export_test.go

   1 package lightning
   2
   3 import (
   4         "bytes"
   5         "io/ioutil"
   6         "os"
   7
   8         "gopkg.in/check.v1"
   9 )
  10
  11 type exportSuite struct{}
  12
  13 var _ = check.Suite(&exportSuite{})
  14
  15 func (s *exportSuite) TestFastaToHGVS(c *check.C) {
  16         tmpdir := c.MkDir()
  17
  18         err := ioutil.WriteFile(tmpdir+"/chr1-12-100.bed", []byte("chr1\t12\t100\ttest.1\n"), 0644)
  19         c.Check(err, check.IsNil)
  20
  21         var buffer bytes.Buffer
  22         exited := (&importer{}).RunCommand("import", []string{"-local=true", "-tag-library", "testdata/tags", "-output-tiles", "-save-incomplete-tiles", "testdata/pipeline1", "testdata/ref.fasta"}, &bytes.Buffer{}, &buffer, os.Stderr)
  23         c.Assert(exited, check.Equals, 0)
  24         ioutil.WriteFile(tmpdir+"/library.gob", buffer.Bytes(), 0644)
  25
  26         exited = (&exporter{}).RunCommand("export", []string{
  27                 "-local=true",
  28                 "-input-dir=" + tmpdir,
  29                 "-output-dir=" + tmpdir,
  30                 "-output-format=hgvs-onehot",
  31                 "-output-labels=" + tmpdir + "/labels.csv",
  32                 "-ref=testdata/ref.fasta",
  33         }, &buffer, os.Stderr, os.Stderr)
  34         c.Check(exited, check.Equals, 0)
  35         output, err := ioutil.ReadFile(tmpdir + "/out.chr1.csv")
  36         c.Check(err, check.IsNil)
  37         c.Check(sortLines(string(output)), check.Equals, sortLines(`chr1.1_3delinsGGC   1       0
  38 chr1.41_42delinsAA      1       0
  39 chr1.161A>T     1       0
  40 chr1.178A>T     1       0
  41 chr1.222_224del 1       0
  42 chr1.302_305delinsAAAA  1       0
  43 `))
  44         output, err = ioutil.ReadFile(tmpdir + "/out.chr2.csv")
  45         c.Check(err, check.IsNil)
  46         c.Check(sortLines(string(output)), check.Equals, sortLines(`chr2.1_3delinsAAA   0       1
  47 chr2.125_127delinsAAA   0       1
  48 chr2.241_254del 1       0
  49 chr2.258_269delinsAA    1       0
  50 chr2.315C>A     1       0
  51 chr2.470_472del 1       0
  52 chr2.471_472delinsAA    1       0
  53 `))
  54         labels, err := ioutil.ReadFile(tmpdir + "/labels.csv")
  55         c.Check(err, check.IsNil)
  56         c.Check(string(labels), check.Equals, `0,"input1","out.csv"
  57 1,"input2","out.csv"
  58 `)
  59
  60         exited = (&exporter{}).RunCommand("export", []string{
  61                 "-local=true",
  62                 "-input-dir=" + tmpdir,
  63                 "-output-dir=" + tmpdir,
  64                 "-output-format=pvcf",
  65                 "-ref=testdata/ref.fasta",
  66         }, &buffer, os.Stderr, os.Stderr)
  67         c.Check(exited, check.Equals, 0)
  68         output, err = ioutil.ReadFile(tmpdir + "/out.chr1.vcf")
  69         c.Check(err, check.IsNil)
  70         c.Log(string(output))
  71         c.Check(sortLines(string(output)), check.Equals, sortLines(`chr1        1       NNN     GGC     .       .       GT      1/1     0/0
  72 chr1    41      TT      AA      .       .       GT      1/0     0/0
  73 chr1    161     A       T       .       .       GT      0/1     0/0
  74 chr1    178     A       T       .       .       GT      0/1     0/0
  75 chr1    221     TCCA    T       .       .       GT      1/1     0/0
  76 chr1    302     TTTT    AAAA    .       .       GT      0/1     0/0
  77 `))
  78         output, err = ioutil.ReadFile(tmpdir + "/out.chr2.vcf")
  79         c.Check(err, check.IsNil)
  80         c.Log(string(output))
  81         c.Check(sortLines(string(output)), check.Equals, sortLines(`chr2        1       TTT     AAA     .       .       GT      0/0     0/1
  82 chr2    125     CTT     AAA     .       .       GT      0/0     1/1
  83 chr2    240     ATTTTTCTTGCTCTC A       .       .       GT      1/0     0/0
  84 chr2    258     CCTTGTATTTTT    AA      .       .       GT      1/0     0/0
  85 chr2    315     C       A       .       .       GT      1/0     0/0
  86 chr2    469     GTGG    G       .       .       GT      1/0     0/0
  87 chr2    471     GG      AA      .       .       GT      0/1     0/0
  88 `))
  89
  90         exited = (&exporter{}).RunCommand("export", []string{
  91                 "-local=true",
  92                 "-input-dir=" + tmpdir,
  93                 "-output-dir=" + tmpdir,
  94                 "-output-format=vcf",
  95                 "-ref=testdata/ref.fasta",
  96         }, &buffer, os.Stderr, os.Stderr)
  97         c.Check(exited, check.Equals, 0)
  98         output, err = ioutil.ReadFile(tmpdir + "/out.chr1.vcf")
  99         c.Check(err, check.IsNil)
 100         c.Log(string(output))
 101         c.Check(sortLines(string(output)), check.Equals, sortLines(`chr1        1       NNN     GGC     .       .       AC=2    GT      0/1
 102 chr1    41      TT      AA      .       .       AC=1    GT      0/1
 103 chr1    161     A       T       .       .       AC=1    GT      0/1
 104 chr1    178     A       T       .       .       AC=1    GT      0/1
 105 chr1    221     TCCA    T       .       .       AC=2    GT      0/1
 106 chr1    302     TTTT    AAAA    .       .       AC=1    GT      0/1
 107 `))
 108         output, err = ioutil.ReadFile(tmpdir + "/out.chr2.vcf")
 109         c.Check(err, check.IsNil)
 110         c.Log(string(output))
 111         c.Check(sortLines(string(output)), check.Equals, sortLines(`chr2        1       TTT     AAA     .       .       AC=1    GT      0/1
 112 chr2    125     CTT     AAA     .       .       AC=2    GT      0/1
 113 chr2    240     ATTTTTCTTGCTCTC A       .       .       AC=1    GT      0/1
 114 chr2    258     CCTTGTATTTTT    AA      .       .       AC=1    GT      0/1
 115 chr2    315     C       A       .       .       AC=1    GT      0/1
 116 chr2    469     GTGG    G       .       .       AC=1    GT      0/1
 117 chr2    471     GG      AA      .       .       AC=1    GT      0/1
 118 `))
 119 }