package main import ( "bytes" "regexp" "strings" "gopkg.in/check.v1" ) type tilelibSuite struct { tag []string taglib tagLibrary } var _ = check.Suite(&tilelibSuite{}) 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: &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) 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: &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) 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: &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) 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: &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) 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: &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) 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: &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[1]+ "ggggggggggggggggggggggg\n"+ s.tag[2]+ "\n"), matchAllChromosomes) 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} 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) 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: &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) c.Assert(err, check.IsNil) c.Check(tseq, check.DeepEquals, tileSeq{"test-seq": []tileLibRef{{0, 1}, {1, 1}, {3, 1}}}) }