Load case/control/neither from csv column, fix Χ² filter.

[lightning.git] / slice_test.go

diff --git a/slice_test.go b/slice_test.go
index 62c0c9181f761ba6685bc30aeea4b37f4946e8d7..10202a4f0a9c848639fd5e046e19314f923fdcc7 100644 (file)
--- a/slice_test.go
+++ b/slice_test.go
@@ -214,13 +214,19 @@ func (s *sliceSuite) TestImportAndSlice(c *check.C) {
 
        c.Log("=== slice-numpy + chunked hgvs matrix ===")
        {
-               err = ioutil.WriteFile(tmpdir+"/cases.txt", []byte("pipeline1/input1\npipeline1dup/input1\n"), 0600)
+               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",
                        "-chunked-hgvs-matrix=true",
-                       "-chi2-cases-file=" + tmpdir + "/cases.txt",
+                       "-chi2-case-control-file=" + tmpdir + "/casecontrol.tsv",
+                       "-chi2-case-control-column=CC",
                        "-chi2-p-value=0.05",
                        "-min-coverage=0.75",
                        "-input-dir=" + slicedir,
@@ -240,13 +246,19 @@ func (s *sliceSuite) TestImportAndSlice(c *check.C) {
 
        c.Log("=== slice-numpy + onehot ===")
        {
-               err = ioutil.WriteFile(tmpdir+"/cases.txt", []byte("pipeline1/input1\npipeline1dup/input1\n"), 0600)
+               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",
                        "-chunked-onehot=true",
-                       "-chi2-cases-file=" + tmpdir + "/cases.txt",
+                       "-chi2-case-control-file=" + tmpdir + "/casecontrol.tsv",
+                       "-chi2-case-control-column=CC",
                        "-chi2-p-value=0.05",
                        "-min-coverage=0.75",
                        "-input-dir=" + slicedir,