tilelib_test.go

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