Export hgvs-onehot.

[lightning.git] / export_test.go

diff --git a/export_test.go b/export_test.go
new file mode 100644 (file)
index 0000000..2a020b9
--- /dev/null
+++ b/export_test.go
@@ -0,0 +1,53 @@
+package lightning
+
+import (
+       "bytes"
+       "io/ioutil"
+       "os"
+
+       "gopkg.in/check.v1"
+)
+
+type exportSuite struct{}
+
+var _ = check.Suite(&exportSuite{})
+
+func (s *exportSuite) TestFastaToHGVS(c *check.C) {
+       tmpdir := c.MkDir()
+
+       err := ioutil.WriteFile(tmpdir+"/chr1-12-100.bed", []byte("chr1\t12\t100\ttest.1\n"), 0644)
+       c.Check(err, check.IsNil)
+
+       var buffer bytes.Buffer
+       exited := (&importer{}).RunCommand("import", []string{"-local=true", "-tag-library", "testdata/tags", "-output-tiles", "-save-incomplete-tiles", "testdata/pipeline1", "testdata/ref.fasta"}, &bytes.Buffer{}, &buffer, os.Stderr)
+       c.Assert(exited, check.Equals, 0)
+       ioutil.WriteFile(tmpdir+"/library.gob", buffer.Bytes(), 0644)
+       var output bytes.Buffer
+       exited = (&exporter{}).RunCommand("export", []string{
+               "-local=true",
+               "-i=" + tmpdir + "/library.gob",
+               "-output-format=hgvs-onehot",
+               "-output-labels=" + tmpdir + "/labels.csv",
+               "-ref=testdata/ref.fasta",
+       }, &buffer, &output, os.Stderr)
+       c.Check(exited, check.Equals, 0)
+       c.Check(output.String(), check.Equals, `chr1.1_3delinsGGC       1       0
+chr1.41_42delinsAA     1       0
+chr1.161A>T    1       0
+chr1.178A>T    1       0
+chr1.222_224del        1       0
+chr1.302_305delinsAAAA 1       0
+chr2.1_3delinsAAA      0       1
+chr2.125_127delinsAAA  0       1
+chr2.241_254del        1       0
+chr2.258_269delinsAA   1       0
+chr2.315C>A    1       0
+chr2.470_472del        1       0
+chr2.471_472delinsAA   1       0
+`)
+       labels, err := ioutil.ReadFile(tmpdir + "/labels.csv")
+       c.Check(err, check.IsNil)
+       c.Check(string(labels), check.Equals, `0,"input1","-"
+1,"input2","-"
+`)
+}