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)
+
+ 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)
+
+ 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) {
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)
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)
+ }, nil, os.Stderr, os.Stderr)
c.Check(exited, check.Equals, 0)
f, err := os.Open(outdir + "/matrix.chr1.npy")
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
- 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, // input2.1.fasta
+ -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 0, 0, // input2.1.fasta
})
f, err = os.Open(outdir + "/matrix.chr2.npy")