-package main
+// 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.GetUint16()
+ 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, uint16(2), check.Commentf("i=%d, v=%v", i, variants))
+ c.Check(variants[i+1], check.Equals, int16(2), check.Commentf("i=%d, v=%v", i, variants))
} else {
- c.Check(variants[i], check.Equals, uint16(2), check.Commentf("i=%d, v=%v", i, variants))
+ c.Check(variants[i], check.Equals, int16(2), check.Commentf("i=%d, v=%v", i, variants))
}
}
- for i := 4; i < 9; i += 2 {
- c.Check(variants[i], check.Equals, uint16(1), check.Commentf("i=%d, v=%v", i, variants))
+ 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 []uint16) {
+func sortUints(variants []int16) {
for i := 0; i < len(variants); i += 2 {
if variants[i] > variants[i+1] {
for j := 0; j < len(variants); j++ {
}
}
-func (s *exportSuite) TestOnehot(c *check.C) {
+func (s *exportNumpySuite) TestOnehot(c *check.C) {
for _, trial := range []struct {
incols int
- in []uint16
+ in []int16
outcols int
- out []uint16
+ out []int16
}{
- {2, []uint16{1, 1, 1, 1}, 2, []uint16{1, 1, 1, 1}},
- {2, []uint16{1, 1, 1, 2}, 3, []uint16{1, 1, 0, 1, 0, 1}},
+ {2, []int16{1, 1, 1, 1}, 2, []int16{1, 1, 1, 1}},
+ {2, []int16{1, 1, 1, 2}, 3, []int16{1, 1, 0, 1, 0, 1}},
{
// 2nd column => 3 one-hot columns
// 4th column => 0 one-hot columns
- 4, []uint16{
+ 4, []int16{
1, 1, 0, 0,
1, 2, 1, 0,
1, 3, 0, 0,
- }, 5, []uint16{
+ }, 5, []int16{
1, 1, 0, 0, 0,
1, 0, 1, 0, 1,
1, 0, 0, 1, 0,
projects / lightning.git / blobdiff