11 type exportSuite struct{}
13 var _ = check.Suite(&exportSuite{})
15 func (s *exportSuite) TestFastaToHGVS(c *check.C) {
18 err := ioutil.WriteFile(tmpdir+"/chr1-12-100.bed", []byte("chr1\t12\t100\ttest.1\n"), 0644)
19 c.Check(err, check.IsNil)
21 var buffer bytes.Buffer
22 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)
23 c.Assert(exited, check.Equals, 0)
24 ioutil.WriteFile(tmpdir+"/library.gob", buffer.Bytes(), 0644)
26 exited = (&exporter{}).RunCommand("export", []string{
28 "-input-dir=" + tmpdir,
29 "-output-dir=" + tmpdir,
30 "-output-format=hgvs-onehot",
31 "-output-labels=" + tmpdir + "/labels.csv",
32 "-ref=testdata/ref.fasta",
33 }, &buffer, os.Stderr, os.Stderr)
34 c.Check(exited, check.Equals, 0)
35 output, err := ioutil.ReadFile(tmpdir + "/out.chr1.csv")
36 c.Check(err, check.IsNil)
37 c.Check(sortLines(string(output)), check.Equals, sortLines(`chr1.1_3delinsGGC 1 0
38 chr1.41_42delinsAA 1 0
42 chr1.302_305delinsAAAA 1 0
44 output, err = ioutil.ReadFile(tmpdir + "/out.chr2.csv")
45 c.Check(err, check.IsNil)
46 c.Check(sortLines(string(output)), check.Equals, sortLines(`chr2.1_3delinsAAA 0 1
47 chr2.125_127delinsAAA 0 1
49 chr2.258_269delinsAA 1 0
52 chr2.471_472delinsAA 1 0
54 labels, err := ioutil.ReadFile(tmpdir + "/labels.csv")
55 c.Check(err, check.IsNil)
56 c.Check(string(labels), check.Equals, `0,"input1","out.csv"
60 exited = (&exporter{}).RunCommand("export", []string{
62 "-input-dir=" + tmpdir,
63 "-output-dir=" + tmpdir,
64 "-output-format=pvcf",
65 "-ref=testdata/ref.fasta",
66 }, &buffer, os.Stderr, os.Stderr)
67 c.Check(exited, check.Equals, 0)
68 output, err = ioutil.ReadFile(tmpdir + "/out.chr1.vcf")
69 c.Check(err, check.IsNil)
71 c.Check(sortLines(string(output)), check.Equals, sortLines(`##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
72 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT testdata/pipeline1/input1.1.fasta testdata/pipeline1/input2.1.fasta
73 chr1 1 . NNN GGC . . . GT 1/1 0/0
74 chr1 41 . TT AA . . . GT 1/0 0/0
75 chr1 161 . A T . . . GT 0/1 0/0
76 chr1 178 . A T . . . GT 0/1 0/0
77 chr1 221 . TCCA T . . . GT 1/1 0/0
78 chr1 302 . TTTT AAAA . . . GT 0/1 0/0
80 output, err = ioutil.ReadFile(tmpdir + "/out.chr2.vcf")
81 c.Check(err, check.IsNil)
83 c.Check(sortLines(string(output)), check.Equals, sortLines(`##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
84 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT testdata/pipeline1/input1.1.fasta testdata/pipeline1/input2.1.fasta
85 chr2 1 . TTT AAA . . . GT 0/0 0/1
86 chr2 125 . CTT AAA . . . GT 0/0 1/1
87 chr2 240 . ATTTTTCTTGCTCTC A . . . GT 1/0 0/0
88 chr2 258 . CCTTGTATTTTT AA . . . GT 1/0 0/0
89 chr2 315 . C A . . . GT 1/0 0/0
90 chr2 469 . GTGG G . . . GT 1/0 0/0
91 chr2 471 . GG AA . . . GT 0/1 0/0
94 exited = (&exporter{}).RunCommand("export", []string{
96 "-input-dir=" + tmpdir,
97 "-output-dir=" + tmpdir,
99 "-ref=testdata/ref.fasta",
100 }, &buffer, os.Stderr, os.Stderr)
101 c.Check(exited, check.Equals, 0)
102 output, err = ioutil.ReadFile(tmpdir + "/out.chr1.vcf")
103 c.Check(err, check.IsNil)
104 c.Log(string(output))
105 c.Check(sortLines(string(output)), check.Equals, sortLines(`#CHROM POS ID REF ALT QUAL FILTER INFO
106 chr1 1 . NNN GGC . . AC=2
107 chr1 41 . TT AA . . AC=1
108 chr1 161 . A T . . AC=1
109 chr1 178 . A T . . AC=1
110 chr1 221 . TCCA T . . AC=2
111 chr1 302 . TTTT AAAA . . AC=1
113 output, err = ioutil.ReadFile(tmpdir + "/out.chr2.vcf")
114 c.Check(err, check.IsNil)
115 c.Log(string(output))
116 c.Check(sortLines(string(output)), check.Equals, sortLines(`#CHROM POS ID REF ALT QUAL FILTER INFO
117 chr2 1 . TTT AAA . . AC=1
118 chr2 125 . CTT AAA . . AC=2
119 chr2 240 . ATTTTTCTTGCTCTC A . . AC=1
120 chr2 258 . CCTTGTATTTTT AA . . AC=1
121 chr2 315 . C A . . AC=1
122 chr2 469 . GTGG G . . AC=1
123 chr2 471 . GG AA . . AC=1