bio-ucsc-api 0.0.1 → 0.0.3

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (25) hide show
  1. data/README.rdoc +9 -2
  2. data/Rakefile +1 -1
  3. data/VERSION +1 -1
  4. data/bio-ucsc-api.gemspec +29 -7
  5. data/lib/bio-ucsc.rb +2 -2
  6. data/lib/bio-ucsc/hg18.rb +3 -0
  7. data/lib/bio-ucsc/hg18/reference.rb +171 -0
  8. data/lib/bio-ucsc/hg19.rb +46 -9
  9. data/lib/bio-ucsc/hg19/description.rb +23 -0
  10. data/lib/bio-ucsc/hg19/gbcdnainfo.rb +24 -0
  11. data/lib/bio-ucsc/hg19/kgxref.rb +19 -0
  12. data/lib/bio-ucsc/hg19/reference.rb +171 -0
  13. data/lib/bio-ucsc/hg19/refseqsummary.rb +23 -0
  14. data/lib/bio-ucsc/hg19/trnas.rb +20 -0
  15. data/samples/hg19-2bit-retrieve.rb +39 -0
  16. data/samples/hg19-sample.rb +22 -1
  17. data/samples/symbol2summary.rb +47 -0
  18. data/spec/hg18/reference_spec.rb +144 -0
  19. data/spec/hg19/description_spec.rb +25 -0
  20. data/spec/hg19/gbcdnainfo_spec.rb +25 -0
  21. data/spec/hg19/kgxref_spec.rb +14 -0
  22. data/spec/hg19/reference_spec.rb +137 -0
  23. data/spec/hg19/refseqsummary_spec.rb +15 -0
  24. data/spec/hg19/trnas_spec.rb +23 -0
  25. metadata +29 -56
data/spec/hg19/description_spec.rb ADDED
@@ -0,0 +1,25 @@
1
+ require 'bio-ucsc'
2
+ describe "Bio::Ucsc::Hg19::Description" do
3
+
4
+ describe "#find" do
5
+ context "given range *(0..9)" do
6
+ it "returens an array of results" do
7
+ Bio::Ucsc::Hg19::DBConnection.default
8
+ Bio::Ucsc::Hg19::DBConnection.connect
9
+ Bio::Ucsc::Hg19::Description.find([*(0..9)]).should have(10).items
10
+ end
11
+ end
12
+ end
13
+
14
+ describe ".gbCndaInfo.acc" do
15
+ context "given id==1" do
16
+ it 'returens "AB004856"' do
17
+ Bio::Ucsc::Hg19::DBConnection.default
18
+ Bio::Ucsc::Hg19::DBConnection.connect
19
+ Bio::Ucsc::Hg19::Description.find(1).gbCdnaInfo.acc.should == "AB004856"
20
+ end
21
+ end
22
+ end
23
+
24
+
25
+ end
data/spec/hg19/gbcdnainfo_spec.rb ADDED
@@ -0,0 +1,25 @@
1
+ require 'bio-ucsc'
2
+ describe "Bio::Ucsc::Hg19::GbCdnaInfo" do
3
+
4
+ describe "#find" do
5
+ context "given range *(1..9)" do
6
+ it "returens an array of results" do
7
+ Bio::Ucsc::Hg19::DBConnection.default
8
+ Bio::Ucsc::Hg19::DBConnection.connect
9
+ Bio::Ucsc::Hg19::GbCdnaInfo.find([*(1..9)]).should have(9).items
10
+ end
11
+ end
12
+ end
13
+
14
+ describe ".description.name" do
15
+ context "given id==1" do
16
+ it 'returens 1' do
17
+ Bio::Ucsc::Hg19::DBConnection.default
18
+ Bio::Ucsc::Hg19::DBConnection.connect
19
+ r = Bio::Ucsc::Hg19::GbCdnaInfo.find(1, :include => :description)
20
+ r.description.id.should == 1
21
+ end
22
+ end
23
+ end
24
+
25
+ end
data/spec/hg19/kgxref_spec.rb ADDED
@@ -0,0 +1,14 @@
1
+ require 'bio-ucsc'
2
+ describe "Bio::Ucsc::Hg19::KgXref" do
3
+
4
+ describe "#find_by_geneSymbol" do
5
+ context 'given "TP53"' do
6
+ it "returens an array of results" do
7
+ Bio::Ucsc::Hg19::DBConnection.default
8
+ Bio::Ucsc::Hg19::DBConnection.connect
9
+ Bio::Ucsc::Hg19::KgXref.find_all_by_geneSymbol("TP53").should have(13).item
10
+ end
11
+ end
12
+ end
13
+
14
+ end
data/spec/hg19/reference_spec.rb ADDED
@@ -0,0 +1,137 @@
1
+ require 'bio-ucsc'
2
+
3
+ describe "Bio::Ucsc::Hg19::Reference" do
4
+
5
+ describe ".load" do
6
+ context 'given "../samples/hg19.2bit"' do
7
+ it "returns true" do
8
+ Bio::Ucsc::Hg19::Reference.load("samples/hg19.2bit")
9
+ end
10
+ end
11
+ end
12
+
13
+ describe ".header.signarue" do
14
+ context 'given "../samples/hg19.2bit"' do
15
+ it "returns 0x1A412743" do
16
+ Bio::Ucsc::Hg19::Reference.load("samples/hg19.2bit")
17
+ Bio::Ucsc::Hg19::Reference.header.signature.should == 0x1A412743
18
+ end
19
+ end
20
+ end
21
+
22
+ describe ".header.version" do
23
+ context 'given "../samples/hg19.2bit"' do
24
+ it "returns 0" do
25
+ Bio::Ucsc::Hg19::Reference.load("samples/hg19.2bit")
26
+ Bio::Ucsc::Hg19::Reference.header.version.should == 0
27
+ end
28
+ end
29
+ end
30
+
31
+ describe ".header.sequence_count" do
32
+ context 'given "../samples/hg19.2bit"' do
33
+ it "returns 0x5d" do
34
+ Bio::Ucsc::Hg19::Reference.load("samples/hg19.2bit")
35
+ Bio::Ucsc::Hg19::Reference.header.sequence_count.should == 0x5d
36
+ end
37
+ end
38
+ end
39
+
40
+ describe '.offsets["chr1"]' do
41
+ context 'given "../samples/hg19.2bit"' do
42
+ it "returns 0x0687" do
43
+ Bio::Ucsc::Hg19::Reference.load("samples/hg19.2bit")
44
+ Bio::Ucsc::Hg19::Reference.offsets["chr1"].should == 0x0687
45
+ end
46
+ end
47
+ end
48
+
49
+ describe ".records" do
50
+ context 'given "chr1"' do
51
+ it 'returns (TwoBitRecord.reserved == 0)' do
52
+ Bio::Ucsc::Hg19::Reference.load("samples/hg19.2bit")
53
+ Bio::Ucsc::Hg19::Reference.records("chr1").reserved == 0
54
+ end
55
+ end
56
+ end
57
+
58
+ describe ".records" do
59
+ context 'given "chr1"' do
60
+ it 'returns (TwoBitRecord.dna_size == 249_250_621)' do
61
+ Bio::Ucsc::Hg19::Reference.load("samples/hg19.2bit")
62
+ Bio::Ucsc::Hg19::Reference.records("chr1").dna_size.should == 249_250_621
63
+ end
64
+ end
65
+ end
66
+
67
+ describe ".byte_to_nucleotides" do
68
+ context 'given 0b00011011' do
69
+ it 'returns "TCAG"' do
70
+ r = Bio::Ucsc::Hg19::Reference.byte_to_nucleotides(0b00011011)
71
+ r.should == "TCAG"
72
+ end
73
+ end
74
+ end
75
+
76
+ describe ".bytes_to_nucleotides" do
77
+ context 'given [0b00011011, 0b11100100]' do
78
+ it 'returns "TCAGGACT"' do
79
+ ary = [0b00011011, 0b11100100]
80
+ r = Bio::Ucsc::Hg19::Reference.bytes_to_nucleotides(ary)
81
+ r.should == "TCAGGACT"
82
+ end
83
+ end
84
+ end
85
+
86
+ describe ".find_by_interval_raw" do
87
+ context "given range chr1:1,000,000-1,000,030" do
88
+ it 'returens "TGGGCACAGCCTCACCCAGGAAAGCAGCTGG"' do
89
+ Bio::Ucsc::Hg19::Reference.load("samples/hg19.2bit")
90
+ itv = Bio::GenomicInterval.parse("chr1:1,000,000-1,000,030")
91
+ r = Bio::Ucsc::Hg19::Reference.find_by_interval_raw(itv)
92
+ r.should == "TGGGCACAGCCTCACCCAGGAAAGCAGCTGG"
93
+ end
94
+ end
95
+
96
+ context "given range chr2:1,123,456-1,123,499" do
97
+ it 'returens "GTACTTAGAACACTATTGATTTCTGTACGTTGATTTTGTATTCT"' do
98
+ Bio::Ucsc::Hg19::Reference.load("samples/hg19.2bit")
99
+ itv = Bio::GenomicInterval.parse("chr2:1,123,456-1,123,499")
100
+ r = Bio::Ucsc::Hg19::Reference.find_by_interval_raw(itv)
101
+ r.should == "GTACTTAGAACACTATTGATTTCTGTACGTTGATTTTGTATTCT"
102
+ end
103
+ end
104
+
105
+ context "given range chr2:1,123,456-1,123,456" do
106
+ it 'returens "G"' do
107
+ Bio::Ucsc::Hg19::Reference.load("samples/hg19.2bit")
108
+ itv = Bio::GenomicInterval.parse("chr2:1,123,456-1,123,456")
109
+ r = Bio::Ucsc::Hg19::Reference.find_by_interval_raw(itv)
110
+ r.should == "G"
111
+ end
112
+ end
113
+ end
114
+
115
+ describe ".find_by_interval" do
116
+ context "given range chr1:9,980-10,020" do
117
+ it 'returns "NNNNNNNNNNNNNNNNNNNNNTAACCCTAACCCTAACCCTA"' do
118
+ Bio::Ucsc::Hg19::Reference.load("samples/hg19.2bit")
119
+ itv = Bio::GenomicInterval.parse("chr1:9,980-10,020")
120
+ r = Bio::Ucsc::Hg19::Reference.find_by_interval(itv)
121
+ r.should == "NNNNNNNNNNNNNNNNNNNNNTAACCCTAACCCTAACCCTA"
122
+ end
123
+ end
124
+
125
+ # N-block => chr1:267,720-317,719
126
+ context "given range chr1:267,690-267,735" do
127
+ it 'returns "GGGACTACAGGCGCCCGCATCCAGCTGGATNNNNNNNNNNNNNNNN' do
128
+ Bio::Ucsc::Hg19::Reference.load("samples/hg19.2bit")
129
+ itv = Bio::GenomicInterval.parse("chr1:267,690-267,735")
130
+ r = Bio::Ucsc::Hg19::Reference.find_by_interval(itv)
131
+ r.should == "GGGACTACAGGCGCCCGCATCCAGCTGGATNNNNNNNNNNNNNNNN"
132
+ end
133
+ end
134
+ end
135
+ end
136
+
137
+
data/spec/hg19/refseqsummary_spec.rb ADDED
@@ -0,0 +1,15 @@
1
+ require 'bio-ucsc'
2
+ describe "Bio::Ucsc::Hg19::RefSeqSummary" do
3
+
4
+ describe "#find_all_by_mrnaAcc" do
5
+ context 'given "NR_036941"' do
6
+ it "returens an array of results" do
7
+ Bio::Ucsc::Hg19::DBConnection.default
8
+ Bio::Ucsc::Hg19::DBConnection.connect
9
+ r = Bio::Ucsc::Hg19::RefSeqSummary.find_all_by_mrnaAcc("NR_036941")
10
+ r.should have(1).item
11
+ end
12
+ end
13
+ end
14
+
15
+ end
data/spec/hg19/trnas_spec.rb ADDED
@@ -0,0 +1,23 @@
1
+ require 'bio-ucsc'
2
+ describe "Bio::Ucsc::Hg19::TRNAs" do
3
+
4
+ describe "#find_by_interval" do
5
+ context "given range chr1:1-10,000,000" do
6
+ it "returens an array of results" do
7
+ Bio::Ucsc::Hg19::DBConnection.default
8
+ Bio::Ucsc::Hg19::DBConnection.connect
9
+ i = Bio::GenomicInterval.parse("chr1:1-10,000,000")
10
+ Bio::Ucsc::Hg19::TRNAs.find_by_interval(i).should have(1).items
11
+ end
12
+
13
+ it "returens an array of results with column accessors" do
14
+ Bio::Ucsc::Hg19::DBConnection.default
15
+ Bio::Ucsc::Hg19::DBConnection.connect
16
+ i = Bio::GenomicInterval.parse("chr1:1-10,000,000")
17
+ r = Bio::Ucsc::Hg19::TRNAs.find_by_interval(i)
18
+ r[0].chrom.should == "chr1"
19
+ end
20
+ end
21
+ end
22
+
23
+ end
metadata CHANGED
@@ -1,12 +1,8 @@
1
1
  --- !ruby/object:Gem::Specification
2
2
  name: bio-ucsc-api
3
3
  version: !ruby/object:Gem::Version
4
- prerelease: false
5
- segments:
6
- - 0
7
- - 0
8
- - 1
9
- version: 0.0.1
4
+ prerelease:
5
+ version: 0.0.3
10
6
  platform: ruby
11
7
  authors:
12
8
  - MISHIMA, Hiroyuki
@@ -16,8 +12,7 @@ autorequire:
16
12
  bindir: bin
17
13
  cert_chain: []
18
14
 
19
- date: 2011-04-22 00:00:00 +09:00
20
- default_executable:
15
+ date: 2011-04-25 00:00:00 Z
21
16
  dependencies:
22
17
  - !ruby/object:Gem::Dependency
23
18
  name: activerecord
@@ -26,10 +21,6 @@ dependencies:
26
21
  requirements:
27
22
  - - ">="
28
23
  - !ruby/object:Gem::Version
29
- segments:
30
- - 3
31
- - 0
32
- - 7
33
24
  version: 3.0.7
34
25
  type: :runtime
35
26
  prerelease: false
@@ -41,10 +32,6 @@ dependencies:
41
32
  requirements:
42
33
  - - ">="
43
34
  - !ruby/object:Gem::Version
44
- segments:
45
- - 2
46
- - 8
47
- - 1
48
35
  version: 2.8.1
49
36
  type: :runtime
50
37
  prerelease: false
@@ -56,10 +43,6 @@ dependencies:
56
43
  requirements:
57
44
  - - ">="
58
45
  - !ruby/object:Gem::Version
59
- segments:
60
- - 0
61
- - 1
62
- - 2
63
46
  version: 0.1.2
64
47
  type: :runtime
65
48
  prerelease: false
@@ -71,10 +54,6 @@ dependencies:
71
54
  requirements:
72
55
  - - ~>
73
56
  - !ruby/object:Gem::Version
74
- segments:
75
- - 2
76
- - 5
77
- - 0
78
57
  version: 2.5.0
79
58
  type: :development
80
59
  prerelease: false
@@ -86,10 +65,6 @@ dependencies:
86
65
  requirements:
87
66
  - - ~>
88
67
  - !ruby/object:Gem::Version
89
- segments:
90
- - 1
91
- - 0
92
- - 0
93
68
  version: 1.0.0
94
69
  type: :development
95
70
  prerelease: false
@@ -101,10 +76,6 @@ dependencies:
101
76
  requirements:
102
77
  - - ~>
103
78
  - !ruby/object:Gem::Version
104
- segments:
105
- - 1
106
- - 5
107
- - 2
108
79
  version: 1.5.2
109
80
  type: :development
110
81
  prerelease: false
@@ -116,8 +87,6 @@ dependencies:
116
87
  requirements:
117
88
  - - ">="
118
89
  - !ruby/object:Gem::Version
119
- segments:
120
- - 0
121
90
  version: "0"
122
91
  type: :development
123
92
  prerelease: false
@@ -129,10 +98,6 @@ dependencies:
129
98
  requirements:
130
99
  - - ">="
131
100
  - !ruby/object:Gem::Version
132
- segments:
133
- - 1
134
- - 4
135
- - 1
136
101
  version: 1.4.1
137
102
  type: :development
138
103
  prerelease: false
@@ -144,10 +109,6 @@ dependencies:
144
109
  requirements:
145
110
  - - ">="
146
111
  - !ruby/object:Gem::Version
147
- segments:
148
- - 3
149
- - 0
150
- - 0
151
112
  version: 3.0.0
152
113
  type: :runtime
153
114
  prerelease: false
@@ -159,10 +120,6 @@ dependencies:
159
120
  requirements:
160
121
  - - ">="
161
122
  - !ruby/object:Gem::Version
162
- segments:
163
- - 3
164
- - 0
165
- - 0
166
123
  version: 3.0.0
167
124
  type: :runtime
168
125
  prerelease: false
@@ -174,11 +131,7 @@ dependencies:
174
131
  requirements:
175
132
  - - ">="
176
133
  - !ruby/object:Gem::Version
177
- segments:
178
- - 0
179
- - 1
180
- - 1
181
- version: 0.1.1
134
+ version: 0.1.2
182
135
  type: :runtime
183
136
  prerelease: false
184
137
  version_requirements: *id011
@@ -211,6 +164,7 @@ files:
211
164
  - lib/bio-ucsc/hg18/cnpsharp2.rb
212
165
  - lib/bio-ucsc/hg18/db_connection.rb
213
166
  - lib/bio-ucsc/hg18/dgv.rb
167
+ - lib/bio-ucsc/hg18/reference.rb
214
168
  - lib/bio-ucsc/hg18/refgene.rb
215
169
  - lib/bio-ucsc/hg18/rmsk.rb
216
170
  - lib/bio-ucsc/hg18/tables.rb
@@ -219,8 +173,10 @@ files:
219
173
  - lib/bio-ucsc/hg19/ccdsgene.rb
220
174
  - lib/bio-ucsc/hg19/cytoband.rb
221
175
  - lib/bio-ucsc/hg19/db_connection.rb
176
+ - lib/bio-ucsc/hg19/description.rb
222
177
  - lib/bio-ucsc/hg19/dgv.rb
223
178
  - lib/bio-ucsc/hg19/ensgene.rb
179
+ - lib/bio-ucsc/hg19/gbcdnainfo.rb
224
180
  - lib/bio-ucsc/hg19/gwascatalog.rb
225
181
  - lib/bio-ucsc/hg19/hapmapalleleschimp.rb
226
182
  - lib/bio-ucsc/hg19/hapmapallelesmacaque.rb
@@ -235,11 +191,14 @@ files:
235
191
  - lib/bio-ucsc/hg19/hapmapsnpsmkk.rb
236
192
  - lib/bio-ucsc/hg19/hapmapsnpstsi.rb
237
193
  - lib/bio-ucsc/hg19/hapmapsnpsyri.rb
194
+ - lib/bio-ucsc/hg19/kgxref.rb
238
195
  - lib/bio-ucsc/hg19/knowngene.rb
239
196
  - lib/bio-ucsc/hg19/omimgene.rb
240
197
  - lib/bio-ucsc/hg19/phastconselements46wayprimates.rb
241
198
  - lib/bio-ucsc/hg19/phylop46wayprimates.rb
199
+ - lib/bio-ucsc/hg19/reference.rb
242
200
  - lib/bio-ucsc/hg19/refgene.rb
201
+ - lib/bio-ucsc/hg19/refseqsummary.rb
243
202
  - lib/bio-ucsc/hg19/rmsk.rb
244
203
  - lib/bio-ucsc/hg19/snp131.rb
245
204
  - lib/bio-ucsc/hg19/snp132.rb
@@ -247,9 +206,12 @@ files:
247
206
  - lib/bio-ucsc/hg19/snp132common.rb
248
207
  - lib/bio-ucsc/hg19/snp132flagged.rb
249
208
  - lib/bio-ucsc/hg19/snp132mult.rb
209
+ - lib/bio-ucsc/hg19/trnas.rb
250
210
  - lib/bio-ucsc/hg19/wgrna.rb
251
211
  - lib/bio-ucsc/ucsc_bin.rb
212
+ - samples/hg19-2bit-retrieve.rb
252
213
  - samples/hg19-sample.rb
214
+ - samples/symbol2summary.rb
253
215
  - spec/hg18/cnpiafrate2_spec.rb
254
216
  - spec/hg18/cnplocke_spec.rb
255
217
  - spec/hg18/cnpredon_spec.rb
@@ -257,13 +219,16 @@ files:
257
219
  - spec/hg18/cnpsharp2_spec.rb
258
220
  - spec/hg18/db_connection_spec.rb
259
221
  - spec/hg18/dgv_spec.rb
222
+ - spec/hg18/reference_spec.rb
260
223
  - spec/hg18/refgene_spec.rb
261
224
  - spec/hg18/rmsk_spec.rb
262
225
  - spec/hg19/ccdsgene_spec.rb
263
226
  - spec/hg19/cytoband_spec.rb
264
227
  - spec/hg19/db_connection_spec.rb
228
+ - spec/hg19/description_spec.rb
265
229
  - spec/hg19/dgv_spec.rb
266
230
  - spec/hg19/ensgene_spec.rb
231
+ - spec/hg19/gbcdnainfo_spec.rb
267
232
  - spec/hg19/gwascatalog_spec.rb
268
233
  - spec/hg19/hapmapalleleschimp_spec.rb
269
234
  - spec/hg19/hapmapallelesmacaque_spec.rb
@@ -278,20 +243,23 @@ files:
278
243
  - spec/hg19/hapmapsnpsmkk_spec.rb
279
244
  - spec/hg19/hapmapsnpstsi_spec.rb
280
245
  - spec/hg19/hapmapsnpsyri_spec.rb
246
+ - spec/hg19/kgxref_spec.rb
281
247
  - spec/hg19/knowngene_spec.rb
282
248
  - spec/hg19/omimGene_spec.rb
283
249
  - spec/hg19/phastconselements46wayprimates_spec.rb
284
250
  - spec/hg19/phyloP46wayPrimates_spec.rb
251
+ - spec/hg19/reference_spec.rb
285
252
  - spec/hg19/refgene_spec.rb
253
+ - spec/hg19/refseqsummary_spec.rb
286
254
  - spec/hg19/rmsk_spec.rb
287
255
  - spec/hg19/snp132Flagged_spec.rb
288
256
  - spec/hg19/snp132_spec.rb
289
257
  - spec/hg19/snp132codingdbsnp_spec.rb
290
258
  - spec/hg19/snp132common_spec.rb
291
259
  - spec/hg19/snp132mult_spec.rb
260
+ - spec/hg19/trnas_spec.rb
292
261
  - spec/hg19/wgrna_spec.rb
293
262
  - spec/spec_helper.rb
294
- has_rdoc: true
295
263
  homepage: http://github.com/misshie/bioruby-ucsc-api
296
264
  licenses:
297
265
  - Ruby (Ruby's/GPLv2 dual)
@@ -305,7 +273,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
305
273
  requirements:
306
274
  - - ">="
307
275
  - !ruby/object:Gem::Version
308
- hash: -300095872068821190
276
+ hash: 2324911911426027047
309
277
  segments:
310
278
  - 0
311
279
  version: "0"
@@ -314,13 +282,11 @@ required_rubygems_version: !ruby/object:Gem::Requirement
314
282
  requirements:
315
283
  - - ">="
316
284
  - !ruby/object:Gem::Version
317
- segments:
318
- - 0
319
285
  version: "0"
320
286
  requirements: []
321
287
 
322
288
  rubyforge_project:
323
- rubygems_version: 1.3.7
289
+ rubygems_version: 1.7.2
324
290
  signing_key:
325
291
  specification_version: 3
326
292
  summary: "A Bioruby plugin: an API for UCSC Genome Browser (experimental)"
@@ -332,13 +298,16 @@ test_files:
332
298
  - spec/hg18/cnpsharp2_spec.rb
333
299
  - spec/hg18/db_connection_spec.rb
334
300
  - spec/hg18/dgv_spec.rb
301
+ - spec/hg18/reference_spec.rb
335
302
  - spec/hg18/refgene_spec.rb
336
303
  - spec/hg18/rmsk_spec.rb
337
304
  - spec/hg19/ccdsgene_spec.rb
338
305
  - spec/hg19/cytoband_spec.rb
339
306
  - spec/hg19/db_connection_spec.rb
307
+ - spec/hg19/description_spec.rb
340
308
  - spec/hg19/dgv_spec.rb
341
309
  - spec/hg19/ensgene_spec.rb
310
+ - spec/hg19/gbcdnainfo_spec.rb
342
311
  - spec/hg19/gwascatalog_spec.rb
343
312
  - spec/hg19/hapmapalleleschimp_spec.rb
344
313
  - spec/hg19/hapmapallelesmacaque_spec.rb
@@ -353,16 +322,20 @@ test_files:
353
322
  - spec/hg19/hapmapsnpsmkk_spec.rb
354
323
  - spec/hg19/hapmapsnpstsi_spec.rb
355
324
  - spec/hg19/hapmapsnpsyri_spec.rb
325
+ - spec/hg19/kgxref_spec.rb
356
326
  - spec/hg19/knowngene_spec.rb
357
327
  - spec/hg19/omimGene_spec.rb
358
328
  - spec/hg19/phastconselements46wayprimates_spec.rb
359
329
  - spec/hg19/phyloP46wayPrimates_spec.rb
330
+ - spec/hg19/reference_spec.rb
360
331
  - spec/hg19/refgene_spec.rb
332
+ - spec/hg19/refseqsummary_spec.rb
361
333
  - spec/hg19/rmsk_spec.rb
362
334
  - spec/hg19/snp132Flagged_spec.rb
363
335
  - spec/hg19/snp132_spec.rb
364
336
  - spec/hg19/snp132codingdbsnp_spec.rb
365
337
  - spec/hg19/snp132common_spec.rb
366
338
  - spec/hg19/snp132mult_spec.rb
339
+ - spec/hg19/trnas_spec.rb
367
340
  - spec/hg19/wgrna_spec.rb
368
341
  - spec/spec_helper.rb