-// Copyright (C) The Lightning Authors. All rights reserved.
-//
-// SPDX-License-Identifier: AGPL-3.0
-
-package lightning
-
-import (
- "io/ioutil"
- "os"
- "os/exec"
-
- "github.com/kshedden/gonpy"
- "gopkg.in/check.v1"
-)
-
-type exportSuite struct{}
-
-var _ = check.Suite(&exportSuite{})
-
-func (s *exportSuite) TestFastaToHGVS(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)
-
- 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)
-
- input := tmpdir + "/library.gob"
-
- exited = (&exporter{}).RunCommand("export", []string{
- "-local=true",
- "-input-dir=" + input,
- "-output-dir=" + tmpdir,
- "-output-format=hgvs-onehot",
- "-output-labels=" + tmpdir + "/labels.csv",
- "-ref=testdata/ref.fasta",
- }, 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) {
- out, _ := exec.Command("find", tmpdir, "-ls").CombinedOutput()
- c.Logf("%s", out)
- }
- c.Check(sortLines(string(output)), check.Equals, sortLines(`chr1.1_3delinsGGC 1 0
-chr1.41_42delinsAA 1 0
-chr1.161A>T 1 0
-chr1.178A>T 1 0
-chr1.222_224del 1 0
-chr1.302_305delinsAAAA 1 0
-`))
- 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
-`))
- labels, err := ioutil.ReadFile(tmpdir + "/labels.csv")
- c.Check(err, check.IsNil)
- 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 . TT AA . . . 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 469 . GTGG G . . . GT 1/0 0/0
-chr2 471 . GG AA . . . 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 . TT AA . . 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 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"
-`)
-}
projects / lightning.git / blobdiff