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 exportNumpySuite struct{}
  13
  14 var _ = check.Suite(&exportNumpySuite{})
  15
  16 func (s *exportNumpySuite) 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         exited = (&exportNumpy{}).RunCommand("export-numpy", []string{"-local=true", "-output-dir", tmpdir, "-output-annotations", tmpdir + "/annotations.csv", "-regions", tmpdir + "/chr1-12-100.bed"}, &buffer, os.Stderr, os.Stderr)
  26         c.Check(exited, check.Equals, 0)
  27         f, err := os.Open(tmpdir + "/matrix.npy")
  28         c.Assert(err, check.IsNil)
  29         defer f.Close()
  30         npy, err := gonpy.NewReader(f)
  31         c.Assert(err, check.IsNil)
  32         variants, err := npy.GetInt16()
  33         c.Assert(err, check.IsNil)
  34         c.Check(variants, check.HasLen, 6)
  35         for i := 0; i < 4 && i < len(variants); i += 2 {
  36                 if variants[i] == 1 {
  37                         c.Check(variants[i+1], check.Equals, int16(2), check.Commentf("i=%d, v=%v", i, variants))
  38                 } else {
  39                         c.Check(variants[i], check.Equals, int16(2), check.Commentf("i=%d, v=%v", i, variants))
  40                 }
  41         }
  42         for i := 4; i < 6 && i < len(variants); i += 2 {
  43                 c.Check(variants[i], check.Equals, int16(1), check.Commentf("i=%d, v=%v", i, variants))
  44         }
  45         annotations, err := ioutil.ReadFile(tmpdir + "/annotations.csv")
  46         c.Check(err, check.IsNil)
  47         c.Logf("%s", string(annotations))
  48         c.Check(string(annotations), check.Matches, `(?ms)(.*\n)?1,1,2,chr1:g.84_85insACTGCGATCTGA\n.*`)
  49         c.Check(string(annotations), check.Matches, `(?ms)(.*\n)?1,1,1,chr1:g.87_96delinsGCATCTGCA\n.*`)
  50 }
  51
  52 func sortUints(variants []int16) {
  53         for i := 0; i < len(variants); i += 2 {
  54                 if variants[i] > variants[i+1] {
  55                         for j := 0; j < len(variants); j++ {
  56                                 variants[j], variants[j+1] = variants[j+1], variants[j]
  57                         }
  58                         return
  59                 }
  60         }
  61 }
  62
  63 func (s *exportNumpySuite) TestOnehot(c *check.C) {
  64         for _, trial := range []struct {
  65                 incols  int
  66                 in      []int16
  67                 outcols int
  68                 out     []int16
  69         }{
  70                 {2, []int16{1, 1, 1, 1}, 2, []int16{1, 1, 1, 1}},
  71                 {2, []int16{1, 1, 1, 2}, 3, []int16{1, 1, 0, 1, 0, 1}},
  72                 {
  73                         // 2nd column => 3 one-hot columns
  74                         // 4th column => 0 one-hot columns
  75                         4, []int16{
  76                                 1, 1, 0, 0,
  77                                 1, 2, 1, 0,
  78                                 1, 3, 0, 0,
  79                         }, 5, []int16{
  80                                 1, 1, 0, 0, 0,
  81                                 1, 0, 1, 0, 1,
  82                                 1, 0, 0, 1, 0,
  83                         },
  84                 },
  85         } {
  86                 out, _, outcols := recodeOnehot(trial.in, trial.incols)
  87                 c.Check(out, check.DeepEquals, trial.out)
  88                 c.Check(outcols, check.Equals, trial.outcols)
  89         }
  90 }