exportnumpy_test.go

   1 package main
   2
   3 import (
   4         "bytes"
   5         "os"
   6
   7         "github.com/kshedden/gonpy"
   8         "gopkg.in/check.v1"
   9 )
  10
  11 type exportSuite struct{}
  12
  13 var _ = check.Suite(&exportSuite{})
  14
  15 func (s *exportSuite) TestFastaToNumpy(c *check.C) {
  16         var buffer bytes.Buffer
  17         exited := (&importer{}).RunCommand("import", []string{"-local=true", "-tag-library", "testdata/tags", "-ref", "testdata/ref", "testdata/a.1.fasta"}, &bytes.Buffer{}, &buffer, os.Stderr)
  18         c.Assert(exited, check.Equals, 0)
  19         var output bytes.Buffer
  20         exited = (&exportNumpy{}).RunCommand("export-numpy", []string{"-local=true"}, &buffer, &output, os.Stderr)
  21         c.Check(exited, check.Equals, 0)
  22         npy, err := gonpy.NewReader(&output)
  23         c.Assert(err, check.IsNil)
  24         variants, err := npy.GetUint16()
  25         c.Assert(err, check.IsNil)
  26         for i := 0; i < 4; i += 2 {
  27                 if variants[i] == 1 {
  28                         c.Check(variants[i+1], check.Equals, uint16(2), check.Commentf("i=%d, v=%v", i, variants))
  29                 } else {
  30                         c.Check(variants[i], check.Equals, uint16(2), check.Commentf("i=%d, v=%v", i, variants))
  31                 }
  32         }
  33         for i := 4; i < 9; i += 2 {
  34                 c.Check(variants[i], check.Equals, uint16(1), check.Commentf("i=%d, v=%v", i, variants))
  35         }
  36 }
  37
  38 func sortUints(variants []uint16) {
  39         for i := 0; i < len(variants); i += 2 {
  40                 if variants[i] > variants[i+1] {
  41                         for j := 0; j < len(variants); j++ {
  42                                 variants[j], variants[j+1] = variants[j+1], variants[j]
  43                         }
  44                         return
  45                 }
  46         }
  47 }
  48
  49 func (s *exportSuite) TestOnehot(c *check.C) {
  50         for _, trial := range []struct {
  51                 incols  int
  52                 in      []uint16
  53                 outcols int
  54                 out     []uint16
  55         }{
  56                 {2, []uint16{1, 1, 1, 1}, 2, []uint16{1, 1, 1, 1}},
  57                 {2, []uint16{1, 1, 1, 2}, 3, []uint16{1, 1, 0, 1, 0, 1}},
  58                 {
  59                         // 2nd column => 3 one-hot columns
  60                         // 4th column => 0 one-hot columns
  61                         4, []uint16{
  62                                 1, 1, 0, 0,
  63                                 1, 2, 1, 0,
  64                                 1, 3, 0, 0,
  65                         }, 5, []uint16{
  66                                 1, 1, 0, 0, 0,
  67                                 1, 0, 1, 0, 1,
  68                                 1, 0, 0, 1, 0,
  69                         },
  70                 },
  71         } {
  72                 out, outcols := recodeOnehot(trial.in, trial.incols)
  73                 c.Check(out, check.DeepEquals, trial.out)
  74                 c.Check(outcols, check.Equals, trial.outcols)
  75         }
  76 }