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Fix interval tree unused node markers.
[lightning.git] / slice_test.go
diff --git a/slice_test.go b/slice_test.go
index c73d3d7dc0cd8496e4e02b9e93f84f41ad18a19b..15dc220a741f585e240fd48c19916082076a989f 100644 (file)
--- a/slice_test.go
+++ b/slice_test.go
@@ -19,8 +19,20 @@ var _ = check.Suite(&sliceSuite{})
 
 func (s *sliceSuite) TestImportAndSlice(c *check.C) {
        tmpdir := c.MkDir()
+       err := os.Mkdir(tmpdir+"/lib1", 0777)
+       c.Assert(err, check.IsNil)
+       err = os.Mkdir(tmpdir+"/lib2", 0777)
+       c.Assert(err, check.IsNil)
+       err = os.Mkdir(tmpdir+"/lib3", 0777)
+       c.Assert(err, check.IsNil)
+       cwd, err := os.Getwd()
+       c.Assert(err, check.IsNil)
+       err = os.Symlink(cwd+"/testdata/pipeline1", tmpdir+"/pipeline1")
+       c.Assert(err, check.IsNil)
+       err = os.Symlink(cwd+"/testdata/pipeline1", tmpdir+"/pipeline1dup")
+       c.Assert(err, check.IsNil)
 
-       err := ioutil.WriteFile(tmpdir+"/chr1-12-100.bed", []byte("chr1\t12\t100\ttest.1\n"), 0644)
+       err = ioutil.WriteFile(tmpdir+"/chr1-12-100.bed", []byte("chr1\t12\t100\ttest.1\n"), 0644)
        c.Check(err, check.IsNil)
 
        c.Log("=== import testdata/ref ===")
@@ -29,7 +41,7 @@ func (s *sliceSuite) TestImportAndSlice(c *check.C) {
                "-tag-library", "testdata/tags",
                "-output-tiles",
                "-save-incomplete-tiles",
-               "-o", tmpdir + "/library1.gob",
+               "-o", tmpdir + "/lib1/library1.gob",
                "testdata/ref.fasta",
        }, nil, os.Stderr, os.Stderr)
        c.Assert(exited, check.Equals, 0)
@@ -39,63 +51,160 @@ func (s *sliceSuite) TestImportAndSlice(c *check.C) {
                "-local=true",
                "-tag-library", "testdata/tags",
                "-output-tiles",
-               "-o", tmpdir + "/library2.gob",
-               "testdata/pipeline1",
+               "-o", tmpdir + "/lib2/library2.gob",
+               tmpdir + "/pipeline1",
        }, nil, os.Stderr, os.Stderr)
        c.Assert(exited, check.Equals, 0)
 
-       c.Log("=== merge ===")
-       exited = (&merger{}).RunCommand("merge", []string{
+       c.Log("=== import pipeline1dup ===")
+       exited = (&importer{}).RunCommand("import", []string{
                "-local=true",
-               "-o", tmpdir + "/library.gob",
-               tmpdir + "/library1.gob",
-               tmpdir + "/library2.gob",
+               "-tag-library", "testdata/tags",
+               "-output-tiles",
+               "-o", tmpdir + "/lib3/library3.gob",
+               tmpdir + "/pipeline1dup",
        }, nil, os.Stderr, os.Stderr)
        c.Assert(exited, check.Equals, 0)
 
-       input := tmpdir + "/library.gob"
        slicedir := c.MkDir()
 
        c.Log("=== slice ===")
        exited = (&slicecmd{}).RunCommand("slice", []string{
                "-local=true",
-               "-input-dir=" + input,
                "-output-dir=" + slicedir,
                "-tags-per-file=2",
+               tmpdir + "/lib1",
+               tmpdir + "/lib2",
+               tmpdir + "/lib3",
        }, nil, os.Stderr, os.Stderr)
        c.Check(exited, check.Equals, 0)
        out, _ := exec.Command("find", slicedir, "-ls").CombinedOutput()
        c.Logf("%s", out)
 
        c.Log("=== slice-numpy ===")
-       npydir := c.MkDir()
-       exited = (&sliceNumpy{}).RunCommand("slice-numpy", []string{
-               "-local=true",
-               "-input-dir=" + slicedir,
-               "-output-dir=" + npydir,
-       }, nil, os.Stderr, os.Stderr)
-       c.Check(exited, check.Equals, 0)
-       out, _ = exec.Command("find", npydir, "-ls").CombinedOutput()
-       c.Logf("%s", out)
+       {
+               npydir := c.MkDir()
+               exited := (&sliceNumpy{}).RunCommand("slice-numpy", []string{
+                       "-local=true",
+                       "-input-dir=" + slicedir,
+                       "-output-dir=" + npydir,
+               }, nil, os.Stderr, os.Stderr)
+               c.Check(exited, check.Equals, 0)
+               out, _ := exec.Command("find", npydir, "-ls").CombinedOutput()
+               c.Logf("%s", out)
 
-       f, err := os.Open(npydir + "/matrix.0000.npy")
-       c.Assert(err, check.IsNil)
-       defer f.Close()
-       npy, err := gonpy.NewReader(f)
-       c.Assert(err, check.IsNil)
-       c.Check(npy.Shape, check.DeepEquals, []int{2, 4})
-       variants, err := npy.GetInt16()
-       c.Check(variants, check.DeepEquals, []int16{3, 2, 1, 2, -1, -1, 1, 1})
+               f, err := os.Open(npydir + "/matrix.0000.npy")
+               c.Assert(err, check.IsNil)
+               defer f.Close()
+               npy, err := gonpy.NewReader(f)
+               c.Assert(err, check.IsNil)
+               c.Check(npy.Shape, check.DeepEquals, []int{4, 4})
+               variants, err := npy.GetInt16()
+               c.Check(variants, check.DeepEquals, []int16{2, 1, 1, 2, -1, -1, 1, 1, 2, 1, 1, 2, -1, -1, 1, 1})
 
-       annotations, err := ioutil.ReadFile(npydir + "/matrix.0000.annotations.csv")
-       c.Assert(err, check.IsNil)
-       c.Logf("%s", annotations)
-       for _, s := range []string{
-               "chr1:g.161A>T",
-               "chr1:g.178A>T",
-               "chr1:g.1_3delinsGGC",
-               "chr1:g.222_224del",
-       } {
-               c.Check(string(annotations), check.Matches, "(?ms).*"+s+".*")
+               annotations, err := ioutil.ReadFile(npydir + "/matrix.0000.annotations.csv")
+               c.Assert(err, check.IsNil)
+               c.Logf("%s", annotations)
+               for _, s := range []string{
+                       "chr1:g.161A>T",
+                       "chr1:g.178A>T",
+                       "chr1:g.1_3delinsGGC",
+                       "chr1:g.222_224del",
+               } {
+                       c.Check(string(annotations), check.Matches, "(?ms).*"+s+".*")
+               }
+
+               annotations, err = ioutil.ReadFile(npydir + "/matrix.0002.annotations.csv")
+               c.Assert(err, check.IsNil)
+               c.Logf("%s", annotations)
+               for _, s := range []string{
+                       ",2,chr2:g.1_3delinsAAA",
+                       ",2,chr2:g.125_127delinsAAA",
+                       ",4,chr2:g.125_127delinsAAA",
+               } {
+                       c.Check(string(annotations), check.Matches, "(?ms).*"+s+".*")
+               }
+       }
+
+       c.Log("=== slice-numpy + regions ===")
+       {
+               npydir := c.MkDir()
+               exited := (&sliceNumpy{}).RunCommand("slice-numpy", []string{
+                       "-local=true",
+                       "-regions=" + tmpdir + "/chr1-12-100.bed",
+                       "-input-dir=" + slicedir,
+                       "-output-dir=" + npydir,
+               }, nil, os.Stderr, os.Stderr)
+               c.Check(exited, check.Equals, 0)
+               out, _ := exec.Command("find", npydir, "-ls").CombinedOutput()
+               c.Logf("%s", out)
+
+               f, err := os.Open(npydir + "/matrix.0000.npy")
+               c.Assert(err, check.IsNil)
+               defer f.Close()
+               npy, err := gonpy.NewReader(f)
+               c.Assert(err, check.IsNil)
+               c.Check(npy.Shape, check.DeepEquals, []int{4, 2})
+               variants, err := npy.GetInt16()
+               c.Check(variants, check.DeepEquals, []int16{2, 1, -1, -1, 2, 1, -1, -1})
+
+               annotations, err := ioutil.ReadFile(npydir + "/matrix.0000.annotations.csv")
+               c.Assert(err, check.IsNil)
+               c.Logf("%s", annotations)
+               for _, s := range []string{
+                       "chr1:g.161A>T",
+                       "chr1:g.178A>T",
+                       "chr1:g.1_3delinsGGC",
+                       "chr1:g.222_224del",
+               } {
+                       c.Check(string(annotations), check.Matches, "(?ms).*"+s+".*")
+               }
+
+               for _, fnm := range []string{
+                       npydir + "/matrix.0001.annotations.csv",
+                       npydir + "/matrix.0002.annotations.csv",
+               } {
+                       annotations, err := ioutil.ReadFile(fnm)
+                       c.Assert(err, check.IsNil)
+                       c.Check(string(annotations), check.Equals, "", check.Commentf(fnm))
+               }
+       }
+
+       err = ioutil.WriteFile(tmpdir+"/chr1and2-100-200.bed", []byte("chr1\t100\t200\ttest.1\nchr2\t100\t200\ttest.2\n"), 0644)
+       c.Check(err, check.IsNil)
+
+       c.Log("=== slice-numpy + regions + merge ===")
+       {
+               npydir := c.MkDir()
+               exited := (&sliceNumpy{}).RunCommand("slice-numpy", []string{
+                       "-local=true",
+                       "-regions=" + tmpdir + "/chr1and2-100-200.bed",
+                       "-input-dir=" + slicedir,
+                       "-output-dir=" + npydir,
+                       "-merge-output=true",
+               }, nil, os.Stderr, os.Stderr)
+               c.Check(exited, check.Equals, 0)
+               out, _ := exec.Command("find", npydir, "-ls").CombinedOutput()
+               c.Logf("%s", out)
+
+               f, err := os.Open(npydir + "/matrix.npy")
+               c.Assert(err, check.IsNil)
+               defer f.Close()
+               npy, err := gonpy.NewReader(f)
+               c.Assert(err, check.IsNil)
+               c.Check(npy.Shape, check.DeepEquals, []int{4, 4})
+               variants, err := npy.GetInt16()
+               c.Check(variants, check.DeepEquals, []int16{2, 1, 3, 1, -1, -1, 4, 2, 2, 1, 3, 1, -1, -1, 4, 2})
+
+               annotations, err := ioutil.ReadFile(npydir + "/matrix.annotations.csv")
+               c.Assert(err, check.IsNil)
+               c.Logf("%s", annotations)
+               for _, s := range []string{
+                       "0,0,1,chr1:g.161A>T",
+                       "0,0,1,chr1:g.178A>T",
+                       "4,1,2,chr2:g.125_127delinsAAA",
+               } {
+                       c.Check(string(annotations), check.Matches, "(?ms).*"+s+".*")
+               }
        }
 }