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