package lightning import ( "bytes" "fmt" "io" "io/ioutil" "os" "sort" "strings" "sync" "gopkg.in/check.v1" ) type pipelineSuite struct{} var _ = check.Suite(&pipelineSuite{}) func (s *pipelineSuite) TestImport(c *check.C) { for _, infile := range []string{ "testdata/pipeline1/", "testdata/ref.fasta", } { c.Logf("TestImport: %s", infile) var wg sync.WaitGroup statsin, importout := io.Pipe() wg.Add(1) go func() { defer wg.Done() code := (&importer{}).RunCommand("lightning import", []string{"-local=true", "-skip-ooo=true", "-output-tiles", "-tag-library", "testdata/tags", infile}, bytes.NewReader(nil), importout, os.Stderr) c.Check(code, check.Equals, 0) importout.Close() }() statsout := &bytes.Buffer{} wg.Add(1) go func() { defer wg.Done() code := (&statscmd{}).RunCommand("lightning stats", []string{"-local"}, statsin, statsout, os.Stderr) c.Check(code, check.Equals, 0) }() wg.Wait() c.Logf("%s", statsout.String()) } } func (s *pipelineSuite) TestImportMerge(c *check.C) { libfile := make([]string, 2) tmpdir := c.MkDir() var wg sync.WaitGroup for i, infile := range []string{ "testdata/ref.fasta", "testdata/pipeline1/", } { i, infile := i, infile c.Logf("TestImportMerge: %s", infile) libfile[i] = fmt.Sprintf("%s/%d.gob", tmpdir, i) wg.Add(1) go func() { defer wg.Done() args := []string{"-local=true", "-o=" + libfile[i], "-skip-ooo=true", "-output-tiles", "-tag-library", "testdata/tags"} if i == 0 { // ref only args = append(args, "-save-incomplete-tiles") } args = append(args, infile) code := (&importer{}).RunCommand("lightning import", args, bytes.NewReader(nil), &bytes.Buffer{}, os.Stderr) c.Check(code, check.Equals, 0) }() } wg.Wait() merged := &bytes.Buffer{} code := (&merger{}).RunCommand("lightning merge", []string{"-local", libfile[0], libfile[1]}, bytes.NewReader(nil), merged, os.Stderr) c.Check(code, check.Equals, 0) c.Logf("len(merged) %d", merged.Len()) statsout := &bytes.Buffer{} code = (&statscmd{}).RunCommand("lightning stats", []string{"-local"}, bytes.NewReader(merged.Bytes()), statsout, os.Stderr) c.Check(code, check.Equals, 0) c.Check(statsout.Len() > 0, check.Equals, true) c.Logf("%s", statsout.String()) c.Check(ioutil.WriteFile(tmpdir+"/merged.gob", merged.Bytes(), 0666), check.IsNil) hgvsout := &bytes.Buffer{} code = (&exporter{}).RunCommand("lightning export", []string{"-local", "-ref", "testdata/ref.fasta", "-output-format", "hgvs", "-i", tmpdir + "/merged.gob"}, bytes.NewReader(nil), hgvsout, os.Stderr) c.Check(code, check.Equals, 0) c.Check(hgvsout.Len() > 0, check.Equals, true) c.Logf("%s", hgvsout.String()) c.Check(hgvsout.String(), check.Equals, `chr1:g.1_3delinsGGC . chr1:g.[41_42delinsAA];[41=] . chr1:g.[161=];[161A>T] . chr1:g.[178=];[178A>T] . chr1:g.222_224del . chr1:g.[302=];[302_305delinsAAAA] . . chr2:g.[1=];[1_3delinsAAA] . chr2:g.125_127delinsAAA chr2:g.[241_254del];[241=] . chr2:g.[258_269delinsAA];[258=] . chr2:g.[315C>A];[315=] . chr2:g.[470_472del];[470=] . chr2:g.[471=];[471_472delinsAA] . `) vcfout := &bytes.Buffer{} code = (&exporter{}).RunCommand("lightning export", []string{"-local", "-ref", "testdata/ref.fasta", "-output-format", "vcf", "-i", tmpdir + "/merged.gob", "-output-bed", tmpdir + "/export.bed"}, bytes.NewReader(nil), vcfout, os.Stderr) c.Check(code, check.Equals, 0) c.Check(vcfout.Len() > 0, check.Equals, true) c.Logf("%s", vcfout.String()) c.Check(vcfout.String(), check.Equals, `chr1 1 NNN GGC 1/1 0/0 chr1 41 TT AA 1/0 0/0 chr1 161 A T 0/1 0/0 chr1 178 A T 0/1 0/0 chr1 221 TCCA T 1/1 0/0 chr1 302 TTTT AAAA 0/1 0/0 chr2 1 TTT AAA 0/0 0/1 chr2 125 CTT AAA 0/0 1/1 chr2 240 ATTTTTCTTGCTCTC A 1/0 0/0 chr2 258 CCTTGTATTTTT AA 1/0 0/0 chr2 315 C A 1/0 0/0 chr2 469 GTGG G 1/0 0/0 chr2 471 GG AA 0/1 0/0 `) bedout, err := ioutil.ReadFile(tmpdir + "/export.bed") c.Check(err, check.IsNil) c.Logf("%s", string(bedout)) c.Check(string(bedout), check.Equals, `chr1 0 248 0 1000 . 0 224 chr1 224 372 1 1000 . 248 348 chr1 348 496 2 1000 . 372 472 chr1 472 572 3 1000 . 496 572 chr2 0 248 4 1000 . 0 224 chr2 224 372 5 750 . 248 348 chr2 348 496 6 1000 . 372 472 chr2 472 572 7 1000 . 496 572 `) annotateout := &bytes.Buffer{} code = (&annotatecmd{}).RunCommand("lightning annotate", []string{"-local", "-variant-hash=true", "-i", tmpdir + "/merged.gob"}, bytes.NewReader(nil), annotateout, os.Stderr) c.Check(code, check.Equals, 0) c.Check(annotateout.Len() > 0, check.Equals, true) sorted := sortLines(annotateout.String()) c.Logf("%s", sorted) c.Check(sorted, check.Equals, sortLines(`0,8d4fe9a63921b,chr1:g.161A>T 0,8d4fe9a63921b,chr1:g.178A>T 0,8d4fe9a63921b,chr1:g.1_3delinsGGC 0,8d4fe9a63921b,chr1:g.222_224del 0,ba4263ca4199c,chr1:g.1_3delinsGGC 0,ba4263ca4199c,chr1:g.222_224del 0,ba4263ca4199c,chr1:g.41_42delinsAA 1,139890345dbb8,chr1:g.302_305delinsAAAA 4,cbfca15d241d3,chr2:g.125_127delinsAAA 4,cbfca15d241d3,chr2:g.1_3delinsAAA 4,f5fafe9450b02,chr2:g.241_245delinsAAAAA 4,f5fafe9450b02,chr2:g.291C>A 4,fe9a71a42adb4,chr2:g.125_127delinsAAA 6,e36dce85efbef,chr2:g.471_472delinsAA 6,f81388b184f4a,chr2:g.470_472del `)) } func sortLines(txt string) string { lines := strings.Split(strings.TrimRightFunc(txt, func(c rune) bool { return c == '\n' }), "\n") sort.Strings(lines) return strings.Join(lines, "\n") + "\n" }