tilelib_test.go

   1 package main
   2
   3 import (
   4         "bytes"
   5         "regexp"
   6         "strings"
   7
   8         "gopkg.in/check.v1"
   9 )
  10
  11 type tilelibSuite struct {
  12         tag    []string
  13         taglib tagLibrary
  14 }
  15
  16 var _ = check.Suite(&tilelibSuite{})
  17
  18 func (s *tilelibSuite) SetUpSuite(c *check.C) {
  19         fasta := `>0000.00
  20 ggagaactgtgctccgccttcaga
  21 acacatgctagcgcgtcggggtgg
  22 gactctagcagagtggccagccac
  23 cctcccgagccgagccacccgtca
  24 gttattaataataacttatcatca
  25 `
  26         err := s.taglib.Load(bytes.NewBufferString(fasta))
  27         c.Assert(err, check.IsNil)
  28         for _, seq := range strings.Split(fasta, "\n") {
  29                 if len(seq) > 0 && seq[0] != '>' {
  30                         s.tag = append(s.tag, seq+"\n")
  31                 }
  32         }
  33 }
  34
  35 func (s *tilelibSuite) TestSkipOOO(c *check.C) {
  36         matchAllChromosomes := regexp.MustCompile(".")
  37
  38         // tags appear in seq: 4, 0, 2 (but skipOOO is false)
  39         tilelib := &tileLibrary{taglib: &s.taglib, skipOOO: false}
  40         tseq, _, err := tilelib.TileFasta("test-label", bytes.NewBufferString(">test-seq\n"+
  41                 s.tag[4]+
  42                 "ggggggggggggggggggggggg\n"+
  43                 s.tag[0]+
  44                 "cccccccccccccccccccc\n"+
  45                 s.tag[2]+
  46                 "\n"), matchAllChromosomes)
  47         c.Assert(err, check.IsNil)
  48         c.Check(tseq, check.DeepEquals, tileSeq{"test-seq": []tileLibRef{{4, 1}, {0, 1}, {2, 1}}})
  49
  50         // tags appear in seq: 0, 1, 2 -> don't skip
  51         tilelib = &tileLibrary{taglib: &s.taglib, skipOOO: true}
  52         tseq, _, err = tilelib.TileFasta("test-label", bytes.NewBufferString(">test-seq\n"+
  53                 s.tag[0]+
  54                 "cccccccccccccccccccc\n"+
  55                 s.tag[1]+
  56                 "ggggggggggggggggggggggg\n"+
  57                 s.tag[2]+
  58                 "\n"), matchAllChromosomes)
  59         c.Assert(err, check.IsNil)
  60         c.Check(tseq, check.DeepEquals, tileSeq{"test-seq": []tileLibRef{{0, 1}, {1, 1}, {2, 1}}})
  61
  62         // tags appear in seq: 2, 3, 4 -> don't skip
  63         tilelib = &tileLibrary{taglib: &s.taglib, skipOOO: true}
  64         tseq, _, err = tilelib.TileFasta("test-label", bytes.NewBufferString(">test-seq\n"+
  65                 s.tag[2]+
  66                 "cccccccccccccccccccc\n"+
  67                 s.tag[3]+
  68                 "ggggggggggggggggggggggg\n"+
  69                 s.tag[4]+
  70                 "\n"), matchAllChromosomes)
  71         c.Assert(err, check.IsNil)
  72         c.Check(tseq, check.DeepEquals, tileSeq{"test-seq": []tileLibRef{{2, 1}, {3, 1}, {4, 1}}})
  73
  74         // tags appear in seq: 4, 0, 2 -> skip 4
  75         tilelib = &tileLibrary{taglib: &s.taglib, skipOOO: true}
  76         tseq, _, err = tilelib.TileFasta("test-label", bytes.NewBufferString(">test-seq\n"+
  77                 s.tag[4]+
  78                 "cccccccccccccccccccc\n"+
  79                 s.tag[0]+
  80                 "ggggggggggggggggggggggg\n"+
  81                 s.tag[2]+
  82                 "\n"), matchAllChromosomes)
  83         c.Assert(err, check.IsNil)
  84         c.Check(tseq, check.DeepEquals, tileSeq{"test-seq": []tileLibRef{{0, 1}, {2, 1}}})
  85
  86         // tags appear in seq: 0, 2, 1 -> skip 2
  87         tilelib = &tileLibrary{taglib: &s.taglib, skipOOO: true}
  88         tseq, _, err = tilelib.TileFasta("test-label", bytes.NewBufferString(">test-seq\n"+
  89                 s.tag[0]+
  90                 "cccccccccccccccccccc\n"+
  91                 s.tag[2]+
  92                 "ggggggggggggggggggggggg\n"+
  93                 s.tag[1]+
  94                 "\n"), matchAllChromosomes)
  95         c.Assert(err, check.IsNil)
  96         c.Check(tseq, check.DeepEquals, tileSeq{"test-seq": []tileLibRef{{0, 1}, {1, 1}}})
  97
  98         // tags appear in seq: 0, 1, 1, 2 -> skip second tag1
  99         tilelib = &tileLibrary{taglib: &s.taglib, skipOOO: true}
 100         tseq, _, err = tilelib.TileFasta("test-label", bytes.NewBufferString(">test-seq\n"+
 101                 s.tag[0]+
 102                 "cccccccccccccccccccc\n"+
 103                 s.tag[1]+
 104                 "ggggggggggggggggggggggg\n"+
 105                 s.tag[1]+
 106                 "ggggggggggggggggggggggg\n"+
 107                 s.tag[2]+
 108                 "\n"), matchAllChromosomes)
 109         c.Assert(err, check.IsNil)
 110         c.Check(tseq, check.DeepEquals, tileSeq{"test-seq": []tileLibRef{{0, 1}, {1, 1}, {2, 1}}})
 111
 112         // tags appear in seq: 0, 1, 3, 0, 4 -> skip second tag0
 113         tilelib = &tileLibrary{taglib: &s.taglib, skipOOO: true}
 114         tseq, _, err = tilelib.TileFasta("test-label", bytes.NewBufferString(">test-seq\n"+
 115                 s.tag[0]+
 116                 "cccccccccccccccccccc\n"+
 117                 s.tag[1]+
 118                 "ggggggggggggggggggggggg\n"+
 119                 s.tag[3]+
 120                 "ggggggggggggggggggggggg\n"+
 121                 s.tag[0]+
 122                 "ggggggggggggggggggggggg\n"+
 123                 s.tag[4]+
 124                 "\n"), matchAllChromosomes)
 125         c.Assert(err, check.IsNil)
 126         c.Check(tseq, check.DeepEquals, tileSeq{"test-seq": []tileLibRef{{0, 1}, {1, 1}, {3, 1}, {4, 1}}})
 127
 128         // tags appear in seq: 0, 1, 3 -> don't skip
 129         tilelib = &tileLibrary{taglib: &s.taglib, skipOOO: true}
 130         tseq, _, err = tilelib.TileFasta("test-label", bytes.NewBufferString(">test-seq\n"+
 131                 s.tag[0]+
 132                 "cccccccccccccccccccc\n"+
 133                 s.tag[1]+
 134                 "ggggggggggggggggggggggg\n"+
 135                 s.tag[3]+
 136                 "\n"), matchAllChromosomes)
 137         c.Assert(err, check.IsNil)
 138         c.Check(tseq, check.DeepEquals, tileSeq{"test-seq": []tileLibRef{{0, 1}, {1, 1}, {3, 1}}})
 139 }