Add -single-onehot output option.

[lightning.git] / slice_test.go

diff --git a/slice_test.go b/slice_test.go
index 10202a4f0a9c848639fd5e046e19314f923fdcc7..4278f13e203aa31e371f989d956488a51f98114a 100644 (file)
--- a/slice_test.go
+++ b/slice_test.go
@@ -244,7 +244,7 @@ pipeline1dup/input2 0
 `)
        }
 
-       c.Log("=== slice-numpy + onehot ===")
+       c.Log("=== slice-numpy + onehotChunked ===")
        {
                err = ioutil.WriteFile(tmpdir+"/casecontrol.tsv", []byte(`SampleID      CC
 pipeline1/input1       1
@@ -287,4 +287,48 @@ pipeline1dup/input2        0
                        })
                }
        }
+
+       c.Log("=== slice-numpy + onehotSingle ===")
+       {
+               err = ioutil.WriteFile(tmpdir+"/casecontrol.tsv", []byte(`SampleID      CC
+pipeline1/input1       1
+pipeline1/input2       0
+pipeline1dup/input1    1
+pipeline1dup/input2    0
+`), 0600)
+               c.Assert(err, check.IsNil)
+               npydir := c.MkDir()
+               exited := (&sliceNumpy{}).RunCommand("slice-numpy", []string{
+                       "-local=true",
+                       "-single-onehot=true",
+                       "-chi2-case-control-file=" + tmpdir + "/casecontrol.tsv",
+                       "-chi2-case-control-column=CC",
+                       "-chi2-p-value=0.05",
+                       "-min-coverage=0.75",
+                       "-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 + "/onehot.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, 16})
+               onehot, err := npy.GetInt8()
+               if c.Check(err, check.IsNil) {
+                       for r := 0; r < npy.Shape[0]; r++ {
+                               c.Logf("%v", onehot[r*npy.Shape[1]:(r+1)*npy.Shape[1]])
+                       }
+                       c.Check(onehot, check.DeepEquals, []int8{
+                               0, 1, 0, 0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 1, 0, 1, // input1
+                               0, 0, 1, 0, 0, 0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0, // input2
+                               0, 1, 0, 0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 1, 0, 1, // dup/input1
+                               0, 0, 1, 0, 0, 0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0, // dup/input2
+                       })
+               }
+       }
 }