pipeline_test.go

   1 package lightning
   2
   3 import (
   4         "bytes"
   5         "fmt"
   6         "io"
   7         "io/ioutil"
   8         "os"
   9         "sort"
  10         "strings"
  11         "sync"
  12
  13         "gopkg.in/check.v1"
  14 )
  15
  16 type pipelineSuite struct{}
  17
  18 var _ = check.Suite(&pipelineSuite{})
  19
  20 func (s *pipelineSuite) TestImport(c *check.C) {
  21         for _, infile := range []string{
  22                 "testdata/pipeline1/",
  23                 "testdata/ref.fasta",
  24         } {
  25                 c.Logf("TestImport: %s", infile)
  26                 var wg sync.WaitGroup
  27
  28                 statsin, importout := io.Pipe()
  29                 wg.Add(1)
  30                 go func() {
  31                         defer wg.Done()
  32                         code := (&importer{}).RunCommand("lightning import", []string{"-local=true", "-skip-ooo=true", "-output-tiles", "-tag-library", "testdata/tags", infile}, bytes.NewReader(nil), importout, os.Stderr)
  33                         c.Check(code, check.Equals, 0)
  34                         importout.Close()
  35                 }()
  36                 statsout := &bytes.Buffer{}
  37                 wg.Add(1)
  38                 go func() {
  39                         defer wg.Done()
  40                         code := (&statscmd{}).RunCommand("lightning stats", []string{"-local"}, statsin, statsout, os.Stderr)
  41                         c.Check(code, check.Equals, 0)
  42                 }()
  43                 wg.Wait()
  44                 c.Logf("%s", statsout.String())
  45         }
  46 }
  47
  48 func (s *pipelineSuite) TestImportMerge(c *check.C) {
  49         libfile := make([]string, 2)
  50         tmpdir := c.MkDir()
  51
  52         var wg sync.WaitGroup
  53         for i, infile := range []string{
  54                 "testdata/ref.fasta",
  55                 "testdata/pipeline1/",
  56         } {
  57                 i, infile := i, infile
  58                 c.Logf("TestImportMerge: %s", infile)
  59                 libfile[i] = fmt.Sprintf("%s/%d.gob", tmpdir, i)
  60                 wg.Add(1)
  61                 go func() {
  62                         defer wg.Done()
  63                         args := []string{"-local=true", "-o=" + libfile[i], "-skip-ooo=true", "-output-tiles", "-tag-library", "testdata/tags"}
  64                         if i == 0 {
  65                                 // ref only
  66                                 args = append(args, "-save-incomplete-tiles")
  67                         }
  68                         args = append(args, infile)
  69                         code := (&importer{}).RunCommand("lightning import", args, bytes.NewReader(nil), &bytes.Buffer{}, os.Stderr)
  70                         c.Check(code, check.Equals, 0)
  71                 }()
  72         }
  73         wg.Wait()
  74
  75         merged := &bytes.Buffer{}
  76         code := (&merger{}).RunCommand("lightning merge", []string{"-local", libfile[0], libfile[1]}, bytes.NewReader(nil), merged, os.Stderr)
  77         c.Check(code, check.Equals, 0)
  78         c.Logf("len(merged) %d", merged.Len())
  79
  80         statsout := &bytes.Buffer{}
  81         code = (&statscmd{}).RunCommand("lightning stats", []string{"-local"}, bytes.NewReader(merged.Bytes()), statsout, os.Stderr)
  82         c.Check(code, check.Equals, 0)
  83         c.Check(statsout.Len() > 0, check.Equals, true)
  84         c.Logf("%s", statsout.String())
  85
  86         err := os.Mkdir(tmpdir+"/merged", 0777)
  87         c.Assert(err, check.IsNil)
  88         c.Check(ioutil.WriteFile(tmpdir+"/merged/library.gob", merged.Bytes(), 0666), check.IsNil)
  89
  90         code = (&exporter{}).RunCommand("lightning export", []string{"-local", "-ref", "testdata/ref.fasta", "-output-format", "hgvs", "-input-dir", tmpdir + "/merged", "-output-dir", tmpdir, "-output-per-chromosome=false"}, bytes.NewReader(nil), os.Stderr, os.Stderr)
  91         c.Check(code, check.Equals, 0)
  92         hgvsout, err := ioutil.ReadFile(tmpdir + "/out.csv")
  93         c.Check(err, check.IsNil)
  94         c.Check(sortLines(string(hgvsout)), check.Equals, sortLines(`chr1:g.1_3delinsGGC        .
  95 chr1:g.[41_42delinsAA];[41=]    .
  96 chr1:g.[161=];[161A>T]  .
  97 chr1:g.[178=];[178A>T]  .
  98 chr1:g.222_224del       .
  99 chr1:g.[302=];[302_305delinsAAAA]       .
 100 .       chr2:g.[1=];[1_3delinsAAA]
 101 .       chr2:g.125_127delinsAAA
 102 chr2:g.[241_254del];[241=]      .
 103 chr2:g.[258_269delinsAA];[258=] .
 104 chr2:g.[315C>A];[315=]  .
 105 chr2:g.[470_472del];[470=]      .
 106 chr2:g.[471=];[471_472delinsAA] .
 107 `))
 108
 109         code = (&exporter{}).RunCommand("lightning export", []string{"-local", "-ref", "testdata/ref.fasta", "-output-dir", tmpdir, "-output-format", "vcf", "-input-dir", tmpdir + "/merged", "-output-bed", tmpdir + "/export.bed", "-output-per-chromosome=false"}, bytes.NewReader(nil), os.Stderr, os.Stderr)
 110         c.Check(code, check.Equals, 0)
 111         vcfout, err := ioutil.ReadFile(tmpdir + "/out.vcf")
 112         c.Check(err, check.IsNil)
 113         c.Check(sortLines(string(vcfout)), check.Equals, sortLines(`chr1        1       NNN     GGC     1/1     0/0
 114 chr1    41      TT      AA      1/0     0/0
 115 chr1    161     A       T       0/1     0/0
 116 chr1    178     A       T       0/1     0/0
 117 chr1    221     TCCA    T       1/1     0/0
 118 chr1    302     TTTT    AAAA    0/1     0/0
 119 chr2    1       TTT     AAA     0/0     0/1
 120 chr2    125     CTT     AAA     0/0     1/1
 121 chr2    240     ATTTTTCTTGCTCTC A       1/0     0/0
 122 chr2    258     CCTTGTATTTTT    AA      1/0     0/0
 123 chr2    315     C       A       1/0     0/0
 124 chr2    469     GTGG    G       1/0     0/0
 125 chr2    471     GG      AA      0/1     0/0
 126 `))
 127         bedout, err := ioutil.ReadFile(tmpdir + "/export.bed")
 128         c.Check(err, check.IsNil)
 129         c.Logf("%s", string(bedout))
 130         c.Check(sortLines(string(bedout)), check.Equals, sortLines(`chr1 0 248 0 1000 . 0 224
 131 chr1 224 372 1 1000 . 248 348
 132 chr1 348 496 2 1000 . 372 472
 133 chr1 472 572 3 1000 . 496 572
 134 chr2 0 248 4 1000 . 0 224
 135 chr2 224 372 5 750 . 248 348
 136 chr2 348 496 6 1000 . 372 472
 137 chr2 472 572 7 1000 . 496 572
 138 `))
 139
 140         annotateout := &bytes.Buffer{}
 141         code = (&annotatecmd{}).RunCommand("lightning annotate", []string{"-local", "-variant-hash=true", "-i", tmpdir + "/merged/library.gob"}, bytes.NewReader(nil), annotateout, os.Stderr)
 142         c.Check(code, check.Equals, 0)
 143         c.Check(annotateout.Len() > 0, check.Equals, true)
 144         sorted := sortLines(annotateout.String())
 145         c.Logf("%s", sorted)
 146         c.Check(sorted, check.Equals, sortLines(`0,0,8d4fe9a63921b,chr1:g.161A>T
 147 0,0,8d4fe9a63921b,chr1:g.178A>T
 148 0,0,8d4fe9a63921b,chr1:g.1_3delinsGGC
 149 0,0,8d4fe9a63921b,chr1:g.222_224del
 150 0,0,ba4263ca4199c,chr1:g.1_3delinsGGC
 151 0,0,ba4263ca4199c,chr1:g.222_224del
 152 0,0,ba4263ca4199c,chr1:g.41_42delinsAA
 153 1,1,139890345dbb8,chr1:g.302_305delinsAAAA
 154 4,4,cbfca15d241d3,chr2:g.125_127delinsAAA
 155 4,4,cbfca15d241d3,chr2:g.1_3delinsAAA
 156 4,4,f5fafe9450b02,chr2:g.241_245delinsAAAAA
 157 4,4,f5fafe9450b02,chr2:g.291C>A
 158 4,4,fe9a71a42adb4,chr2:g.125_127delinsAAA
 159 6,6,e36dce85efbef,chr2:g.471_472delinsAA
 160 6,6,f81388b184f4a,chr2:g.470_472del
 161 `))
 162 }
 163
 164 func sortLines(txt string) string {
 165         lines := strings.Split(strings.TrimRightFunc(txt, func(c rune) bool { return c == '\n' }), "\n")
 166         sort.Strings(lines)
 167         return strings.Join(lines, "\n") + "\n"
 168 }