tilelib_test.go

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