Implement -regions and -expand-regions for slice-numpy.

[lightning.git] / slice_test.go

diff --git a/slice_test.go b/slice_test.go
index d84d95f30fa402c9130c27c6d476f68a57a133f6..73321006342303c94671b5598a544fefbe519a14 100644 (file)
--- a/slice_test.go
+++ b/slice_test.go
@@ -82,45 +82,87 @@ func (s *sliceSuite) TestImportAndSlice(c *check.C) {
        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)
-
-       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+".*")
+       {
+               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{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.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+".*")
+               }
        }
 
-       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+".*")
+               }
+
+               annotations, err = ioutil.ReadFile(npydir + "/matrix.0002.annotations.csv")
+               c.Assert(err, check.IsNil)
+               c.Logf("%s", annotations)
+               c.Check(string(annotations), check.Equals, "")
        }
 }