Fix some tests.

[lightning.git] / exportnumpy_test.go

diff --git a/exportnumpy_test.go b/exportnumpy_test.go
index 9dd71da82b833014ef826cbad6c9e0db05988e87..2de95d285975a3e0d81242283fdf35e226cdf6d7 100644 (file)
--- 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