slice_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         "io/ioutil"
   9         "os"
  10         "os/exec"
  11
  12         "github.com/kshedden/gonpy"
  13         "gopkg.in/check.v1"
  14 )
  15
  16 type sliceSuite struct{}
  17
  18 var _ = check.Suite(&sliceSuite{})
  19
  20 func (s *sliceSuite) TestImportAndSlice(c *check.C) {
  21         tmpdir := c.MkDir()
  22         err := os.Mkdir(tmpdir+"/lib1", 0777)
  23         c.Assert(err, check.IsNil)
  24         err = os.Mkdir(tmpdir+"/lib2", 0777)
  25         c.Assert(err, check.IsNil)
  26         err = os.Mkdir(tmpdir+"/lib3", 0777)
  27         c.Assert(err, check.IsNil)
  28         cwd, err := os.Getwd()
  29         c.Assert(err, check.IsNil)
  30         err = os.Symlink(cwd+"/testdata/pipeline1", tmpdir+"/pipeline1")
  31         c.Assert(err, check.IsNil)
  32         err = os.Symlink(cwd+"/testdata/pipeline1", tmpdir+"/pipeline1dup")
  33         c.Assert(err, check.IsNil)
  34
  35         err = ioutil.WriteFile(tmpdir+"/chr1-12-100.bed", []byte("chr1\t12\t100\ttest.1\n"), 0644)
  36         c.Check(err, check.IsNil)
  37
  38         c.Log("=== import testdata/ref ===")
  39         exited := (&importer{}).RunCommand("import", []string{
  40                 "-local=true",
  41                 "-tag-library", "testdata/tags",
  42                 "-output-tiles",
  43                 "-save-incomplete-tiles",
  44                 "-o", tmpdir + "/lib1/library1.gob",
  45                 "testdata/ref.fasta",
  46         }, nil, os.Stderr, os.Stderr)
  47         c.Assert(exited, check.Equals, 0)
  48
  49         c.Log("=== import testdata/pipeline1 ===")
  50         exited = (&importer{}).RunCommand("import", []string{
  51                 "-local=true",
  52                 "-tag-library", "testdata/tags",
  53                 "-output-tiles",
  54                 "-o", tmpdir + "/lib2/library2.gob",
  55                 tmpdir + "/pipeline1",
  56         }, nil, os.Stderr, os.Stderr)
  57         c.Assert(exited, check.Equals, 0)
  58
  59         c.Log("=== import pipeline1dup ===")
  60         exited = (&importer{}).RunCommand("import", []string{
  61                 "-local=true",
  62                 "-tag-library", "testdata/tags",
  63                 "-output-tiles",
  64                 "-o", tmpdir + "/lib3/library3.gob",
  65                 tmpdir + "/pipeline1dup",
  66         }, nil, os.Stderr, os.Stderr)
  67         c.Assert(exited, check.Equals, 0)
  68
  69         slicedir := c.MkDir()
  70
  71         c.Log("=== slice ===")
  72         exited = (&slicecmd{}).RunCommand("slice", []string{
  73                 "-local=true",
  74                 "-output-dir=" + slicedir,
  75                 "-tags-per-file=2",
  76                 tmpdir + "/lib1",
  77                 tmpdir + "/lib2",
  78                 tmpdir + "/lib3",
  79         }, nil, os.Stderr, os.Stderr)
  80         c.Check(exited, check.Equals, 0)
  81         out, _ := exec.Command("find", slicedir, "-ls").CombinedOutput()
  82         c.Logf("%s", out)
  83
  84         c.Log("=== slice-numpy ===")
  85         {
  86                 npydir := c.MkDir()
  87                 exited := (&sliceNumpy{}).RunCommand("slice-numpy", []string{
  88                         "-local=true",
  89                         "-input-dir=" + slicedir,
  90                         "-output-dir=" + npydir,
  91                 }, nil, os.Stderr, os.Stderr)
  92                 c.Check(exited, check.Equals, 0)
  93                 out, _ := exec.Command("find", npydir, "-ls").CombinedOutput()
  94                 c.Logf("%s", out)
  95
  96                 f, err := os.Open(npydir + "/matrix.0000.npy")
  97                 c.Assert(err, check.IsNil)
  98                 defer f.Close()
  99                 npy, err := gonpy.NewReader(f)
 100                 c.Assert(err, check.IsNil)
 101                 c.Check(npy.Shape, check.DeepEquals, []int{4, 4})
 102                 variants, err := npy.GetInt16()
 103                 c.Check(variants, check.DeepEquals, []int16{2, 1, 1, 2, -1, -1, 1, 1, 2, 1, 1, 2, -1, -1, 1, 1})
 104
 105                 annotations, err := ioutil.ReadFile(npydir + "/matrix.0000.annotations.csv")
 106                 c.Assert(err, check.IsNil)
 107                 c.Logf("%s", annotations)
 108                 for _, s := range []string{
 109                         "chr1:g.161A>T",
 110                         "chr1:g.178A>T",
 111                         "chr1:g.1_3delinsGGC",
 112                         "chr1:g.222_224del",
 113                 } {
 114                         c.Check(string(annotations), check.Matches, "(?ms).*"+s+".*")
 115                 }
 116
 117                 annotations, err = ioutil.ReadFile(npydir + "/matrix.0002.annotations.csv")
 118                 c.Assert(err, check.IsNil)
 119                 c.Logf("%s", annotations)
 120                 for _, s := range []string{
 121                         ",2,chr2:g.1_3delinsAAA",
 122                         ",2,chr2:g.125_127delinsAAA",
 123                         ",4,chr2:g.125_127delinsAAA",
 124                 } {
 125                         c.Check(string(annotations), check.Matches, "(?ms).*"+s+".*")
 126                 }
 127         }
 128
 129         c.Log("=== slice-numpy + regions ===")
 130         {
 131                 npydir := c.MkDir()
 132                 exited := (&sliceNumpy{}).RunCommand("slice-numpy", []string{
 133                         "-local=true",
 134                         "-regions=" + tmpdir + "/chr1-12-100.bed",
 135                         "-input-dir=" + slicedir,
 136                         "-output-dir=" + npydir,
 137                         "-chunked-hgvs-matrix=true",
 138                 }, nil, os.Stderr, os.Stderr)
 139                 c.Check(exited, check.Equals, 0)
 140                 out, _ := exec.Command("find", npydir, "-ls").CombinedOutput()
 141                 c.Logf("%s", out)
 142
 143                 f, err := os.Open(npydir + "/matrix.0000.npy")
 144                 c.Assert(err, check.IsNil)
 145                 defer f.Close()
 146                 npy, err := gonpy.NewReader(f)
 147                 c.Assert(err, check.IsNil)
 148                 c.Check(npy.Shape, check.DeepEquals, []int{4, 2})
 149                 variants, err := npy.GetInt16()
 150                 c.Check(variants, check.DeepEquals, []int16{2, 1, -1, -1, 2, 1, -1, -1})
 151
 152                 annotations, err := ioutil.ReadFile(npydir + "/matrix.0000.annotations.csv")
 153                 c.Assert(err, check.IsNil)
 154                 c.Logf("%s", annotations)
 155                 for _, s := range []string{
 156                         "chr1:g.161A>T",
 157                         "chr1:g.178A>T",
 158                         "chr1:g.1_3delinsGGC",
 159                         "chr1:g.222_224del",
 160                 } {
 161                         c.Check(string(annotations), check.Matches, "(?ms).*"+s+".*")
 162                 }
 163
 164                 for _, fnm := range []string{
 165                         npydir + "/matrix.0001.annotations.csv",
 166                         npydir + "/matrix.0002.annotations.csv",
 167                 } {
 168                         annotations, err := ioutil.ReadFile(fnm)
 169                         c.Assert(err, check.IsNil)
 170                         c.Check(string(annotations), check.Equals, "", check.Commentf(fnm))
 171                 }
 172         }
 173
 174         err = ioutil.WriteFile(tmpdir+"/chr1and2-100-200.bed", []byte("chr1\t100\t200\ttest.1\nchr2\t100\t200\ttest.2\n"), 0644)
 175         c.Check(err, check.IsNil)
 176
 177         c.Log("=== slice-numpy + regions + merge ===")
 178         {
 179                 npydir := c.MkDir()
 180                 exited := (&sliceNumpy{}).RunCommand("slice-numpy", []string{
 181                         "-local=true",
 182                         "-regions=" + tmpdir + "/chr1and2-100-200.bed",
 183                         "-input-dir=" + slicedir,
 184                         "-output-dir=" + npydir,
 185                         "-merge-output=true",
 186                         "-single-hgvs-matrix=true",
 187                 }, nil, os.Stderr, os.Stderr)
 188                 c.Check(exited, check.Equals, 0)
 189                 out, _ := exec.Command("find", npydir, "-ls").CombinedOutput()
 190                 c.Logf("%s", out)
 191
 192                 f, err := os.Open(npydir + "/matrix.npy")
 193                 c.Assert(err, check.IsNil)
 194                 defer f.Close()
 195                 npy, err := gonpy.NewReader(f)
 196                 c.Assert(err, check.IsNil)
 197                 c.Check(npy.Shape, check.DeepEquals, []int{4, 4})
 198                 variants, err := npy.GetInt16()
 199                 c.Check(variants, check.DeepEquals, []int16{2, 1, 3, 1, -1, -1, 4, 2, 2, 1, 3, 1, -1, -1, 4, 2})
 200
 201                 annotations, err := ioutil.ReadFile(npydir + "/matrix.annotations.csv")
 202                 c.Assert(err, check.IsNil)
 203                 c.Logf("%s", annotations)
 204                 for _, s := range []string{
 205                         "0,0,1,chr1:g.161A>T",
 206                         "0,0,1,chr1:g.178A>T",
 207                         "4,1,2,chr2:g.125_127delinsAAA",
 208                 } {
 209                         c.Check(string(annotations), check.Matches, "(?ms).*"+s+".*")
 210                 }
 211         }
 212 }