.Seq, tubeOffset int, maxMem uint64
t := &linear.Seq{Seq: make(alphabet.Letters, 29940)}
for _, p := range P {
pa := New(t, t, true, nil, 0, nil, nil)
err := pa.Optimise(p.l, p.id)
if err == nil {
c.Check(*pa.FilterParams, check.Equals, filter.Params{WordSize: p.k, MinMatch: p.s, MaxError: p.d, TubeOffset: p.t})
c.Check(*pa.DPParams, check.Equals, dp.Params{MinHitLength: p.l, MinId: p.id})
c.Check(pa.AvgIndexListLength(pa.FilterParams), floatApprox, p.list, 0.05)
}
}
}
func (s *S) TestPack(c *check.C) {
p := NewPacker("")
for k := byte(1); k <= maxk; k++ {
a := &linear.Seq{
Annotation: seq.Annotation{
ID: fmt.Sprintf("deBruijn%d", k),
},
Seq: make(alphabet.Letters, 0, util.Pow(Q, k)),
}
for _, i := range util.DeBruijn(byte(Q), k) {
a.Seq = append(a.Seq, alphabet.Letter(l[i]))
}
ps, _ := p.Pack(a)
c.Logf("%d: %s", k, ps)
}
c.Check(p.FinalisePack().Len(), check.Equals, 94208)
}
func (s *S) TestFeaturise(c *check.C) {
for _, t := range T {
f, err := ps.feature(t.start, t.end, false)
if err != nil {
c.Fatal(err)
}
c.Check(f, check.DeepEquals, t.result)
}
}
func (s *S) TestWrite(c *check.C) {
b := &B{&bytes.Buffer{}}
w := NewWriter(b, 4, 60, false)
for _, t := range T {
if f1, err := ps.feature(t.start, t.end, false); err != nil {
c.Fatal(err)
} else {
if f2, err := ps.feature(t.start, t.end, false); err != nil {
c.Fatal(err)
} else {
n, err := w.Write(&Pair{A: f1, B: f2})
c.Check(n, check.Not(check.Equals), 0)
c.Check(err, check.Equals, nil)
}
}
}
c.Check(string(b.Bytes()), check.Equals,
`deBruijn2 pals hit 1 6 0.0000 . . Target deBruijn2 1 6; maxe 0
deBruijn2 pals hit 2 6 0.0000 . . Target deBruijn2 2 6; maxe 0
deBruijn2 pals hit 1 16 0.0000 . . Target deBruijn2 1 16; maxe 0
deBruijn1 pals hit 1 4 0.0000 . . Target deBruijn1 1 4; maxe 0
deBruijn5 pals hit 1 904 0.0000 . . Target deBruijn5 1 904; maxe 0
deBruijn8 pals hit 1025 4095 0.0000 . . Target deBruijn8 1025 4095; maxe 0
`)
}
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