Mention undiffable variants in annotations, write -2 in hgvs matrix.

[lightning.git] / export_test.go

diff --git a/export_test.go b/export_test.go
index 959bd85d1b16b33f9a2cb3770a1ad83ab8334ac4..ac7063d2fc625f28b583550d5ed06ced823a6f13 100644 (file)
--- a/export_test.go
+++ b/export_test.go
@@ -1,7 +1,10 @@
+// Copyright (C) The Lightning Authors. All rights reserved.
+//
+// SPDX-License-Identifier: AGPL-3.0
+
 package lightning
 
 import (
-       "bytes"
        "io/ioutil"
        "os"
        "os/exec"
@@ -20,19 +23,44 @@ func (s *exportSuite) TestFastaToHGVS(c *check.C) {
        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) {
@@ -64,11 +92,11 @@ chr2.471_472delinsAA        1       0
 
        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)
@@ -98,11 +126,11 @@ chr2       471     .       GG      AA      .       .       .       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)
@@ -128,14 +156,16 @@ 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=" + 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")
@@ -148,7 +178,7 @@ chr2        471     .       GG      AA      .       .       AC=1
        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")
@@ -184,4 +214,21 @@ chr2       471     .       GG      AA      .       .       AC=1
 5,"chr2.470_472del"
 6,"chr2.471_472delinsAA"
 `)
+
+       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)
+
 }