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", nil, &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 }