-package main
+// Copyright (C) The Lightning Authors. All rights reserved.
+//
+// SPDX-License-Identifier: AGPL-3.0
+
+package lightning
import (
"bytes"
+ "regexp"
+ "strings"
"gopkg.in/check.v1"
)
-type tilelibSuite struct{}
+type tilelibSuite struct {
+ tag []string
+ taglib tagLibrary
+}
var _ = check.Suite(&tilelibSuite{})
-func (s *tilelibSuite) TestSkipOOO(c *check.C) {
- var taglib tagLibrary
- err := taglib.Load(bytes.NewBufferString(`>0000.00
+func (s *tilelibSuite) SetUpSuite(c *check.C) {
+ fasta := `>0000.00
ggagaactgtgctccgccttcaga
acacatgctagcgcgtcggggtgg
gactctagcagagtggccagccac
cctcccgagccgagccacccgtca
gttattaataataacttatcatca
-`))
+`
+ err := s.taglib.Load(bytes.NewBufferString(fasta))
c.Assert(err, check.IsNil)
+ for _, seq := range strings.Split(fasta, "\n") {
+ if len(seq) > 0 && seq[0] != '>' {
+ s.tag = append(s.tag, seq+"\n")
+ }
+ }
+}
+
+func (s *tilelibSuite) TestSkipOOO(c *check.C) {
+ matchAllChromosomes := regexp.MustCompile(".")
// tags appear in seq: 4, 0, 2 (but skipOOO is false)
- tilelib := &tileLibrary{taglib: &taglib, skipOOO: false}
- tseq, err := tilelib.TileFasta("test-label", bytes.NewBufferString(`>test-seq
-gttattaataataacttatcatca
-ggggggggggggggggggggggg
-ggagaactgtgctccgccttcaga
-cccccccccccccccccccc
-gactctagcagagtggccagccac
-`))
+ tilelib := &tileLibrary{taglib: &s.taglib, skipOOO: false}
+ tseq, _, err := tilelib.TileFasta("test-label", bytes.NewBufferString(">test-seq\n"+
+ s.tag[4]+
+ "ggggggggggggggggggggggg\n"+
+ s.tag[0]+
+ "cccccccccccccccccccc\n"+
+ s.tag[2]+
+ "\n"), matchAllChromosomes, false)
c.Assert(err, check.IsNil)
c.Check(tseq, check.DeepEquals, tileSeq{"test-seq": []tileLibRef{{4, 1}, {0, 1}, {2, 1}}})
// tags appear in seq: 0, 1, 2 -> don't skip
- tilelib = &tileLibrary{taglib: &taglib, skipOOO: true}
- tseq, err = tilelib.TileFasta("test-label", bytes.NewBufferString(`>test-seq
-ggagaactgtgctccgccttcaga
-cccccccccccccccccccc
-acacatgctagcgcgtcggggtgg
-ggggggggggggggggggggggg
-gactctagcagagtggccagccac
-`))
+ tilelib = &tileLibrary{taglib: &s.taglib, skipOOO: true}
+ tseq, _, err = tilelib.TileFasta("test-label", bytes.NewBufferString(">test-seq\n"+
+ s.tag[0]+
+ "cccccccccccccccccccc\n"+
+ s.tag[1]+
+ "ggggggggggggggggggggggg\n"+
+ s.tag[2]+
+ "\n"), matchAllChromosomes, false)
c.Assert(err, check.IsNil)
c.Check(tseq, check.DeepEquals, tileSeq{"test-seq": []tileLibRef{{0, 1}, {1, 1}, {2, 1}}})
// tags appear in seq: 2, 3, 4 -> don't skip
- tilelib = &tileLibrary{taglib: &taglib, skipOOO: true}
- tseq, err = tilelib.TileFasta("test-label", bytes.NewBufferString(`>test-seq
-gactctagcagagtggccagccac
-cccccccccccccccccccc
-cctcccgagccgagccacccgtca
-ggggggggggggggggggggggg
-gttattaataataacttatcatca
-`))
+ tilelib = &tileLibrary{taglib: &s.taglib, skipOOO: true}
+ tseq, _, err = tilelib.TileFasta("test-label", bytes.NewBufferString(">test-seq\n"+
+ s.tag[2]+
+ "cccccccccccccccccccc\n"+
+ s.tag[3]+
+ "ggggggggggggggggggggggg\n"+
+ s.tag[4]+
+ "\n"), matchAllChromosomes, false)
c.Assert(err, check.IsNil)
c.Check(tseq, check.DeepEquals, tileSeq{"test-seq": []tileLibRef{{2, 1}, {3, 1}, {4, 1}}})
// tags appear in seq: 4, 0, 2 -> skip 4
- tilelib = &tileLibrary{taglib: &taglib, skipOOO: true}
- tseq, err = tilelib.TileFasta("test-label", bytes.NewBufferString(`>test-seq
-gttattaataataacttatcatca
-cccccccccccccccccccc
-ggagaactgtgctccgccttcaga
-ggggggggggggggggggggggg
-gactctagcagagtggccagccac
-`))
+ tilelib = &tileLibrary{taglib: &s.taglib, skipOOO: true}
+ tseq, _, err = tilelib.TileFasta("test-label", bytes.NewBufferString(">test-seq\n"+
+ s.tag[4]+
+ "cccccccccccccccccccc\n"+
+ s.tag[0]+
+ "ggggggggggggggggggggggg\n"+
+ s.tag[2]+
+ "\n"), matchAllChromosomes, false)
c.Assert(err, check.IsNil)
c.Check(tseq, check.DeepEquals, tileSeq{"test-seq": []tileLibRef{{0, 1}, {2, 1}}})
// tags appear in seq: 0, 2, 1 -> skip 2
- tilelib = &tileLibrary{taglib: &taglib, skipOOO: true}
- tseq, err = tilelib.TileFasta("test-label", bytes.NewBufferString(`>test-seq
-ggagaactgtgctccgccttcaga
-cccccccccccccccccccc
-gactctagcagagtggccagccac
-ggggggggggggggggggggggg
-acacatgctagcgcgtcggggtgg
-`))
+ tilelib = &tileLibrary{taglib: &s.taglib, skipOOO: true}
+ tseq, _, err = tilelib.TileFasta("test-label", bytes.NewBufferString(">test-seq\n"+
+ s.tag[0]+
+ "cccccccccccccccccccc\n"+
+ s.tag[2]+
+ "ggggggggggggggggggggggg\n"+
+ s.tag[1]+
+ "\n"), matchAllChromosomes, false)
c.Assert(err, check.IsNil)
c.Check(tseq, check.DeepEquals, tileSeq{"test-seq": []tileLibRef{{0, 1}, {1, 1}}})
// tags appear in seq: 0, 1, 1, 2 -> skip second tag1
- tilelib = &tileLibrary{taglib: &taglib, skipOOO: true}
- tseq, err = tilelib.TileFasta("test-label", bytes.NewBufferString(`>test-seq
-ggagaactgtgctccgccttcaga
-cccccccccccccccccccc
-acacatgctagcgcgtcggggtgg
-ggggggggggggggggggggggg
-acacatgctagcgcgtcggggtgg
-ggggggggggggggggggggggg
-gactctagcagagtggccagccac
-`))
+ tilelib = &tileLibrary{taglib: &s.taglib, skipOOO: true, useDups: true}
+ tseq, _, err = tilelib.TileFasta("test-label", bytes.NewBufferString(">test-seq\n"+
+ s.tag[0]+
+ "cccccccccccccccccccc\n"+
+ s.tag[1]+
+ "ggggggggggggggggggggggg\n"+
+ s.tag[1]+
+ "ggggggggggggggggggggggg\n"+
+ s.tag[2]+
+ "\n"), matchAllChromosomes, false)
c.Assert(err, check.IsNil)
c.Check(tseq, check.DeepEquals, tileSeq{"test-seq": []tileLibRef{{0, 1}, {1, 1}, {2, 1}}})
+ // tags appear in seq: 0, 1, 3, 0, 4 -> skip second tag0
+ tilelib = &tileLibrary{taglib: &s.taglib, skipOOO: true, useDups: true}
+ tseq, _, err = tilelib.TileFasta("test-label", bytes.NewBufferString(">test-seq\n"+
+ s.tag[0]+
+ "cccccccccccccccccccc\n"+
+ s.tag[1]+
+ "ggggggggggggggggggggggg\n"+
+ s.tag[3]+
+ "ggggggggggggggggggggggg\n"+
+ s.tag[0]+
+ "ggggggggggggggggggggggg\n"+
+ s.tag[4]+
+ "\n"), matchAllChromosomes, false)
+ c.Assert(err, check.IsNil)
+ c.Check(tseq, check.DeepEquals, tileSeq{"test-seq": []tileLibRef{{0, 1}, {1, 1}, {3, 1}, {4, 1}}})
+
// tags appear in seq: 0, 1, 3 -> don't skip
- tilelib = &tileLibrary{taglib: &taglib, skipOOO: true}
- tseq, err = tilelib.TileFasta("test-label", bytes.NewBufferString(`>test-seq
-ggagaactgtgctccgccttcaga
-cccccccccccccccccccc
-acacatgctagcgcgtcggggtgg
-ggggggggggggggggggggggg
-cctcccgagccgagccacccgtca
-`))
+ tilelib = &tileLibrary{taglib: &s.taglib, skipOOO: true}
+ tseq, _, err = tilelib.TileFasta("test-label", bytes.NewBufferString(">test-seq\n"+
+ s.tag[0]+
+ "cccccccccccccccccccc\n"+
+ s.tag[1]+
+ "ggggggggggggggggggggggg\n"+
+ s.tag[3]+
+ "\n"), matchAllChromosomes, false)
c.Assert(err, check.IsNil)
c.Check(tseq, check.DeepEquals, tileSeq{"test-seq": []tileLibRef{{0, 1}, {1, 1}, {3, 1}}})
}
projects / lightning.git / blobdiff