X-Git-Url: https://git.arvados.org/lightning.git/blobdiff_plain/f35bf68935079b520da1418fa75b08394d68b1ef..ed9183d5e6ce23f1cf6f9a7d65d3e68214393e8a:/slice_test.go

diff --git a/slice_test.go b/slice_test.go
index c73d3d7dc0..15dc220a74 100644
--- 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+".*")
+		}
 	}
 }