tilelib_test.go

   1 // Copyright (C) The Lightning Authors. All rights reserved.
   2 //
   3 // SPDX-License-Identifier: AGPL-3.0
   4
   5 package lightning
   6
   7 import (
   8         "bytes"
   9         "regexp"
  10         "strings"
  11
  12         "gopkg.in/check.v1"
  13 )
  14
  15 type tilelibSuite struct {
  16         tag    []string
  17         taglib tagLibrary
  18 }
  19
  20 var _ = check.Suite(&tilelibSuite{})
  21
  22 func (s *tilelibSuite) SetUpSuite(c *check.C) {
  23         fasta := `>0000.00
  24 ggagaactgtgctccgccttcaga
  25 acacatgctagcgcgtcggggtgg
  26 gactctagcagagtggccagccac
  27 cctcccgagccgagccacccgtca
  28 gttattaataataacttatcatca
  29 `
  30         err := s.taglib.Load(bytes.NewBufferString(fasta))
  31         c.Assert(err, check.IsNil)
  32         for _, seq := range strings.Split(fasta, "\n") {
  33                 if len(seq) > 0 && seq[0] != '>' {
  34                         s.tag = append(s.tag, seq+"\n")
  35                 }
  36         }
  37 }
  38
  39 func (s *tilelibSuite) TestSkipOOO(c *check.C) {
  40         matchAllChromosomes := regexp.MustCompile(".")
  41
  42         // tags appear in seq: 4, 0, 2 (but skipOOO is false)
  43         tilelib := &tileLibrary{taglib: &s.taglib, skipOOO: false}
  44         tseq, _, err := tilelib.TileFasta("test-label", bytes.NewBufferString(">test-seq\n"+
  45                 s.tag[4]+
  46                 "ggggggggggggggggggggggg\n"+
  47                 s.tag[0]+
  48                 "cccccccccccccccccccc\n"+
  49                 s.tag[2]+
  50                 "\n"), matchAllChromosomes, false)
  51         c.Assert(err, check.IsNil)
  52         c.Check(tseq, check.DeepEquals, tileSeq{"test-seq": []tileLibRef{{4, 1}, {0, 1}, {2, 1}}})
  53
  54         // tags appear in seq: 0, 1, 2 -> don't skip
  55         tilelib = &tileLibrary{taglib: &s.taglib, skipOOO: true}
  56         tseq, _, err = tilelib.TileFasta("test-label", bytes.NewBufferString(">test-seq\n"+
  57                 s.tag[0]+
  58                 "cccccccccccccccccccc\n"+
  59                 s.tag[1]+
  60                 "ggggggggggggggggggggggg\n"+
  61                 s.tag[2]+
  62                 "\n"), matchAllChromosomes, false)
  63         c.Assert(err, check.IsNil)
  64         c.Check(tseq, check.DeepEquals, tileSeq{"test-seq": []tileLibRef{{0, 1}, {1, 1}, {2, 1}}})
  65
  66         // tags appear in seq: 2, 3, 4 -> don't skip
  67         tilelib = &tileLibrary{taglib: &s.taglib, skipOOO: true}
  68         tseq, _, err = tilelib.TileFasta("test-label", bytes.NewBufferString(">test-seq\n"+
  69                 s.tag[2]+
  70                 "cccccccccccccccccccc\n"+
  71                 s.tag[3]+
  72                 "ggggggggggggggggggggggg\n"+
  73                 s.tag[4]+
  74                 "\n"), matchAllChromosomes, false)
  75         c.Assert(err, check.IsNil)
  76         c.Check(tseq, check.DeepEquals, tileSeq{"test-seq": []tileLibRef{{2, 1}, {3, 1}, {4, 1}}})
  77
  78         // tags appear in seq: 4, 0, 2 -> skip 4
  79         tilelib = &tileLibrary{taglib: &s.taglib, skipOOO: true}
  80         tseq, _, err = tilelib.TileFasta("test-label", bytes.NewBufferString(">test-seq\n"+
  81                 s.tag[4]+
  82                 "cccccccccccccccccccc\n"+
  83                 s.tag[0]+
  84                 "ggggggggggggggggggggggg\n"+
  85                 s.tag[2]+
  86                 "\n"), matchAllChromosomes, false)
  87         c.Assert(err, check.IsNil)
  88         c.Check(tseq, check.DeepEquals, tileSeq{"test-seq": []tileLibRef{{0, 1}, {2, 1}}})
  89
  90         // tags appear in seq: 0, 2, 1 -> skip 2
  91         tilelib = &tileLibrary{taglib: &s.taglib, skipOOO: true}
  92         tseq, _, err = tilelib.TileFasta("test-label", bytes.NewBufferString(">test-seq\n"+
  93                 s.tag[0]+
  94                 "cccccccccccccccccccc\n"+
  95                 s.tag[2]+
  96                 "ggggggggggggggggggggggg\n"+
  97                 s.tag[1]+
  98                 "\n"), matchAllChromosomes, false)
  99         c.Assert(err, check.IsNil)
 100         c.Check(tseq, check.DeepEquals, tileSeq{"test-seq": []tileLibRef{{0, 1}, {1, 1}}})
 101
 102         // tags appear in seq: 0, 1, 1, 2 -> skip second tag1
 103         tilelib = &tileLibrary{taglib: &s.taglib, skipOOO: true, useDups: true}
 104         tseq, _, err = tilelib.TileFasta("test-label", bytes.NewBufferString(">test-seq\n"+
 105                 s.tag[0]+
 106                 "cccccccccccccccccccc\n"+
 107                 s.tag[1]+
 108                 "ggggggggggggggggggggggg\n"+
 109                 s.tag[1]+
 110                 "ggggggggggggggggggggggg\n"+
 111                 s.tag[2]+
 112                 "\n"), matchAllChromosomes, false)
 113         c.Assert(err, check.IsNil)
 114         c.Check(tseq, check.DeepEquals, tileSeq{"test-seq": []tileLibRef{{0, 1}, {1, 1}, {2, 1}}})
 115
 116         // tags appear in seq: 0, 1, 3, 0, 4 -> skip second tag0
 117         tilelib = &tileLibrary{taglib: &s.taglib, skipOOO: true, useDups: true}
 118         tseq, _, err = tilelib.TileFasta("test-label", bytes.NewBufferString(">test-seq\n"+
 119                 s.tag[0]+
 120                 "cccccccccccccccccccc\n"+
 121                 s.tag[1]+
 122                 "ggggggggggggggggggggggg\n"+
 123                 s.tag[3]+
 124                 "ggggggggggggggggggggggg\n"+
 125                 s.tag[0]+
 126                 "ggggggggggggggggggggggg\n"+
 127                 s.tag[4]+
 128                 "\n"), matchAllChromosomes, false)
 129         c.Assert(err, check.IsNil)
 130         c.Check(tseq, check.DeepEquals, tileSeq{"test-seq": []tileLibRef{{0, 1}, {1, 1}, {3, 1}, {4, 1}}})
 131
 132         // tags appear in seq: 0, 1, 3 -> don't skip
 133         tilelib = &tileLibrary{taglib: &s.taglib, skipOOO: true}
 134         tseq, _, err = tilelib.TileFasta("test-label", bytes.NewBufferString(">test-seq\n"+
 135                 s.tag[0]+
 136                 "cccccccccccccccccccc\n"+
 137                 s.tag[1]+
 138                 "ggggggggggggggggggggggg\n"+
 139                 s.tag[3]+
 140                 "\n"), matchAllChromosomes, false)
 141         c.Assert(err, check.IsNil)
 142         c.Check(tseq, check.DeepEquals, tileSeq{"test-seq": []tileLibRef{{0, 1}, {1, 1}, {3, 1}}})
 143 }