exportnumpy_test.go

   1 // Copyright (C) The Lightning Authors. All rights reserved.
   2 //
   3 // SPDX-License-Identifier: AGPL-3.0
   4
   5 package lightning
   6
   7 import (
   8         "bytes"
   9         "io/ioutil"
  10         "os"
  11
  12         "github.com/kshedden/gonpy"
  13         "gopkg.in/check.v1"
  14 )
  15
  16 type exportNumpySuite struct{}
  17
  18 var _ = check.Suite(&exportNumpySuite{})
  19
  20 func (s *exportNumpySuite) TestFastaToNumpy(c *check.C) {
  21         tmpdir := c.MkDir()
  22
  23         err := ioutil.WriteFile(tmpdir+"/chr1-12-100.bed", []byte("chr1\t12\t100\ttest.1\n"), 0644)
  24         c.Check(err, check.IsNil)
  25
  26         var buffer bytes.Buffer
  27         exited := (&importer{}).RunCommand("import", []string{"-local=true", "-o", tmpdir + "/library.gob.gz", "-tag-library", "testdata/tags", "-output-tiles", "-save-incomplete-tiles", "testdata/a.1.fasta", "testdata/tinyref.fasta"}, &bytes.Buffer{}, os.Stderr, os.Stderr)
  28         c.Assert(exited, check.Equals, 0)
  29         exited = (&exportNumpy{}).RunCommand("export-numpy", []string{"-local=true", "-input-dir", tmpdir, "-output-dir", tmpdir, "-output-annotations", tmpdir + "/annotations.csv", "-regions", tmpdir + "/chr1-12-100.bed"}, &buffer, os.Stderr, os.Stderr)
  30         c.Check(exited, check.Equals, 0)
  31         f, err := os.Open(tmpdir + "/matrix.npy")
  32         c.Assert(err, check.IsNil)
  33         defer f.Close()
  34         npy, err := gonpy.NewReader(f)
  35         c.Assert(err, check.IsNil)
  36         variants, err := npy.GetInt16()
  37         c.Assert(err, check.IsNil)
  38         c.Check(variants, check.HasLen, 6)
  39         for i := 0; i < 4 && i < len(variants); i += 2 {
  40                 if variants[i] == 1 {
  41                         c.Check(variants[i+1], check.Equals, int16(2), check.Commentf("i=%d, v=%v", i, variants))
  42                 } else {
  43                         c.Check(variants[i], check.Equals, int16(2), check.Commentf("i=%d, v=%v", i, variants))
  44                 }
  45         }
  46         for i := 4; i < 6 && i < len(variants); i += 2 {
  47                 c.Check(variants[i], check.Equals, int16(1), check.Commentf("i=%d, v=%v", i, variants))
  48         }
  49         annotations, err := ioutil.ReadFile(tmpdir + "/annotations.csv")
  50         c.Check(err, check.IsNil)
  51         c.Logf("%s", string(annotations))
  52         c.Check(string(annotations), check.Matches, `(?ms)(.*\n)?1,1,2,chr1:g.84_85insACTGCGATCTGA\n.*`)
  53         c.Check(string(annotations), check.Matches, `(?ms)(.*\n)?1,1,1,chr1:g.87_96delinsGCATCTGCA\n.*`)
  54 }
  55
  56 func sortUints(variants []int16) {
  57         for i := 0; i < len(variants); i += 2 {
  58                 if variants[i] > variants[i+1] {
  59                         for j := 0; j < len(variants); j++ {
  60                                 variants[j], variants[j+1] = variants[j+1], variants[j]
  61                         }
  62                         return
  63                 }
  64         }
  65 }
  66
  67 func (s *exportNumpySuite) TestOnehot(c *check.C) {
  68         for _, trial := range []struct {
  69                 incols  int
  70                 in      []int16
  71                 outcols int
  72                 out     []int16
  73         }{
  74                 {2, []int16{1, 1, 1, 1}, 2, []int16{1, 1, 1, 1}},
  75                 {2, []int16{1, 1, 1, 2}, 3, []int16{1, 1, 0, 1, 0, 1}},
  76                 {
  77                         // 2nd column => 3 one-hot columns
  78                         // 4th column => 0 one-hot columns
  79                         4, []int16{
  80                                 1, 1, 0, 0,
  81                                 1, 2, 1, 0,
  82                                 1, 3, 0, 0,
  83                         }, 5, []int16{
  84                                 1, 1, 0, 0, 0,
  85                                 1, 0, 1, 0, 1,
  86                                 1, 0, 0, 1, 0,
  87                         },
  88                 },
  89         } {
  90                 out, _, outcols := recodeOnehot(trial.in, trial.incols)
  91                 c.Check(out, check.DeepEquals, trial.out)
  92                 c.Check(outcols, check.Equals, trial.outcols)
  93         }
  94 }