taglib_test.go

   1 package main
   2
   3 import (
   4         "bufio"
   5         "fmt"
   6         "io"
   7         "math/rand"
   8         "os"
   9         "strings"
  10         "testing"
  11         "time"
  12
  13         "gopkg.in/check.v1"
  14 )
  15
  16 func Test(t *testing.T) { check.TestingT(t) }
  17
  18 type taglibSuite struct{}
  19
  20 var _ = check.Suite(&taglibSuite{})
  21
  22 type tagMatch struct {
  23         id     tagID
  24         pos    int
  25         taglen int
  26 }
  27
  28 func (s *taglibSuite) TestFindAllTinyData(c *check.C) {
  29         pr, pw, err := os.Pipe()
  30         c.Assert(err, check.IsNil)
  31         go func() {
  32                 defer pw.Close()
  33                 fmt.Fprintf(pw, `>0000.00
  34 ggagaactgtgctccgccttcaga
  35 acacatgctagcgcgtcggggtgg
  36 gactctagcagagtggccagccac
  37 `)
  38         }()
  39         var taglib tagLibrary
  40         err = taglib.Load(pr)
  41         c.Assert(err, check.IsNil)
  42         haystack := []byte(`ggagaactgtgctccgccttcagaccccccccccccccccccccacacatgctagcgcgtcggggtgggggggggggggggggggggggggggactctagcagagtggccagccac`)
  43         var matches []tagMatch
  44         taglib.FindAll(haystack, func(id tagID, pos, taglen int) {
  45                 matches = append(matches, tagMatch{id, pos, taglen})
  46         })
  47         c.Check(matches, check.DeepEquals, []tagMatch{{0, 0, 24}, {1, 44, 24}, {2, 92, 24}})
  48 }
  49
  50 func (s *taglibSuite) TestFindAllRealisticSize(c *check.C) {
  51         start := time.Now()
  52         acgt := []byte{'a', 'c', 'g', 't'}
  53         haystack := make([]byte, 25000000) // ~1/2 smallest human chromosome
  54         c.Logf("@%v haystack", time.Since(start))
  55         rand.Read(haystack)
  56         for i := range haystack {
  57                 haystack[i] = acgt[int(haystack[i]&3)]
  58         }
  59
  60         tagcount := 12500
  61         tagsize := 24
  62         var tags []string
  63         pr, pw := io.Pipe()
  64         go func() {
  65                 defer pw.Close()
  66                 w := bufio.NewWriter(pw)
  67                 defer w.Flush()
  68                 used := map[string]bool{}
  69                 fmt.Fprint(w, ">000\n")
  70                 for i := 0; len(tags) < tagcount; i += (len(haystack) - tagsize) / tagcount {
  71                         i := i
  72                         tag := haystack[i : i+tagsize]
  73                         for used[string(tag)] {
  74                                 i++
  75                                 tag = haystack[i : i+tagsize]
  76                         }
  77                         used[string(tag)] = true
  78                         tags = append(tags, strings.ToLower(string(tag)))
  79                         w.Write(tag)
  80                         w.Write([]byte{'\n'})
  81                 }
  82         }()
  83         c.Logf("@%v build library", time.Since(start))
  84         var taglib tagLibrary
  85         err := taglib.Load(pr)
  86         c.Assert(err, check.IsNil)
  87         c.Logf("@%v find tags in input", time.Since(start))
  88         var matches []tagMatch
  89         taglib.FindAll(haystack, func(id tagID, pos, taglen int) {
  90                 matches = append(matches, tagMatch{id, pos, taglen})
  91         })
  92         c.Logf("@%v done", time.Since(start))
  93         c.Check(matches[0], check.Equals, tagMatch{0, 0, tagsize})
  94         c.Check(matches[1].id, check.Equals, tagID(1))
  95 }