exportnumpy_test.go

   1 package lightning
   2
   3 import (
   4         "bytes"
   5         "io/ioutil"
   6         "os"
   7
   8         "github.com/kshedden/gonpy"
   9         "gopkg.in/check.v1"
  10 )
  11
  12 type exportSuite struct{}
  13
  14 var _ = check.Suite(&exportSuite{})
  15
  16 func (s *exportSuite) TestFastaToNumpy(c *check.C) {
  17         tmpdir := c.MkDir()
  18
  19         err := ioutil.WriteFile(tmpdir+"/chr1-12-100.bed", []byte("chr1\t12\t100\ttest.1\n"), 0644)
  20         c.Check(err, check.IsNil)
  21
  22         var buffer bytes.Buffer
  23         exited := (&importer{}).RunCommand("import", []string{"-local=true", "-tag-library", "testdata/tags", "-output-tiles", "-save-incomplete-tiles", "testdata/a.1.fasta", "testdata/tinyref.fasta"}, &bytes.Buffer{}, &buffer, os.Stderr)
  24         c.Assert(exited, check.Equals, 0)
  25         var output bytes.Buffer
  26         exited = (&exportNumpy{}).RunCommand("export-numpy", []string{"-local=true", "-output-annotations", tmpdir + "/annotations.csv", "-regions", tmpdir + "/chr1-12-100.bed"}, &buffer, &output, os.Stderr)
  27         c.Check(exited, check.Equals, 0)
  28         npy, err := gonpy.NewReader(&output)
  29         c.Assert(err, check.IsNil)
  30         variants, err := npy.GetInt16()
  31         c.Assert(err, check.IsNil)
  32         c.Check(variants, check.HasLen, 6)
  33         for i := 0; i < 4 && i < len(variants); i += 2 {
  34                 if variants[i] == 1 {
  35                         c.Check(variants[i+1], check.Equals, int16(2), check.Commentf("i=%d, v=%v", i, variants))
  36                 } else {
  37                         c.Check(variants[i], check.Equals, int16(2), check.Commentf("i=%d, v=%v", i, variants))
  38                 }
  39         }
  40         for i := 4; i < 6 && i < len(variants); i += 2 {
  41                 c.Check(variants[i], check.Equals, int16(1), check.Commentf("i=%d, v=%v", i, variants))
  42         }
  43         annotations, err := ioutil.ReadFile(tmpdir + "/annotations.csv")
  44         c.Check(err, check.IsNil)
  45         c.Logf("%s", string(annotations))
  46         c.Check(string(annotations), check.Matches, `(?ms)(.*\n)?1,1,2,chr1:g.84_85insACTGCGATCTGA\n.*`)
  47         c.Check(string(annotations), check.Matches, `(?ms)(.*\n)?1,1,1,chr1:g.87_96delinsGCATCTGCA\n.*`)
  48 }
  49
  50 func sortUints(variants []int16) {
  51         for i := 0; i < len(variants); i += 2 {
  52                 if variants[i] > variants[i+1] {
  53                         for j := 0; j < len(variants); j++ {
  54                                 variants[j], variants[j+1] = variants[j+1], variants[j]
  55                         }
  56                         return
  57                 }
  58         }
  59 }
  60
  61 func (s *exportSuite) TestOnehot(c *check.C) {
  62         for _, trial := range []struct {
  63                 incols  int
  64                 in      []int16
  65                 outcols int
  66                 out     []int16
  67         }{
  68                 {2, []int16{1, 1, 1, 1}, 2, []int16{1, 1, 1, 1}},
  69                 {2, []int16{1, 1, 1, 2}, 3, []int16{1, 1, 0, 1, 0, 1}},
  70                 {
  71                         // 2nd column => 3 one-hot columns
  72                         // 4th column => 0 one-hot columns
  73                         4, []int16{
  74                                 1, 1, 0, 0,
  75                                 1, 2, 1, 0,
  76                                 1, 3, 0, 0,
  77                         }, 5, []int16{
  78                                 1, 1, 0, 0, 0,
  79                                 1, 0, 1, 0, 1,
  80                                 1, 0, 0, 1, 0,
  81                         },
  82                 },
  83         } {
  84                 out, _, outcols := recodeOnehot(trial.in, trial.incols)
  85                 c.Check(out, check.DeepEquals, trial.out)
  86                 c.Check(outcols, check.Equals, trial.outcols)
  87         }
  88 }