+// Copyright (C) The Lightning Authors. All rights reserved.
+//
+// SPDX-License-Identifier: AGPL-3.0
+
package lightning
import (
- "bytes"
"io/ioutil"
"os"
"os/exec"
+ "github.com/kshedden/gonpy"
"gopkg.in/check.v1"
)
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)
+ exited := (&importer{}).RunCommand("import", []string{
+ "-local=true",
+ "-tag-library", "testdata/tags",
+ "-output-tiles",
+ "-save-incomplete-tiles",
+ "-o", tmpdir + "/library1.gob",
+ "testdata/ref.fasta",
+ }, nil, os.Stderr, os.Stderr)
+ c.Assert(exited, check.Equals, 0)
+
+ exited = (&importer{}).RunCommand("import", []string{
+ "-local=true",
+ "-tag-library", "testdata/tags",
+ "-output-tiles",
+ // "-save-incomplete-tiles",
+ "-o", tmpdir + "/library2.gob",
+ "testdata/pipeline1",
+ }, nil, os.Stderr, os.Stderr)
+ c.Assert(exited, check.Equals, 0)
+
+ exited = (&merger{}).RunCommand("merge", []string{
+ "-local=true",
+ "-o", tmpdir + "/library.gob",
+ tmpdir + "/library1.gob",
+ tmpdir + "/library2.gob",
+ }, nil, os.Stderr, os.Stderr)
c.Assert(exited, check.Equals, 0)
- ioutil.WriteFile(tmpdir+"/library.gob", buffer.Bytes(), 0644)
+
+ input := tmpdir + "/library.gob"
exited = (&exporter{}).RunCommand("export", []string{
"-local=true",
- "-input-dir=" + tmpdir,
+ "-input-dir=" + input,
"-output-dir=" + tmpdir,
"-output-format=hgvs-onehot",
"-output-labels=" + tmpdir + "/labels.csv",
"-ref=testdata/ref.fasta",
- }, &buffer, os.Stderr, os.Stderr)
+ }, nil, os.Stderr, os.Stderr)
c.Check(exited, check.Equals, 0)
output, err := ioutil.ReadFile(tmpdir + "/out.chr1.tsv")
if !c.Check(err, check.IsNil) {
exited = (&exporter{}).RunCommand("export", []string{
"-local=true",
- "-input-dir=" + tmpdir,
+ "-input-dir=" + input,
"-output-dir=" + tmpdir,
"-output-format=pvcf",
"-ref=testdata/ref.fasta",
- }, &buffer, os.Stderr, os.Stderr)
+ }, os.Stderr, os.Stderr, os.Stderr)
c.Check(exited, check.Equals, 0)
output, err = ioutil.ReadFile(tmpdir + "/out.chr1.vcf")
c.Check(err, check.IsNil)
exited = (&exporter{}).RunCommand("export", []string{
"-local=true",
- "-input-dir=" + tmpdir,
+ "-input-dir=" + input,
"-output-dir=" + tmpdir,
"-output-format=vcf",
"-ref=testdata/ref.fasta",
- }, &buffer, os.Stderr, os.Stderr)
+ }, nil, os.Stderr, os.Stderr)
c.Check(exited, check.Equals, 0)
output, err = ioutil.ReadFile(tmpdir + "/out.chr1.vcf")
c.Check(err, check.IsNil)
chr2 469 . GTGG G . . AC=1
chr2 471 . GG AA . . AC=1
`))
+
+ c.Logf("export hgvs-numpy")
+ outdir := c.MkDir()
+ exited = (&exporter{}).RunCommand("export", []string{
+ "-local=true",
+ "-input-dir=" + input,
+ "-output-dir=" + outdir,
+ "-output-format=hgvs-numpy",
+ "-ref=testdata/ref.fasta",
+ "-match-genome=input[12]",
+ }, nil, os.Stderr, os.Stderr)
+ c.Check(exited, check.Equals, 0)
+
+ f, err := os.Open(outdir + "/matrix.chr1.npy")
+ c.Assert(err, check.IsNil)
+ defer f.Close()
+ npy, err := gonpy.NewReader(f)
+ c.Assert(err, check.IsNil)
+ variants, err := npy.GetInt8()
+ c.Assert(err, check.IsNil)
+ c.Check(variants, check.HasLen, 6*2*2) // 6 variants * 2 alleles * 2 genomes
+ c.Check(variants, check.DeepEquals, []int8{
+ 1, 0, 0, 1, 0, 1, 0, 1, 1, 0, 0, 1, // input1.1.fasta
+ -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 0, 0, // input2.1.fasta
+ })
+
+ f, err = os.Open(outdir + "/matrix.chr2.npy")
+ c.Assert(err, check.IsNil)
+ defer f.Close()
+ npy, err = gonpy.NewReader(f)
+ c.Assert(err, check.IsNil)
+ variants, err = npy.GetInt8()
+ c.Assert(err, check.IsNil)
+ c.Check(variants, check.HasLen, 7*2*2) // 6 variants * 2 alleles * 2 genomes
+ c.Check(variants, check.DeepEquals, []int8{
+ 0, 0, 0, 0, 0, 1, 0, 1, 0, 1, 0, 1, 0, 1, // input1.1.fasta
+ 0, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, // input2.1.fasta
+ })
+
+ annotations, err := ioutil.ReadFile(outdir + "/annotations.chr1.csv")
+ c.Check(err, check.IsNil)
+ c.Logf("%s", string(annotations))
+ c.Check(string(annotations), check.Equals, `0,"chr1.1_3delinsGGC"
+1,"chr1.41_42delinsAA"
+2,"chr1.161A>T"
+3,"chr1.178A>T"
+4,"chr1.222_224del"
+5,"chr1.302_305delinsAAAA"
+`)
+ annotations, err = ioutil.ReadFile(outdir + "/annotations.chr2.csv")
+ c.Check(err, check.IsNil)
+ c.Check(string(annotations), check.Equals, `0,"chr2.1_3delinsAAA"
+1,"chr2.125_127delinsAAA"
+2,"chr2.241_254del"
+3,"chr2.258_269delinsAA"
+4,"chr2.315C>A"
+5,"chr2.470_472del"
+6,"chr2.471_472delinsAA"
+`)
+
+ c.Logf("export hgvs-numpy with p-value threshold")
+ outdir = c.MkDir()
+ err = ioutil.WriteFile(tmpdir+"/cases", []byte("input1\n"), 0777)
+ c.Assert(err, check.IsNil)
+ exited = (&exporter{}).RunCommand("export", []string{
+ "-local=true",
+ "-input-dir=" + input,
+ "-p-value=0.05",
+ "-cases=" + tmpdir + "/cases",
+ "-output-dir=" + outdir,
+ "-output-format=hgvs-numpy",
+ "-ref=testdata/ref.fasta",
+ "-match-genome=input[12]",
+ }, nil, os.Stderr, os.Stderr)
+ c.Check(exited, check.Equals, 0)
+
}