Export hgvs one-hot numpy.

[lightning.git] / export_test.go

diff --git a/export_test.go b/export_test.go
index 2b7772c3829fc07f15c9b875cb4216bc7f8c0b01..959bd85d1b16b33f9a2cb3770a1ad83ab8334ac4 100644 (file)
--- a/export_test.go
+++ b/export_test.go
@@ -6,6 +6,7 @@ import (
        "os"
        "os/exec"
 
+       "github.com/kshedden/gonpy"
        "gopkg.in/check.v1"
 )
 
@@ -126,4 +127,61 @@ chr2       315     .       C       A       .       .       AC=1
 chr2   469     .       GTGG    G       .       .       AC=1
 chr2   471     .       GG      AA      .       .       AC=1
 `))
+
+       outdir := c.MkDir()
+       exited = (&exporter{}).RunCommand("export", []string{
+               "-local=true",
+               "-input-dir=" + tmpdir,
+               "-output-dir=" + outdir,
+               "-output-format=hgvs-numpy",
+               "-ref=testdata/ref.fasta",
+       }, &buffer, 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
+               0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 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"
+`)
 }