X-Git-Url: https://git.arvados.org/lightning.git/blobdiff_plain/00b2acd54dd1aa412f6f2bddc24b1bbb31c7ae3f..79e0bd0ff72ae1759e8b780e5d8b61b09c9a0399:/exportnumpy_test.go

diff --git a/exportnumpy_test.go b/exportnumpy_test.go
index 9dd71da82b..2de95d2859 100644
--- a/exportnumpy_test.go
+++ b/exportnumpy_test.go
@@ -1,38 +1,56 @@
+// Copyright (C) The Lightning Authors. All rights reserved.
+//
+// SPDX-License-Identifier: AGPL-3.0
+
 package lightning
 
 import (
 	"bytes"
+	"io/ioutil"
 	"os"
 
 	"github.com/kshedden/gonpy"
 	"gopkg.in/check.v1"
 )
 
-type exportSuite struct{}
+type exportNumpySuite struct{}
+
+var _ = check.Suite(&exportNumpySuite{})
 
-var _ = check.Suite(&exportSuite{})
+func (s *exportNumpySuite) TestFastaToNumpy(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)
 
-func (s *exportSuite) TestFastaToNumpy(c *check.C) {
 	var buffer bytes.Buffer
-	exited := (&importer{}).RunCommand("import", []string{"-local=true", "-tag-library", "testdata/tags", "-ref", "testdata/ref", "-output-tiles", "testdata/a.1.fasta"}, &bytes.Buffer{}, &buffer, os.Stderr)
+	exited := (&importer{}).RunCommand("import", []string{"-local=true", "-o", tmpdir + "/library.gob.gz", "-tag-library", "testdata/tags", "-output-tiles", "-save-incomplete-tiles", "testdata/a.1.fasta", "testdata/tinyref.fasta"}, &bytes.Buffer{}, os.Stderr, os.Stderr)
 	c.Assert(exited, check.Equals, 0)
-	var output bytes.Buffer
-	exited = (&exportNumpy{}).RunCommand("export-numpy", []string{"-local=true"}, &buffer, &output, os.Stderr)
+	exited = (&exportNumpy{}).RunCommand("export-numpy", []string{"-local=true", "-input-dir", tmpdir, "-output-dir", tmpdir, "-output-annotations", tmpdir + "/annotations.csv", "-regions", tmpdir + "/chr1-12-100.bed"}, &buffer, os.Stderr, os.Stderr)
 	c.Check(exited, check.Equals, 0)
-	npy, err := gonpy.NewReader(&output)
+	f, err := os.Open(tmpdir + "/matrix.npy")
+	c.Assert(err, check.IsNil)
+	defer f.Close()
+	npy, err := gonpy.NewReader(f)
 	c.Assert(err, check.IsNil)
 	variants, err := npy.GetInt16()
 	c.Assert(err, check.IsNil)
-	for i := 0; i < 4; i += 2 {
+	c.Check(variants, check.HasLen, 6)
+	for i := 0; i < 4 && i < len(variants); i += 2 {
 		if variants[i] == 1 {
 			c.Check(variants[i+1], check.Equals, int16(2), check.Commentf("i=%d, v=%v", i, variants))
 		} else {
 			c.Check(variants[i], check.Equals, int16(2), check.Commentf("i=%d, v=%v", i, variants))
 		}
 	}
-	for i := 4; i < 9; i += 2 {
+	for i := 4; i < 6 && i < len(variants); i += 2 {
 		c.Check(variants[i], check.Equals, int16(1), check.Commentf("i=%d, v=%v", i, variants))
 	}
+	annotations, err := ioutil.ReadFile(tmpdir + "/annotations.csv")
+	c.Check(err, check.IsNil)
+	c.Logf("%s", string(annotations))
+	c.Check(string(annotations), check.Matches, `(?ms)(.*\n)?1,1,2,chr1:g.84_85insACTGCGATCTGA\n.*`)
+	c.Check(string(annotations), check.Matches, `(?ms)(.*\n)?1,1,1,chr1:g.87_96delinsGCATCTGCA\n.*`)
 }
 
 func sortUints(variants []int16) {
@@ -46,7 +64,7 @@ func sortUints(variants []int16) {
 	}
 }
 
-func (s *exportSuite) TestOnehot(c *check.C) {
+func (s *exportNumpySuite) TestOnehot(c *check.C) {
 	for _, trial := range []struct {
 		incols  int
 		in      []int16