X-Git-Url: https://git.arvados.org/lightning.git/blobdiff_plain/127e7220c13792cea1cf5f31c4ccfc2a61c11f77..2ce4195e773941a3f625e5e2d5f0a36aa082ecf2:/export_test.go

diff --git a/export_test.go b/export_test.go
new file mode 100644
index 0000000000..2a020b9eba
--- /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","-"
+`)
+}