pipeline_test.go

   1 package main
   2
   3 import (
   4         "bytes"
   5         "fmt"
   6         "io"
   7         "io/ioutil"
   8         "os"
   9         "sync"
  10
  11         "gopkg.in/check.v1"
  12 )
  13
  14 type pipelineSuite struct{}
  15
  16 var _ = check.Suite(&pipelineSuite{})
  17
  18 func (s *pipelineSuite) TestImport(c *check.C) {
  19         for _, infile := range []string{
  20                 "testdata/pipeline1/",
  21                 "testdata/ref.fasta",
  22         } {
  23                 c.Logf("TestImport: %s", infile)
  24                 var wg sync.WaitGroup
  25
  26                 statsin, importout := io.Pipe()
  27                 wg.Add(1)
  28                 go func() {
  29                         defer wg.Done()
  30                         code := (&importer{}).RunCommand("lightning import", []string{"-local=true", "-skip-ooo=true", "-output-tiles", "-tag-library", "testdata/tags", infile}, bytes.NewReader(nil), importout, os.Stderr)
  31                         c.Check(code, check.Equals, 0)
  32                         importout.Close()
  33                 }()
  34                 statsout := &bytes.Buffer{}
  35                 wg.Add(1)
  36                 go func() {
  37                         defer wg.Done()
  38                         code := (&stats{}).RunCommand("lightning stats", []string{"-local"}, statsin, statsout, os.Stderr)
  39                         c.Check(code, check.Equals, 0)
  40                 }()
  41                 wg.Wait()
  42                 c.Logf("%s", statsout.String())
  43         }
  44 }
  45
  46 func (s *pipelineSuite) TestImportMerge(c *check.C) {
  47         libfile := make([]string, 2)
  48         tmpdir := c.MkDir()
  49
  50         var wg sync.WaitGroup
  51         for i, infile := range []string{
  52                 "testdata/pipeline1/",
  53                 "testdata/ref.fasta",
  54         } {
  55                 i, infile := i, infile
  56                 c.Logf("TestImportMerge: %s", infile)
  57                 libfile[i] = fmt.Sprintf("%s/%d.gob", tmpdir, i)
  58                 wg.Add(1)
  59                 go func() {
  60                         defer wg.Done()
  61                         code := (&importer{}).RunCommand("lightning import", []string{"-local=true", "-o=" + libfile[i], "-skip-ooo=true", "-output-tiles", "-tag-library", "testdata/tags", infile}, bytes.NewReader(nil), &bytes.Buffer{}, os.Stderr)
  62                         c.Check(code, check.Equals, 0)
  63                 }()
  64         }
  65         wg.Wait()
  66
  67         merged := &bytes.Buffer{}
  68         code := (&merger{}).RunCommand("lightning merge", []string{"-local", libfile[0], libfile[1]}, bytes.NewReader(nil), merged, os.Stderr)
  69         c.Check(code, check.Equals, 0)
  70         c.Logf("len(merged) %d", merged.Len())
  71
  72         statsout := &bytes.Buffer{}
  73         code = (&stats{}).RunCommand("lightning stats", []string{"-local"}, bytes.NewReader(merged.Bytes()), statsout, os.Stderr)
  74         c.Check(code, check.Equals, 0)
  75         c.Check(statsout.Len() > 0, check.Equals, true)
  76         c.Logf("%s", statsout.String())
  77
  78         c.Check(ioutil.WriteFile(tmpdir+"/merged.gob", merged.Bytes(), 0666), check.IsNil)
  79
  80         hgvsout := &bytes.Buffer{}
  81         code = (&exportHGVS{}).RunCommand("lightning export-hgvs", []string{"-local", "-ref", "testdata/ref.fasta", "-i", tmpdir + "/merged.gob"}, bytes.NewReader(nil), hgvsout, os.Stderr)
  82         c.Check(code, check.Equals, 0)
  83         c.Check(hgvsout.Len() > 0, check.Equals, true)
  84         c.Logf("%s", hgvsout.String())
  85         c.Check(hgvsout.String(), check.Equals, `chr1:g.[41_42delinsAA];[41=]
  86 chr1:g.[161=];[161A>T]
  87 chr1:g.[178=];[178A>T]
  88 chr1:g.222_224del
  89 chr1:g.[302=];[302_305delinsAAAA]
  90 chr2:g.[813_826del];[813=]
  91 chr2:g.[830_841delinsAA];[830=]
  92 chr2:g.[887C>A];[887=]
  93 chr2:g.[1042_1044del];[1042=]
  94 chr2:g.[1043=];[1043_1044delinsAA]
  95 `)
  96 }