+// 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)
- ioutil.WriteFile(tmpdir+"/library.gob", buffer.Bytes(), 0644)
- var output bytes.Buffer
+
+ 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)
+
+ input := tmpdir + "/library.gob"
+
exited = (&exporter{}).RunCommand("export", []string{
"-local=true",
- "-i=" + tmpdir + "/library.gob",
+ "-input-dir=" + input,
+ "-output-dir=" + tmpdir,
"-output-format=hgvs-onehot",
"-output-labels=" + tmpdir + "/labels.csv",
"-ref=testdata/ref.fasta",
- }, &buffer, &output, os.Stderr)
+ }, nil, os.Stderr, os.Stderr)
c.Check(exited, check.Equals, 0)
- c.Check(output.String(), check.Equals, `chr1.1_3delinsGGC 1 0
-chr1.41_42delinsAA 1 0
+ output, err := ioutil.ReadFile(tmpdir + "/out.chr1.tsv")
+ if !c.Check(err, check.IsNil) {
+ out, _ := exec.Command("find", tmpdir, "-ls").CombinedOutput()
+ c.Logf("%s", out)
+ }
+ c.Check(sortLines(string(output)), check.Equals, sortLines(`chr1.1_3delinsGGC 1 0
+chr1.41T>A 1 0
+chr1.42T>A 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
+`))
+ output, err = ioutil.ReadFile(tmpdir + "/out.chr2.tsv")
+ c.Check(err, check.IsNil)
+ c.Check(sortLines(string(output)), check.Equals, sortLines(`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
-`)
+chr2.469_471del 1 0
+chr2.471G>A 1 0
+chr2.472G>A 1 0
+`))
labels, err := ioutil.ReadFile(tmpdir + "/labels.csv")
c.Check(err, check.IsNil)
- c.Check(string(labels), check.Equals, `0,"input1","-"
-1,"input2","-"
+ c.Check(string(labels), check.Equals, `0,"input1","out.tsv"
+1,"input2","out.tsv"
+`)
+
+ exited = (&exporter{}).RunCommand("export", []string{
+ "-local=true",
+ "-input-dir=" + input,
+ "-output-dir=" + tmpdir,
+ "-output-format=pvcf",
+ "-ref=testdata/ref.fasta",
+ }, 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)
+ c.Log(string(output))
+ c.Check(sortLines(string(output)), check.Equals, sortLines(`##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT testdata/pipeline1/input1.1.fasta testdata/pipeline1/input2.1.fasta
+chr1 1 . NNN GGC . . . GT 1/1 0/0
+chr1 41 . T A . . . GT 1/0 0/0
+chr1 42 . T A . . . GT 1/0 0/0
+chr1 161 . A T . . . GT 0/1 0/0
+chr1 178 . A T . . . GT 0/1 0/0
+chr1 221 . TCCA T . . . GT 1/1 0/0
+chr1 302 . TTTT AAAA . . . GT 0/1 0/0
+`))
+ output, err = ioutil.ReadFile(tmpdir + "/out.chr2.vcf")
+ c.Check(err, check.IsNil)
+ c.Log(string(output))
+ c.Check(sortLines(string(output)), check.Equals, sortLines(`##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT testdata/pipeline1/input1.1.fasta testdata/pipeline1/input2.1.fasta
+chr2 1 . TTT AAA . . . GT 0/0 0/1
+chr2 125 . CTT AAA . . . GT 0/0 1/1
+chr2 240 . ATTTTTCTTGCTCTC A . . . GT 1/0 0/0
+chr2 258 . CCTTGTATTTTT AA . . . GT 1/0 0/0
+chr2 315 . C A . . . GT 1/0 0/0
+chr2 468 . CGTG C . . . GT 1/0 0/0
+chr2 471 . G A . . . GT 0/1 0/0
+chr2 472 . G A . . . GT 0/1 0/0
+`))
+
+ exited = (&exporter{}).RunCommand("export", []string{
+ "-local=true",
+ "-input-dir=" + input,
+ "-output-dir=" + tmpdir,
+ "-output-format=vcf",
+ "-ref=testdata/ref.fasta",
+ }, nil, os.Stderr, os.Stderr)
+ c.Check(exited, check.Equals, 0)
+ output, err = ioutil.ReadFile(tmpdir + "/out.chr1.vcf")
+ c.Check(err, check.IsNil)
+ c.Log(string(output))
+ c.Check(sortLines(string(output)), check.Equals, sortLines(`#CHROM POS ID REF ALT QUAL FILTER INFO
+chr1 1 . NNN GGC . . AC=2
+chr1 41 . T A . . AC=1
+chr1 42 . T A . . AC=1
+chr1 161 . A T . . AC=1
+chr1 178 . A T . . AC=1
+chr1 221 . TCCA T . . AC=2
+chr1 302 . TTTT AAAA . . AC=1
+`))
+ output, err = ioutil.ReadFile(tmpdir + "/out.chr2.vcf")
+ c.Check(err, check.IsNil)
+ c.Log(string(output))
+ c.Check(sortLines(string(output)), check.Equals, sortLines(`#CHROM POS ID REF ALT QUAL FILTER INFO
+chr2 1 . TTT AAA . . AC=1
+chr2 125 . CTT AAA . . AC=2
+chr2 240 . ATTTTTCTTGCTCTC A . . AC=1
+chr2 258 . CCTTGTATTTTT AA . . AC=1
+chr2 315 . C A . . AC=1
+chr2 468 . CGTG C . . AC=1
+chr2 471 . G A . . AC=1
+chr2 472 . G A . . 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, 7*2*2) // 7 variants * 2 alleles * 2 genomes
+ c.Check(variants, check.DeepEquals, []int8{
+ 1, 0, 0, 1, 0, 1, 0, 1, 0, 1, 1, 0, 0, 1, // input1.1.fasta
+ -1, -1, -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, 8*2*2) // 8 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, 0, 1, // input1.1.fasta
+ 0, 1, 1, 0, 0, 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,"chr1.41T>A"
+2,"chr1.42T>A"
+3,"chr1.161A>T"
+4,"chr1.178A>T"
+5,"chr1.222_224del"
+6,"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,"chr2.469_471del"
+6,"chr2.471G>A"
+7,"chr2.472G>A"
+`)
+
+ 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)
+
}
projects / lightning.git / blobdiff