package lightning
import (
- "bytes"
"io/ioutil"
"os"
"os/exec"
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)
- ioutil.WriteFile(tmpdir+"/library.gob", buffer.Bytes(), 0644)
+
+ 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=" + 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) {
c.Logf("%s", out)
}
c.Check(sortLines(string(output)), check.Equals, sortLines(`chr1.1_3delinsGGC 1 0
-chr1.41_42delinsAA 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
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)
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)
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 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
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
+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=" + 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)
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 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
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
+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=" + tmpdir,
+ "-input-dir=" + input,
"-output-dir=" + outdir,
"-output-format=hgvs-numpy",
"-ref=testdata/ref.fasta",
- }, &buffer, os.Stderr, os.Stderr)
+ "-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)
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.HasLen, 7*2*2) // 7 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
- 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, // input2.1.fasta
+ 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)
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.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, // input1.1.fasta
- 0, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, // input2.1.fasta
+ 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,"chr1.41_42delinsAA"
-2,"chr1.161A>T"
-3,"chr1.178A>T"
-4,"chr1.222_224del"
-5,"chr1.302_305delinsAAAA"
+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)
2,"chr2.241_254del"
3,"chr2.258_269delinsAA"
4,"chr2.315C>A"
-5,"chr2.470_472del"
-6,"chr2.471_472delinsAA"
+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