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