12 type exportSuite struct{}
14 var _ = check.Suite(&exportSuite{})
16 func (s *exportSuite) TestFastaToHGVS(c *check.C) {
19 err := ioutil.WriteFile(tmpdir+"/chr1-12-100.bed", []byte("chr1\t12\t100\ttest.1\n"), 0644)
20 c.Check(err, check.IsNil)
22 var buffer bytes.Buffer
23 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)
24 c.Assert(exited, check.Equals, 0)
25 ioutil.WriteFile(tmpdir+"/library.gob", buffer.Bytes(), 0644)
27 exited = (&exporter{}).RunCommand("export", []string{
29 "-input-dir=" + tmpdir,
30 "-output-dir=" + tmpdir,
31 "-output-format=hgvs-onehot",
32 "-output-labels=" + tmpdir + "/labels.csv",
33 "-ref=testdata/ref.fasta",
34 }, &buffer, os.Stderr, os.Stderr)
35 c.Check(exited, check.Equals, 0)
36 output, err := ioutil.ReadFile(tmpdir + "/out.chr1.tsv")
37 if !c.Check(err, check.IsNil) {
38 out, _ := exec.Command("find", tmpdir, "-ls").CombinedOutput()
41 c.Check(sortLines(string(output)), check.Equals, sortLines(`chr1.1_3delinsGGC 1 0
42 chr1.41_42delinsAA 1 0
46 chr1.302_305delinsAAAA 1 0
48 output, err = ioutil.ReadFile(tmpdir + "/out.chr2.tsv")
49 c.Check(err, check.IsNil)
50 c.Check(sortLines(string(output)), check.Equals, sortLines(`chr2.1_3delinsAAA 0 1
51 chr2.125_127delinsAAA 0 1
53 chr2.258_269delinsAA 1 0
56 chr2.471_472delinsAA 1 0
58 labels, err := ioutil.ReadFile(tmpdir + "/labels.csv")
59 c.Check(err, check.IsNil)
60 c.Check(string(labels), check.Equals, `0,"input1","out.tsv"
64 exited = (&exporter{}).RunCommand("export", []string{
66 "-input-dir=" + tmpdir,
67 "-output-dir=" + tmpdir,
68 "-output-format=pvcf",
69 "-ref=testdata/ref.fasta",
70 }, &buffer, os.Stderr, os.Stderr)
71 c.Check(exited, check.Equals, 0)
72 output, err = ioutil.ReadFile(tmpdir + "/out.chr1.vcf")
73 c.Check(err, check.IsNil)
75 c.Check(sortLines(string(output)), check.Equals, sortLines(`##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
76 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT testdata/pipeline1/input1.1.fasta testdata/pipeline1/input2.1.fasta
77 chr1 1 . NNN GGC . . . GT 1/1 0/0
78 chr1 41 . TT AA . . . GT 1/0 0/0
79 chr1 161 . A T . . . GT 0/1 0/0
80 chr1 178 . A T . . . GT 0/1 0/0
81 chr1 221 . TCCA T . . . GT 1/1 0/0
82 chr1 302 . TTTT AAAA . . . GT 0/1 0/0
84 output, err = ioutil.ReadFile(tmpdir + "/out.chr2.vcf")
85 c.Check(err, check.IsNil)
87 c.Check(sortLines(string(output)), check.Equals, sortLines(`##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
88 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT testdata/pipeline1/input1.1.fasta testdata/pipeline1/input2.1.fasta
89 chr2 1 . TTT AAA . . . GT 0/0 0/1
90 chr2 125 . CTT AAA . . . GT 0/0 1/1
91 chr2 240 . ATTTTTCTTGCTCTC A . . . GT 1/0 0/0
92 chr2 258 . CCTTGTATTTTT AA . . . GT 1/0 0/0
93 chr2 315 . C A . . . GT 1/0 0/0
94 chr2 469 . GTGG G . . . GT 1/0 0/0
95 chr2 471 . GG AA . . . GT 0/1 0/0
98 exited = (&exporter{}).RunCommand("export", []string{
100 "-input-dir=" + tmpdir,
101 "-output-dir=" + tmpdir,
102 "-output-format=vcf",
103 "-ref=testdata/ref.fasta",
104 }, &buffer, os.Stderr, os.Stderr)
105 c.Check(exited, check.Equals, 0)
106 output, err = ioutil.ReadFile(tmpdir + "/out.chr1.vcf")
107 c.Check(err, check.IsNil)
108 c.Log(string(output))
109 c.Check(sortLines(string(output)), check.Equals, sortLines(`#CHROM POS ID REF ALT QUAL FILTER INFO
110 chr1 1 . NNN GGC . . AC=2
111 chr1 41 . TT AA . . AC=1
112 chr1 161 . A T . . AC=1
113 chr1 178 . A T . . AC=1
114 chr1 221 . TCCA T . . AC=2
115 chr1 302 . TTTT AAAA . . AC=1
117 output, err = ioutil.ReadFile(tmpdir + "/out.chr2.vcf")
118 c.Check(err, check.IsNil)
119 c.Log(string(output))
120 c.Check(sortLines(string(output)), check.Equals, sortLines(`#CHROM POS ID REF ALT QUAL FILTER INFO
121 chr2 1 . TTT AAA . . AC=1
122 chr2 125 . CTT AAA . . AC=2
123 chr2 240 . ATTTTTCTTGCTCTC A . . AC=1
124 chr2 258 . CCTTGTATTTTT AA . . AC=1
125 chr2 315 . C A . . AC=1
126 chr2 469 . GTGG G . . AC=1
127 chr2 471 . GG AA . . AC=1