Option to merge matrices and annotations.

[lightning.git] / slice_test.go

diff --git a/slice_test.go b/slice_test.go
index 73321006342303c94671b5598a544fefbe519a14..15dc220a741f585e240fd48c19916082076a989f 100644 (file)
--- a/slice_test.go
+++ b/slice_test.go
@@ -160,9 +160,51 @@ func (s *sliceSuite) TestImportAndSlice(c *check.C) {
                        c.Check(string(annotations), check.Matches, "(?ms).*"+s+".*")
                }
 
-               annotations, err = ioutil.ReadFile(npydir + "/matrix.0002.annotations.csv")
+               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)
-               c.Check(string(annotations), check.Equals, "")
+               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+".*")
+               }
        }
 }