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
  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         c.Log("=== import testdata/ref ===")
  27         exited := (&importer{}).RunCommand("import", []string{
  28                 "-local=true",
  29                 "-tag-library", "testdata/tags",
  30                 "-output-tiles",
  31                 "-save-incomplete-tiles",
  32                 "-o", tmpdir + "/library1.gob",
  33                 "testdata/ref.fasta",
  34         }, nil, os.Stderr, os.Stderr)
  35         c.Assert(exited, check.Equals, 0)
  36
  37         c.Log("=== import testdata/pipeline1 ===")
  38         exited = (&importer{}).RunCommand("import", []string{
  39                 "-local=true",
  40                 "-tag-library", "testdata/tags",
  41                 "-output-tiles",
  42                 "-o", tmpdir + "/library2.gob",
  43                 "testdata/pipeline1",
  44         }, nil, os.Stderr, os.Stderr)
  45         c.Assert(exited, check.Equals, 0)
  46
  47         c.Log("=== merge ===")
  48         exited = (&merger{}).RunCommand("merge", []string{
  49                 "-local=true",
  50                 "-o", tmpdir + "/library.gob",
  51                 tmpdir + "/library1.gob",
  52                 tmpdir + "/library2.gob",
  53         }, nil, os.Stderr, os.Stderr)
  54         c.Assert(exited, check.Equals, 0)
  55
  56         input := tmpdir + "/library.gob"
  57         slicedir := c.MkDir()
  58
  59         c.Log("=== slice ===")
  60         exited = (&slicecmd{}).RunCommand("slice", []string{
  61                 "-local=true",
  62                 "-input-dir=" + input,
  63                 "-output-dir=" + slicedir,
  64                 "-tags-per-file=2",
  65         }, nil, os.Stderr, os.Stderr)
  66         c.Check(exited, check.Equals, 0)
  67         out, _ := exec.Command("find", slicedir, "-ls").CombinedOutput()
  68         c.Logf("%s", out)
  69
  70         c.Log("=== slice-numpy ===")
  71         npydir := c.MkDir()
  72         exited = (&sliceNumpy{}).RunCommand("slice-numpy", []string{
  73                 "-local=true",
  74                 "-input-dir=" + slicedir,
  75                 "-output-dir=" + npydir,
  76         }, nil, os.Stderr, os.Stderr)
  77         c.Check(exited, check.Equals, 0)
  78         out, _ = exec.Command("find", npydir, "-ls").CombinedOutput()
  79         c.Logf("%s", out)
  80
  81         f, err := os.Open(npydir + "/matrix.0000.npy")
  82         c.Assert(err, check.IsNil)
  83         defer f.Close()
  84         npy, err := gonpy.NewReader(f)
  85         c.Assert(err, check.IsNil)
  86         c.Check(npy.Shape, check.DeepEquals, []int{2, 4})
  87         variants, err := npy.GetInt16()
  88         if c.Check(variants, check.HasLen, 8) {
  89                 c.Check(variants[4:], check.DeepEquals, []int16{-1, -1, 1, 1}) // TODO: check first row too, when stable
  90         }
  91
  92         annotations, err := ioutil.ReadFile(npydir + "/matrix.0000.annotations.csv")
  93         c.Assert(err, check.IsNil)
  94         c.Logf("%s", annotations)
  95         for _, s := range []string{
  96                 "chr1:g.161A>T",
  97                 "chr1:g.178A>T",
  98                 "chr1:g.1_3delinsGGC",
  99                 "chr1:g.222_224del",
 100         } {
 101                 c.Check(string(annotations), check.Matches, "(?ms).*"+s+".*")
 102         }
 103 }