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         exited = (&exporter{}).RunCommand("export", []string{
  26                 "-local=true",
  27                 "-input-dir=" + tmpdir,
  28                 "-output-dir=" + tmpdir,
  29                 "-output-format=hgvs-onehot",
  30                 "-output-labels=" + tmpdir + "/labels.csv",
  31                 "-ref=testdata/ref.fasta",
  32         }, &buffer, os.Stderr, os.Stderr)
  33         c.Check(exited, check.Equals, 0)
  34         output, err := ioutil.ReadFile(tmpdir + "/out.chr1.csv")
  35         c.Check(err, check.IsNil)
  36         c.Check(sortLines(string(output)), check.Equals, sortLines(`chr1.1_3delinsGGC   1       0
  37 chr1.41_42delinsAA      1       0
  38 chr1.161A>T     1       0
  39 chr1.178A>T     1       0
  40 chr1.222_224del 1       0
  41 chr1.302_305delinsAAAA  1       0
  42 `))
  43         output, err = ioutil.ReadFile(tmpdir + "/out.chr2.csv")
  44         c.Check(err, check.IsNil)
  45         c.Check(sortLines(string(output)), check.Equals, sortLines(`chr2.1_3delinsAAA   0       1
  46 chr2.125_127delinsAAA   0       1
  47 chr2.241_254del 1       0
  48 chr2.258_269delinsAA    1       0
  49 chr2.315C>A     1       0
  50 chr2.470_472del 1       0
  51 chr2.471_472delinsAA    1       0
  52 `))
  53         labels, err := ioutil.ReadFile(tmpdir + "/labels.csv")
  54         c.Check(err, check.IsNil)
  55         c.Check(string(labels), check.Equals, `0,"input1","out.csv"
  56 1,"input2","out.csv"
  57 `)
  58 }