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         var buffer bytes.Buffer
  20         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)
  21         c.Assert(exited, check.Equals, 0)
  22         var output bytes.Buffer
  23         exited = (&exportNumpy{}).RunCommand("export-numpy", []string{"-local=true", "-output-annotations", tmpdir + "/annotations.csv"}, &buffer, &output, os.Stderr)
  24         c.Check(exited, check.Equals, 0)
  25         npy, err := gonpy.NewReader(&output)
  26         c.Assert(err, check.IsNil)
  27         variants, err := npy.GetInt16()
  28         c.Assert(err, check.IsNil)
  29         for i := 0; i < 4; i += 2 {
  30                 if variants[i] == 1 {
  31                         c.Check(variants[i+1], check.Equals, int16(2), check.Commentf("i=%d, v=%v", i, variants))
  32                 } else {
  33                         c.Check(variants[i], check.Equals, int16(2), check.Commentf("i=%d, v=%v", i, variants))
  34                 }
  35         }
  36         for i := 4; i < 9; i += 2 {
  37                 c.Check(variants[i], check.Equals, int16(1), check.Commentf("i=%d, v=%v", i, variants))
  38         }
  39         annotations, err := ioutil.ReadFile(tmpdir + "/annotations.csv")
  40         c.Check(err, check.IsNil)
  41         c.Check(string(annotations), check.Matches, `(?ms).*1,2,chr1:g.84_85insACTGCGATCTGA\n.*`)
  42         c.Check(string(annotations), check.Matches, `(?ms).*1,1,chr1:g.87_96delinsGCATCTGCA\n.*`)
  43 }
  44
  45 func sortUints(variants []int16) {
  46         for i := 0; i < len(variants); i += 2 {
  47                 if variants[i] > variants[i+1] {
  48                         for j := 0; j < len(variants); j++ {
  49                                 variants[j], variants[j+1] = variants[j+1], variants[j]
  50                         }
  51                         return
  52                 }
  53         }
  54 }
  55
  56 func (s *exportSuite) TestOnehot(c *check.C) {
  57         for _, trial := range []struct {
  58                 incols  int
  59                 in      []int16
  60                 outcols int
  61                 out     []int16
  62         }{
  63                 {2, []int16{1, 1, 1, 1}, 2, []int16{1, 1, 1, 1}},
  64                 {2, []int16{1, 1, 1, 2}, 3, []int16{1, 1, 0, 1, 0, 1}},
  65                 {
  66                         // 2nd column => 3 one-hot columns
  67                         // 4th column => 0 one-hot columns
  68                         4, []int16{
  69                                 1, 1, 0, 0,
  70                                 1, 2, 1, 0,
  71                                 1, 3, 0, 0,
  72                         }, 5, []int16{
  73                                 1, 1, 0, 0, 0,
  74                                 1, 0, 1, 0, 1,
  75                                 1, 0, 0, 1, 0,
  76                         },
  77                 },
  78         } {
  79                 out, _, outcols := recodeOnehot(trial.in, trial.incols)
  80                 c.Check(out, check.DeepEquals, trial.out)
  81                 c.Check(outcols, check.Equals, trial.outcols)
  82         }
  83 }