X-Git-Url: https://git.arvados.org/lightning.git/blobdiff_plain/93e063d8357b8682c0a730fc702f8b05ece6c46f..HEAD:/export_test.go diff --git a/export_test.go b/export_test.go deleted file mode 100644 index a2452c6ca3..0000000000 --- a/export_test.go +++ /dev/null @@ -1,217 +0,0 @@ -// 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= -#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= -#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" -`) -}