bio-ensembl 1.1.0

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  1. data/.document +5 -0
  2. data/Gemfile +20 -0
  3. data/Gemfile.lock +40 -0
  4. data/LICENSE.txt +20 -0
  5. data/README.rdoc +19 -0
  6. data/Rakefile +71 -0
  7. data/VERSION +1 -0
  8. data/bin/ensembl +40 -0
  9. data/bin/variation_effect_predictor +106 -0
  10. data/bio-ensembl.gemspec +190 -0
  11. data/lib/bio-ensembl.rb +65 -0
  12. data/lib/bio-ensembl/core/activerecord.rb +1812 -0
  13. data/lib/bio-ensembl/core/collection.rb +64 -0
  14. data/lib/bio-ensembl/core/project.rb +262 -0
  15. data/lib/bio-ensembl/core/slice.rb +657 -0
  16. data/lib/bio-ensembl/core/transcript.rb +409 -0
  17. data/lib/bio-ensembl/core/transform.rb +95 -0
  18. data/lib/bio-ensembl/db_connection.rb +205 -0
  19. data/lib/bio-ensembl/variation/activerecord.rb +536 -0
  20. data/lib/bio-ensembl/variation/variation_feature.rb +376 -0
  21. data/lib/bio-ensembl/variation/variation_feature62.rb +444 -0
  22. data/samples/ensembl_genomes_example.rb +60 -0
  23. data/samples/examples_perl_tutorial.rb +125 -0
  24. data/samples/small_example_ruby_api.rb +34 -0
  25. data/samples/variation_effect_predictor_data.txt +4 -0
  26. data/samples/variation_example.rb +67 -0
  27. data/test/data/seq_c6qbl.fa +10 -0
  28. data/test/data/seq_cso19_coding.fa +16 -0
  29. data/test/data/seq_cso19_transcript.fa +28 -0
  30. data/test/data/seq_drd3_gene.fa +838 -0
  31. data/test/data/seq_drd3_transcript.fa +22 -0
  32. data/test/data/seq_drd4_transcript.fa +24 -0
  33. data/test/data/seq_forward_composite.fa +1669 -0
  34. data/test/data/seq_par_boundary.fa +169 -0
  35. data/test/data/seq_rnd3_transcript.fa +47 -0
  36. data/test/data/seq_ub2r1_coding.fa +13 -0
  37. data/test/data/seq_ub2r1_gene.fa +174 -0
  38. data/test/data/seq_ub2r1_transcript.fa +26 -0
  39. data/test/data/seq_y.fa +2 -0
  40. data/test/default/test_connection.rb +60 -0
  41. data/test/default/test_releases.rb +130 -0
  42. data/test/ensembl_genomes/test_collection.rb +122 -0
  43. data/test/ensembl_genomes/test_gene.rb +46 -0
  44. data/test/ensembl_genomes/test_slice.rb +65 -0
  45. data/test/ensembl_genomes/test_variation.rb +38 -0
  46. data/test/helper.rb +18 -0
  47. data/test/release_50/core/test_project.rb +210 -0
  48. data/test/release_50/core/test_project_human.rb +52 -0
  49. data/test/release_50/core/test_relationships.rb +72 -0
  50. data/test/release_50/core/test_sequence.rb +170 -0
  51. data/test/release_50/core/test_slice.rb +116 -0
  52. data/test/release_50/core/test_transcript.rb +125 -0
  53. data/test/release_50/core/test_transform.rb +217 -0
  54. data/test/release_50/variation/test_activerecord.rb +138 -0
  55. data/test/release_50/variation/test_variation.rb +79 -0
  56. data/test/release_53/core/test_gene.rb +61 -0
  57. data/test/release_53/core/test_project.rb +91 -0
  58. data/test/release_53/core/test_project_human.rb +61 -0
  59. data/test/release_53/core/test_slice.rb +42 -0
  60. data/test/release_53/core/test_transform.rb +57 -0
  61. data/test/release_53/variation/test_activerecord.rb +137 -0
  62. data/test/release_53/variation/test_variation.rb +66 -0
  63. data/test/release_56/core/test_gene.rb +61 -0
  64. data/test/release_56/core/test_project.rb +91 -0
  65. data/test/release_56/core/test_slice.rb +49 -0
  66. data/test/release_56/core/test_transform.rb +57 -0
  67. data/test/release_56/variation/test_activerecord.rb +141 -0
  68. data/test/release_56/variation/test_consequence.rb +131 -0
  69. data/test/release_56/variation/test_variation.rb +63 -0
  70. data/test/release_60/core/test_gene.rb +61 -0
  71. data/test/release_60/core/test_project_human.rb +34 -0
  72. data/test/release_60/core/test_slice.rb +42 -0
  73. data/test/release_60/core/test_transcript.rb +120 -0
  74. data/test/release_60/core/test_transform.rb +57 -0
  75. data/test/release_60/variation/test_activerecord.rb +216 -0
  76. data/test/release_60/variation/test_consequence.rb +153 -0
  77. data/test/release_60/variation/test_variation.rb +64 -0
  78. data/test/release_62/core/test_gene.rb +42 -0
  79. data/test/release_62/variation/test_activerecord.rb +86 -0
  80. data/test/release_62/variation/test_consequence.rb +191 -0
  81. metadata +287 -0
data/test/data/seq_par_boundary.fa ADDED
@@ -0,0 +1,169 @@
1
+ >Y dna:chromosome chromosome:NCBI36:Y:2705106:2715105:1
2
+ TCCAAATGATGCTCTGCCATAAGAAGAAATTCACACCCTGAATAGCACAGCAGGATGCGA
3
+ ATAGCAATGCCAGCCAAAGACATTGCAAACAAGCCGGTAAAACTAAGTGATTGTTAGCTG
4
+ TTTAAAAAAATAATAATAACTGGTGTTAACAACAAAGTGAAACTTAACTTCTGAAGATGA
5
+ GGCTACCTTCACAGAGAGGATAAGAAAGGAAGAACTGAGTAAAAGTAGTTAGATATTGCT
6
+ GGATTTTGACATTTTAAGGTTAAGTGTTCCTGCTAAAAATAAAAATTGAACATATAACTC
7
+ CTGAACTAGTGGATGAAAATGAAGAATGAAGAATAAAATTAAATACAAAAAAAATGAAGA
8
+ GTAAAATTAAATACCAAAATTAGCCAAGTGTTGTGGTGAATGCCTGTAGTCCCAGCTACT
9
+ CAGGAGGCTGAGGTGGGAGGATCACTTGAGCCCCAGAGGTGGAGGTTGCAGTGAGCTGAG
10
+ ATTGCGCCACTGCACTTCCGCCTGGGTGGCAGAGCCAGGCTTTGTCTCAAAAATAAAAAA
11
+ AAATAATAAATTAAAAACCTGAATACTAAATGGAAGTTAAGAAGGAAGGAATTAAAAAAG
12
+ AAGAAAAGTAAAATAAAATAGTAGGAATAGTGAATCCTTAGTTATGTTAGATGTTCAGTG
13
+ ATTTAATAAATCTGTAAAAAGACGGAGATGAGATGATGCAATTTAAAATGTTTCGGCTGG
14
+ GCGCAGTGGCTCACGCCTGTAATCCCAGCACTGTAGGAAGCCGAGGCGGGTGGATCACGA
15
+ GGTCAGGAGATCGAGACCATCCTGGCTAACACGGTGAAACCCCATCTCTACTAAAAATAC
16
+ AAATAAAATGTTTCATGCTATTTACGAGAGAAGCATTTGCAACAAAATGCCAAAGAGAAG
17
+ GTGAAAATAGCTGGAAAAAAAATGCGCAAAGCAAATAACCAATAGAAAGAAAGCCAAGTT
18
+ GGGCTAGCAAAATCAGACAAAATAACCTTCGAGGTGCAAACAACTTTGAGGCCCAAATAG
19
+ AGGTTCTTCCCACTAAAAGAATGATTCCCTGAATGATAATGGAATCTTGACCCAGCCTGC
20
+ ACCTCAGGTTAAGTTAAAAGTGGAAATTTAAAGATCTAAGTGTGAGATTTTAAAAAGCAT
21
+ TTCCCCAGAAATACCAGGATCTGTAGATGGAAATGTTATTAAGAATAAAGATGTGGAGCT
22
+ GGGCGTGGTGGCTCACGCCTGTAATCCCAGAACTTTGGGAGGCTGAGACTGGCTGATTTC
23
+ TTGAGCCCAGGAGTTTGAGACTAGCCTGGACAACATAGTGAGACCCCATCTTTACAAAAA
24
+ AATTAAAAAAAATTAGTGGACATGGTGGCATGCACCTCTAGTCCCAGTTACTCAGGAGGC
25
+ TGAGGTGGGAGGATCACCTGTGCCCAGGCTGAGGCTGCAGTGAGCCATGATCACGCCACT
26
+ GCACTCCAGCCTGCGTGACAGAGCAAGACCCTGTCTCAAAAGAAAAGAAAAAAAAAGAAG
27
+ AAAGAAATGAAAACCGTAGCTCAGAGACAGAGAAACTGAGCAATGCATAGGTTCAGAAGG
28
+ GTTTGAAACAGACTGAATTGTGTCTTGGCATATGAGAGAGGTCGCAGCTATAAAACAATG
29
+ AGAGAAGAAACCAAATTCCACATAGGCAGGACTGAGACAATTGGCTGTTCTTGTGGATGA
30
+ TACGTGATCAAATCTCAACCTCATGCGATACTTTTTTTTTTTTTTTTGAGATGGAGTCTC
31
+ GCTCTGTCACCCAGGCTGCAGTGCAGTGGTGTGATCTCACCTCCCCGCAAACTTCTCCTC
32
+ CCGGGTTCAAGTAATTCTCGTGCCTCAGCTGGGACTACAGGCATGTGCCACCACGCCTGG
33
+ CTAATTTTTGCATTTTTTTAGTAGAGACGGGGTTTCACCAAGTTGGCCAGGCTGGTCTCG
34
+ AACTCCTGACCTCAGGTGATCTGTCCACCTCGGTGTCCCAAAGTGCTGGGATTACAGGTG
35
+ TGAACCACCACACCCAGCCTCATGTAATACTTAAAAATGAACTACAGGTGGATTACAAAC
36
+ CTGAATATAAAAGAAAACTTTTTTTTTTGAAAAATAGAGGGAAATGTCTTATAACCTCAG
37
+ AGTTAGGAGGTTTTTCTTAGATACAATACAAAAAGCATAACCACGCCCATAGTCCCAGCT
38
+ ACTCAGGAGGCTGAGGCATAAGAATCACTTGAGCTCGAGAGGTGGAGGTTGCAGTGAGCC
39
+ GAGATCCTGCCATTGCACTCCAGCTGAGGCTACAGAGTGAGAGTATAAAAAAAAAAAAAA
40
+ AAAAGCATAACCTTTAAAAATGGGTTAGCCTATGTCTACATTTAAATAATAATAATAATA
41
+ ATAATGTTCCAACTTCAGGCTCTGAAAAAAGTCAAAAGATGAGCTGTCAACTAGAAGAGG
42
+ CTCCTTACTGCTCATACCACCAGGGAAAGTTTAATATGCAAAATGCAGTCATCCTTCAGA
43
+ ATTCATGGGGGATTAGTTTTAAGACGCCTTCTTCCCCGCAGACACCAAAATCCACAGCTG
44
+ CTGAAGTCTCTGATATAAAACGTGCAGTACTTGCATATAATGCAAGTATATGTTCCTGTA
45
+ TATTTTTATTTATTTATTTGGAGACAGAATCTCACTCTGTTGCCCAGGCTGGAGTGCAGT
46
+ GGCGTGATCTTGGCTCACTGTAACCTCCACCTCCCGGGTTCAAGAGATTCTCCTGACTCA
47
+ ACCTCCCAAGTAGCTGGGATTACAGGTATGCGCCACCACCCCCAGCTAATTTTTGTATTT
48
+ TTGGTAGAGACGGGTTTTAACCATGTTGTCCAGGCTGGTTTCGAACTCCTGACCTCACAT
49
+ AATCTGCCCACCTTGGCCTCCCAAAGTGCTGGGATTACAGGGATGAGCCACCGTGTCCAG
50
+ CCTCTGGTATACTTTAAATTATCTCTAGGTTACTCATAACTCCTGATACGCTGTAAATGC
51
+ TATGCAAATAGTTGTTATACTATATTATTTTTTATTTGTATTACTTTTTATTGGATTGCT
52
+ ATATTTTATTTTTTGAAATATTTTCAATACAAGACTGGTTGGATCTATAGATGCAGAAAT
53
+ TCTGGTTATAGAGCACAAACTGTGTATAGATAGCTCCTACCAAAACAGACGGATGGTGAA
54
+ AAAAAGAAAAGAAAAGAAAAGAAAAAGAAAATGGAGGAGAGAGACTATGAGGCGACTAAA
55
+ AGAAGAGGGATATGATCATTCCATTCGCTGACAAGAAAAATTCAAAGAAGAGGGAATTAT
56
+ GCAATTGACCAGCTGATGTGTGTTAGAAATGCTCAGGGTCACACATATTCATTGAAAGCC
57
+ AATTTAAGCCACTATTTAAATTTAAACCGATTTAAACAATTGGGCTTTTTTTTTTTTTTC
58
+ TAAAAAAAAAAAAAAGTCAATTAGGCCAGGCGAGGTGGCTCACACCTGTCATCCCGGCAC
59
+ TTTGGGAGGCCGAGGTGGGTGGATCACAAGGTCAGGAGTTTGAGACCAGCCTGGCCAACA
60
+ TGGTGAAACCCTGTTTCTACTAAAAATACAAAAGTTAGCTGGGCATGGTGGTGTGTGCCT
61
+ GAGGCTGTGAGACTGAGGCAGGAGAATCACTTGAACCCAGGAGGCGGAGGTTGCAGGGAG
62
+ CGGAGATCATGCCACTGCACTCCAGCTTGGGCGACAGACCAAGACTCTGTCTCAAAAAAA
63
+ AAAAAGAAGAAGTATATTGGTTCCGTCTGGAAAGGTGGAGCACTTGAAGCAAAGGCAGGA
64
+ AGACTGGAAGCAGGGAGAGGGTTTTCAGGTCACAAACAGGTGAGAGACAAAACAGTTGCC
65
+ TTCTTTTGAGTTTCTGATTAGCCTTTCCAAAGGAGGCGATCAGATACGAATCTGCCTCAG
66
+ GGAGCAGAGGGGGGACTTTGAATAGAATGGGAGGCAGGTTGGCCCTAAGCAGTTCCCAGC
67
+ TGGACTTTTCCCTTTAGCTTAGTGACTTGGGGGTCCCGAGATTTATGTTCCCTTCACAGT
68
+ GTATGAGTGAGAGCACTTGGAAACTGAGAGTGGAAGTGTCGCAGGCCAGGTCTCACTAAC
69
+ ACAGGCCCCCACAACACCTGTTTCAGTATTGACTGAGTGGTTAAATATTAAAAGCCAGTG
70
+ CTGTTATACAAAGGCTGGAATGTAACAAAAGCCCACCGAGAGTTTTTCCCAGGACTTTCC
71
+ CGGGCCTTAAAGCATGACAAAATAATGAATGAATTCTTAACAGGACCCATTTAGGATTAA
72
+ ACAAGTTTTACTGGGGGTCTGCAGAAACTCCCCAGGCCTCCACAAACAAGTTTATTGGGG
73
+ CTTTGAAGGAACTCTGCAAACCTCCTGGATTTAGCAGGAGACAACATGAGGGTAATCACC
74
+ CCGGCACCTGGACCCATTAGATTAAGTCAATTTACTGAGGCTCCTGAGGAAGATCCTCAG
75
+ GACTCAGACCTTAGTTATAGATTAAAAGAAGTTAAGGCCGGGCGCGGTGGCTCACGCCTG
76
+ TAATCCCAGCACTTTGGGAGGCCAAGATGGGCGGATCACGAGGTCAGGAGATCGAGACCA
77
+ TCTTGGCTAACACCGCGAAACCCCGTCTCTACTAAAAATACAAAAAAATCAGCCGGGCGT
78
+ AGTGGCGGGCGCCTATAGTGCCAGCTACGCCGGAGGCTGAGGCAGGAGAGTGGCGTGAAC
79
+ CCGGGAGGCGGCGCTTGCAGTGAGCTGAGATTGCGCCACTGCACTCCAGCCTGGGCGACA
80
+ GAGCGAGACTCCGCCTCAAAAAAAAAAAAAAAAAAAAAAAAGTTAATCATTTATGTCGTT
81
+ ACATAAATGGGCACTTACACATAGACGTATAGCTCAGAAGGTATATAAGCTCTATAAAAC
82
+ TTTATCATTTTGAGTGGGTCTGGTAATATTATCTACATGCCTTCTCCCTGTAACCACTTG
83
+ TAGAAATAAAAACTCTCTTCCTTCTCAGTTCATCTGCATCTCATTATTGGGCCACAAAAA
84
+ AATAGCAGCCTGACCCTCAATTTGCTCAGGAAAGACAAGGGGACTTGGGAACACTCCTTA
85
+ CACTTCAAAGAGAAGGCTCAAGGCCATTAAGAAAGACCTGTTGGGGTGCCATCCTTCCAT
86
+ CTGGCTTAGTTAGTTCTTAAAAAGATTTACATATACCTCAAAAAACAGAGGGGAAAATAC
87
+ TAGTTTTCTAAAGGTAGTACTCTAATGAAAAGTAGGAGGAAGGATTACTTTCTTACCTGA
88
+ CAACAAGGAAAACTCAAATTACATAGATTTTAGACTTACAAAAATTTTCTGGACAGATAT
89
+ GAAGAACATTATTAAACTAACAAACAGCAATCCAGAACTTTTTTTGTTGTTGTTTTTGCT
90
+ AAACGTATTTGTAGTTCTGTTAATTTCCTTACTGTAATCTACCAACTTTATGTGATCTCT
91
+ GTCTAAAAAGCAGAACTTTCTGGTCATTTCTAAAGAGCATAGAGATTTTAAGGAACATCA
92
+ GCAATATTCAAATTTAAGAAAACTGATTATAACTTAGAAATTCTGAGGAAGAAGAGTAAT
93
+ GAGGGGTAACTTGTTCTAGCAGAAAATCAAGTATATTTTTATAACCACTTTAATTATTTT
94
+ AACTACATACCTTCATTCTGTGGTTAAAATTTAAGACACTAACAGTTCCAAATTTTGGTG
95
+ AGCATGTATAGCAACGGAAAGCTCAGACATTGCTGTGGCAGTGTGAAATAGCACAAAAAC
96
+ CCTGGAAAATTCTTGGAAAGGTACACACAAAATTAACTGAGCTGAAAATTTCACTCCTAG
97
+ ATGTTGGCCCAGGTACATTAAAAACAGATGTCCACTTAGAGACTTGAGCTCAACTGTTGA
98
+ TAGCAGCTTTATTAATAAAAGCCTCAAGCTCAAAATAGCCCAGTGTTCACCACCAACAGT
99
+ GTACATAAACTGTGGTAAATTCATGCAAATTTCAACCTGAATGAAAGAAGCCAGATGCCC
100
+ TTCAGAATACAGCTCCGTTGATATAAAGCCTTGAACTCAGCCGGGCGTGGTGGCTCACGC
101
+ CTGTCATCCCAGCACTTTGAGAGGTCGAGGTGGGCAGATCACGAGGTCAGGAGATCGAGA
102
+ CCATCCTGGCTAACACGGTGAAACCCTGGCTGTACTAAAAATACAAAAAATTATCCAGGC
103
+ GTGGTGGCGGGCGCCTGTAGTCCCAGCTACTAGGGAGGCTGAGGCAGGAGAATGGCGTGA
104
+ ACCGGGAGGCGGAGCTTGTGGTGAGCCTAGATTGGGCCACTGTACTCCATCCTGAGTGAC
105
+ AGAGCAAGACTCTGTCTCAAAAAAAAAAAAAAAAGATCTCTCAATTGCATGATAGAAATC
106
+ ATGCAATTGACAGAGGAATTGCAAAAGGGCACAGGAAATTTTAAGGGTTGAAGGAATGAT
107
+ GTAAATAGCTTGTAACCTAGTTGGGGTGATAGTTACTCAGGCATATGCATTTGCCAAAGT
108
+ TCATGCATCTATAAATAAAAGATCTGTGCACAATATCTCATGAAGATTTTTACTCTTGAC
109
+ ATTATTACATAGTCCAATATGAAATAAAATATTAATTAAATTTCTTGAAATACTAGAACT
110
+ CTGATAACTACCTTTTGTTTCTACACCTTGTAGAAACAAATCTTTGTGGAACAGATTTGG
111
+ AACAAATATGGAAAATTAATGTATTTCACATCAGTAAAATCGTGACATTGGGAAAAACAT
112
+ TACCCACTTCAATGCCTAATGAAATAATGTCTAATCAATCATGAATATCTACATTACTCT
113
+ TCACTAAGATATTTTTTAGATGGAGCAATTACTTTCAGGTTAATAATAGCAAATATTTAG
114
+ TTAATTCTTCACTAATGCTGATGTCTGTTCTAAGTATTTCTTTTTTTCTTTTCTTTTCTT
115
+ TTTTTTTTTTTTTTTTTGTTGAGATGGAGTCTTGCTCTGTCGCCCAGGCTGGAGTGCAGT
116
+ GGCGCCATCTTGGCTCACTGCAAGCTCCATCTACTGGATTCAAGCCCTCTCCTGCCTCAG
117
+ CCTCCCAAGTAGCTGGGACTACAGGCGCCCGCCACCAAGCCTGGCTAATTTTTTGTATTT
118
+ TTAGTAGAGACGGGGTTTCACCATGTTAGCTAGGATGATCTCAATCTCCTGACCTCGTGA
119
+ TCCACCCACCTTGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACTGCTCCCAGCC
120
+ TGTTCTAAGTATTTCTTATATACACTCACTTATTTAATGCTTGTGTACCTTAATTCATGT
121
+ AGCCTTCACATCTCTTCATGGGTTGGTTTTATTAGTAAATAGCATTTCAACTAACAAAAT
122
+ TATTACAGAATTGAAAAAACTGAGACTCAGACAGCGAAGTAAATTGTTCAAGCTCAAGCC
123
+ TGTAAGTGGCACTCAAGTGAGCCAAAGCTGAAGGGTTTACCTTCCAGAGCCTGTGTTCTT
124
+ TATTCAGTACCAAGCTCCCTCTTAATGTATTTTAAGTGTTGGCATTTTAAAATATAGCAA
125
+ ACATCCATTGGCAGCCAAAGCACACTTGATACTTATAGTTAGAATTTGTTTGTTTATTGA
126
+ TGTTTGTTTAAACATCACAAAAATACAAAAATGCTTCATTTCAGTAATTCCTAAGTAAAC
127
+ CATACATAAAGTATCAATTCCTCTCCTGGGAGTGTGCTTCACAGAAATTCTTATAAATGT
128
+ TCTCCATTGTACATGTATAAGAATGTATAAAAAAGCACTGTTTGTAATAATTGAAACCAG
129
+ TAAGTGTCCATTCATTTGTCCAACAAAAATAGAATGAAATACGCACAACAATTTTTTCTT
130
+ AAAAATTCTAGTTTGGGCAGCATATACACTAAAATTAGAATGGTATGGAGAAGAATAACA
131
+ CTGTCCCTGGGCCAGGAGGGTATTCAAATGTGAAGTCTTTCATATTTTTGGGAGTAGAAT
132
+ TGTGGCTACCCTCTAGTAGGGTCAGGTGAAGAGATGAGTATTGTTATTCAAAAATTATAA
133
+ TATTTCATCTAGATAGAAGCAATTAGTTCAGATCTATTGTAAAGCATGTTGAATATAGGT
134
+ AATAAGAATGTATTGTATGCTTGAAAATTGCTAAGAGAATACAATTTAAATGTTCCCAGT
135
+ GCAAAAGGAAAGGGAAGTATATGAGGTAGTAGATACATTAGCTTGATTTAGTCTTTCCAA
136
+ AATGTATACATGCATGATGTCATAATTTTTAATAATCTGAAAACCACCAAAATGTATTAA
137
+ GCAAAAGAAGCTCCACATAATATTTTGTATTTATATTTATTCACATTGTTAAGGAAAAAT
138
+ GGTATTCAGTGATACTTGTTCAAACTTGATAAGGAAGACTATTCACGACCAACAGCACAG
139
+ CAATGAGGTCTTGCACTGGGGGAGAGATTGGCCTTAGCTCCACATACACAGCTGGGTAGG
140
+ TGGGGATTTATAGCCAAGGAGCAGGGAGTAGGGTCAATGGATGGACAATCACTAAGAGAA
141
+ GACATCATAGATAAGGAGGATTCTTGCTGAAGACAGGCTAGGCTGATCAGACATCACCTA
142
+ GAGGGTGGTGGAGGATGAGAAACCTGATCAGATATTGAGGGTGATCGATCAAGTGTTGAG
143
+ TGTGATCAGATATGCGGTGGGGGTACAGTCTGGCTAACCTGGCTTAGGAGAGTTCTTTGC
144
+ CAAAACTGAGTTTGGCAAGGAAGTGCACAGGCGAGTCTAGGAGAAGGTTCAGAAACCTGA
145
+ CTAAAGTTTGGTCAAACAGAGAATCTGTGTCAGAGGTTCAAGAAAAGGAAAATTAATGTA
146
+ TGGTAATGAAGGTCAGAATGGGTGTTATTTTTGGGAGAGTGAAAAGAGTGGTTTTAAATA
147
+ TTACAAAGTAGTTTTGAGTCAGTGTTTAAAAGGTAATGGGCAATATACAGTTCTCATTTG
148
+ GCATAAAGCTCAGATTAAGTAATATTGTCTCTGGAATAAAGCTTTTTTTAAACCCTGAAC
149
+ TTTGAGAAACATGACATCCATCTCTAATATACACTCTTTTAGTGTTTGAGTTTTATTATT
150
+ TAAGGTAATGTCTCTGAAAAGTTTTGAAATATTGGAAAGCTGACTTTGATACATACCATT
151
+ AATTTTGACTTTTGATTTATTTTTATTGTAGAAAAATTTATTTGTAATTTATACTTTAAA
152
+ CTGTGGTTTACAGTTATTTGTAAACTTCTAGTTTCCTGCTTTAGCTTATGTGCAAATTTT
153
+ ATGAAGTCTTGGCATTACATTTTTATTTAAATCCCATCAAATTAAACCAGTTGGGTCACC
154
+ AGCCCCCGCCCTTCCATCTCCATAATCTGGGTAGTCGGCGTTCTCAACATTCCTGTTGAG
155
+ AATGAAAATTCTGTATTTTTCATTCCACAGGCTTAAAAGTTAATAGGCCATGGAAACAAG
156
+ TAGATTGCCATTTTAAAAGATAGTTTTCAGAAGAAAGGCAAAATGATAAGTTTCATAGAG
157
+ ATACAAAAATGACAAGGAATTAAATATTTTGTTTTACCAGAGGCATTTTATAACTAGTTG
158
+ AAAGGAAATGTCAACCGTTTGGATTTATATGGAGTAAAGGAACTGAATTGCAAGTGGAGG
159
+ TAAAACTGGTTTTTTCCACAGCGTGAAGGGGAGAGAAAGAAACAAGTTTGATCCTGCTTA
160
+ CATATCCATTCCTTAGTTACCTGCAATTTATAGACACGTACAAAGTAGCTGAAAGACCAA
161
+ TGAATACACGGTCTAGAGAGGACTGCTTAACACGCTGCATATAGAAGTGTGATTTTTTTT
162
+ GGTACAATTTTCAAGTGTGTTTCTCATTAGAGCATTTAAAGTAAGCCACAGTGTCCGTTT
163
+ GTATCAAGTTAGTACTCTGACGGCCACAAACATAGGCAGGCTCACTTCTGGATGTCTTAT
164
+ TTCTTTGCATGTTAATCGTGTTGACACAACTTGTCTTGAAATTAAGTTTAAAATGAAATA
165
+ CCAGTAAAACTGAAATGAATAAGGCCTTTATTAGCCAGAGAAAAGAAAACAATATTGAAA
166
+ CTAAACATAAGAAAGTGAGGGCTGTAAGTTATCGTAAAAAGGAGCATCTAGGTAGGTCTT
167
+ TGTAGCCAATGTTACCCGATTGTCCTACAGCTTTGTCCAGTGGCTGTAGCGGTCCCGTTG
168
+ CTGCGGTGAGCTGGCTGCGTTGATGGGCGGTAAGTGGCCT
169
+
data/test/data/seq_rnd3_transcript.fa ADDED
@@ -0,0 +1,47 @@
1
+ >ENSG00000115963|ENST00000263895
2
+ CAGTCGGCTCGGAATTGGACTTGGGAGGCGCGGTGAGGAGTCAGGCTTAAAACTTGTTGG
3
+ AGGGGAGTAACCAGCCTGCTCCTCTCGCTCTCCTCCTCGTCTGCGCCGCGTTTCAGAGAG
4
+ AAAATTCCTGTTCCAAGAGAAAATAAGGCAACATCAATGAAGGAGAGAAGAGCCAGCCAG
5
+ AAATTATCCAGCAAATCTATCATGGATCCTAATCAGAACGTGAAATGCAAGATAGTTGTG
6
+ GTGGGAGACAGTCAGTGTGGAAAAACTGCGCTGCTCCATGTCTTCGCCAAGGACTGCTTC
7
+ CCCGAGAATTACGTTCCTACAGTGTTTGAGAATTACACGGCCAGTTTTGAAATCGACACA
8
+ CAAAGAATAGAGTTGAGCCTGTGGGACACTTCGGGTTCTCCTTACTATGACAATGTCCGC
9
+ CCCCTCTCTTACCCTGATTCGGATGCTGTGCTGATTTGCTTTGACATCAGTAGACCAGAG
10
+ ACCCTGGACAGTGTCCTCAAAAAGTGGAAAGGTGAAATCCAGGAATTTTGTCCAAATACC
11
+ AAAATGCTCTTGGTCGGCTGCAAGTCTGATCTGCGGACAGATGTTAGTACATTAGTAGAG
12
+ CTCTCCAATCACAGGCAGACGCCAGTGTCCTATGACCAGGGGGCAAATATGGCCAAACAG
13
+ ATTGGAGCAGCTACTTATATCGAATGCTCAGCTTTACAGTCGGAAAATAGCGTCAGAGAC
14
+ ATTTTTCACGTTGCCACCTTGGCATGTGTAAATAAGACAAATAAAAACGTTAAGCGGAAC
15
+ AAATCACAGAGAGCCACAAAGCGGATTTCACACATGCCTAGCAGACCAGAACTCTCGGCA
16
+ GTTGCTACGGACTTACGAAAGGACAAAGCGAAGAGCTGCACTGTGATGTGAATCTTTCAT
17
+ TATCTTTAATGAAGACAAAGGAATCTAGTGTAAAAAACAACAGCAAACAAAAAGGTGAAG
18
+ TCTAAATGAAGTGCACAGCCAAAGTCATGTATACCAGAGGCTTAGGAGGCGTTTGAGAGG
19
+ ATACTCATCTTTTTGGAATCCTGACCTTAGGTTCGGCATGTAGACCAAGTGATGAGAAGT
20
+ GAATACATGGAAGAGTTTTTAAGTGTGACTTGAAAAATATGCCAAAAAATGAGAGATACA
21
+ AATGAGCTAGAGGAAGATGAGGGGGGATGCGAGTACCTCCAAGAAGAAAAATCACACTCT
22
+ GAATGGTGCTTGCATTTTTGGGTTTTTTTTTTTTGTTATAATCTATTCATGGATCTCCAC
23
+ TTTGATTTAATTTTTAAATGTTTTAATCTCCTTTACAAAAAGTATACGTTAATATACCGT
24
+ CCTCAAGGGGGAACTGGCACTGTGACCTTAGCATTTAGTTTTCTAGAGGATGTGATCTAA
25
+ TTTCTTTCTAGCTCATCATTAAAAAGGAAATTGTATCAGGACCCATGGGATATATCCAGA
26
+ GGCAAACTTTATGAGGCTTTGAAATCTTGCCTTCCTGAAGATAGCTGAGTAGGATGGTTC
27
+ TAAGGAAAGCCTTTGCAATCTTGCAAGATTTGTAGACCAGCACTACAAAGATCGCATAGA
28
+ TCAAATAGGAAAAAAAATGTCGATTTTTATTCAGTCTGATGGTTCTGTTCTTCATTGTGA
29
+ TTGTCATTAAAAAGTGGTAAATTGCTCAATGTAATATTTTTGTGCGCTGTTTAGAAGTTG
30
+ TGTGATTTTTTGCCATCGTTGATAAAAATGCAAAGTCAAATAAAAGGTGTCTTGGTTTGA
31
+ TGTCATAGAATGATCCAAGGAGAGAAAAAAGGTAGTTACTGTTTTCACCAGAAAAGGTAA
32
+ TGAGTGAAGGAAAGAATAGTAGCAGAAAGCACAGTTTGTGAGTAAAGCTGTCTGGAATTA
33
+ AGTTACCAAAAATACAAAGCAAAAGGACTATTATTTTGGGTTGAAGCTCCAAAACTGACA
34
+ GCATCTGATAATCTGTTGGTTTATTTCACTTTTCATTAAATGAACATTGATGAGAGAAGA
35
+ TGCCACTTACCCAAGCTTTAGAGAATCCCTAGTGGAAGATTATATGATAAACTTTCAGTC
36
+ CTGACATAACACTAGGGCATTTCTAGAGTGTCATTGCTAAAACCTCACTGAACAGATGCA
37
+ GCCAAGGTCTGTGTTCAGCACTTGGTCTCTGTTGTTACGTAAAATAATAAGCATTTAAAA
38
+ TAGTTTACAGATATTTTTGACCAGTTCCTTTTAGAGATTCTTTCAGAGAAGAAACCAGAT
39
+ CTGACCTGTTTATTGTTGGCGCTTGTTGAAAACGAGCTTTCTTTCCCATGATAGTGCTTC
40
+ GTTTTTGAAGTGTTGAAGCTGTGCTCCCCTTAAATCGTGGCAGGAGAGATTAAGGTAATT
41
+ ACAACACTCAGTTCTATGTCTTACAAGCACTTTGTCTTGTCTCTGCAAGAAAATTCGATT
42
+ CCAGTCATTTCCCATAAAATACAGACATTTTACCAACATAATATGCTTTGATTGATGCAG
43
+ CATTATGCTTTGGGCAGTATTACAAAATAGCTGGCGAGTGCTTTCTGTATTTAAATATTG
44
+ TAAAAAGAAAATAAGTTATAACTGTTATAAAGCAGAACTTTTGTTGCATTTTTTAAACTG
45
+ TTGAAGTCACTGTGTATGTTTGTTTGGTCAATGTTTCCGCAGTATTTATTAAAACATACT
46
+ TTTTTTTTCTTCAAATAAAAAAGTAACCATGTCTTTGTCTAAA
47
+
data/test/data/seq_ub2r1_coding.fa ADDED
@@ -0,0 +1,13 @@
1
+ >UB2R1_coding
2
+ ATGGCTCGGCCGCTAGTGCCCAGCTCGCAGAAGGCGCTGCTGCTGGAGCTCAAGGGGCTG
3
+ CAGGAAGAGCCGGTCGAGGGATTCCGCGTGACACTGGTGGACGAGGGCGATCTATACAAC
4
+ TGGGAGGTGGCCATCTTCGGGCCCCCCAACACCTACTACGAGGGCGGCTACTTCAAGGCG
5
+ CGCCTCAAGTTCCCCATCGACTACCCATACTCTCCACCAGCCTTTCGGTTCCTGACCAAG
6
+ ATGTGGCACCCTAACATCTACGAGACGGGGGACGTGTGTATCTCCATCCTCCACCCGCCG
7
+ GTGGACGACCCCCAGAGCGGGGAGCTGCCCTCAGAGAGGTGGAACCCCACGCAGAACGTC
8
+ AGGACCATTCTCCTGAGTGTGATCTCCCTCCTGAACGAGCCCAACACCTTCTCGCCCGCA
9
+ AACGTGGACGCCTCCGTGATGTACAGGAAGTGGAAAGAGAGCAAGGGGAAGGATCGGGAG
10
+ TACACAGACATCATCCGGAAGCAGGTCCTGGGGACCAAGGTGGACGCGGAGCGTGACGGC
11
+ GTGAAGGTGCCCACCACGCTGGCCGAGTACTGCGTGAAGACCAAGGCGCCGGCGCCCGAC
12
+ GAGGGCTCAGACCTCTTCTACGACGACTACTACGAGGACGGCGAGGTGGAGGAGGAGGCC
13
+ GACAGCTGCTTCGGGGACGATGAGGATGACTCTGGCACGGAGGAGTCCTGA
data/test/data/seq_ub2r1_gene.fa ADDED
@@ -0,0 +1,174 @@
1
+ >UB2R1_gene
2
+ GGCAAGCGCCGGTGGGGCGGCGGCGCCAGAGCTGCTGGAGCGCTCGGGGTCCCCGGGCGG
3
+ CGGCGGCGGCGCAGAGGAGGAGGCAGGCGGCGGCCCCGGTGGCTCCCCCCCGGACGGTGC
4
+ GCGGCCCGGCCCGTCTCGCGAACTCGCGGTGGTCGCGCGGCCCCGCGCTGCTCCGACCCC
5
+ GGGCCCCTCCGCCGCCGCCATGGCTCGGCCGCTAGTGCCCAGCTCGCAGAAGGCGCTGCT
6
+ GCTGGAGCTCAAGGGGCTGCAGGAAGAGCCGGTCGAGGGATTCCGCGTGACACTGGTGGA
7
+ CGAGGGCGATCTATACAACTGGGAGGTGGCCATCTTCGGGCCCCCCAACACCTACTACGA
8
+ GGGCGGCTACTTCAAGGTGAGCGCGGCGACCCCCGCCCGGGTCCCGGAGCCCACGAGCGA
9
+ CCTCGGGCGCCGGGAACCAGCTCCCTGCCCCGCGGTCCTAGCGCTGTTGCTGGGCGGGCC
10
+ CCGAAGCCTCCTGGCTTGGGCTCGTTTCCCTTCTATGGCCACGTTCCCCCACCCAGCTCT
11
+ GCCCGGCCCCCTCCTCGGACCGTCTCGGGGACCTTCAGCCTCTGCTGCAGTCCTCGAAAA
12
+ TCCCCAGTTCCCTTCAAGGCATCGTCCGGTCCCCTGTTAGGCTCTTGGCCCCCGGAGGGG
13
+ TGGCCGGGGGCCCTCCCTGTAGCATCTGGGCGTGGGGCTCTTGCCCACCTCCTCCTTGGC
14
+ GGGGGCTGGACCCCGGCTGCCTCCCCCTCCGCCCCTGCGAGAAAGAGGGAGCGGAGCCCA
15
+ GGCCGCGCCGGCCTTTCAGCTGCCCTCCCCGCCCTCCCCGGAGGAGACAAAGAGGCCCCC
16
+ CCAGACCCCGTAGCTGCTATTGTTGGGGAGCTGGGCCCGTGAGCGGGGGAGCGAGGCCAG
17
+ CCTGGGGGTGGCTGGCGCGGCCACTCGCTCAGTCTCCAACAAAGGCCCGGATGAGCCTTG
18
+ GCAGCCAGGACCCGCCTGGAAAGCGGCCACCCTTGCCAGTAGCAGCCGGCCAGGCGCCCT
19
+ GGGCTCCATCCCCTGCTTTATGTAACCTGCGCCCTCGGGAAGGCCGAAGTAGGGGCGTGC
20
+ CTCCCACCTGCTCCCTGCAGCTCTCTCCAGGCCTCCCGGCTCGGGCCCGCGTCCCGGACC
21
+ CCGACCTCAGAAGCTCCGGGCTCGCTCATCCCAGCTGGTCTTGGCCTTTCTCAGAGTCCA
22
+ CTGAACAGGTGGCTTCTTGGGACCCAAACCCCGAGTTCTGGGCCGTTTCTTCTGCCCTCT
23
+ GGCGGTTTAATTCCAAGCAGTTTCTGGATGTTTTTGTTGTTGTTGGGAGCGGGGAGGCTG
24
+ TTTCTGTCTCATGTGAAAAGGACTCAGGCCAAAACCAGGGCAGTTTTCTTGATCTCACGA
25
+ TCCAGACGTGACCTTTGACTTCTTTTAGCGTTCAGGGACCTCGTTCTTGGGGCCAGAGGG
26
+ ACAAAGCGAGGGGCCCTGTGTGAGCGGTGGGGAACGAGCACCCTGTCCAGGAATCTCCCC
27
+ CTCCCACCGTCACTTCCTGCCAAGAGCCTGGACACGACACGACACTGCAGGGCCCGGCCC
28
+ GCTCTGCCCCGGCCAGCTGCGGGCGTGGGGCCGAGGGACCGATGCCTCCCGCACGATATG
29
+ TGTCTGCTCTCCGAGCTAATTAGTGTCTGAACCGCACCCGCTCAGCGGCTGTGAGGGCAG
30
+ CAGCCTGGTCTGCTGGGGGCGATTCCTGAGCAGAGAGTGGGACGCCCGTGGGTTCTGCAT
31
+ CTGGAATCCTGCGTCCCCACACAGGGAACAGAGTTTGGGTCTCGAGGTTGCCAAATGGTT
32
+ TTAGCAGCTCCTCCGCCAGCCCCTTCTGTCTGCTTGGGGGAGCAGCTGGCTGAGGAGCCG
33
+ CAGCCCCACCTCGAAGCCAGGCCTGTGAGGCGGCTGCTGTTCTGGAAGGAGGGGATGGGG
34
+ GTTTCTGGCTGCTGTGCCCACCAGACCGGTTGCCAGGGATTGTGGGCAGAGCTTCCTGGG
35
+ CCAGCATTAGGGGATAATCCGGTTTTCCGGATTTCCCAGGGAGGGGGCCTCTAGACATCT
36
+ GCCACAGGGTCAGTCCTCAGAAGCCAGTGTTGAGACGGGGGTGCTGCCACCCACGAGGAC
37
+ TCTCCCTTCCCGCTGTGCCTGGGAGGGAGTTGGGGGAGCGTGGAAATACAGAACCTGCTG
38
+ AGTGCCCAGGGCCGCTGCTGCCCAGCCACTGCCTGCAGCTGCTGTTCCTTCAGGAGCCAA
39
+ AGTGAGCCCTGGGGCAGGGGCCGCCAGAGAGAGCCCTCCACAGCCGACTTGCTGTCTGCC
40
+ CTTGGCAGGGCGCTTTCCTTTTCTGAGCCTGGGTTTGCTCCGGGGAAAAGACATTCTTAG
41
+ AGGTGCCCAAAATAAGAGGCTCATTGGGACTTGGTGGGGTTTGGTACAGATGAGGCCTTG
42
+ GCTGTTGTCAAGGATTGCCGCCTGAAACCCAGCACCAGGCTTGGGGGGCCTGAAGTCTTG
43
+ GGGAACCGCAGGACAGTTCTGAGACTGAAGTTCCAGCCTTGCTCTGTGGCCGCGGCCAAG
44
+ TCACTTGCCTTACGGGGCACCAGTGAGTTCCCTGTCAAACAGAGGACACCCCCCAAGACA
45
+ CCCCGCGTGCCCTCCCTGTCCAGGAGGGGCCCGTCCACGATCCAAGACCCCCAAAGTGCC
46
+ CTGCCTGTCCGGGAGGGGCCTCGCCCACAATCCAAGACCCCCGAGTACCCTCCCTGTCCA
47
+ GACCTCGCCCACGATCCAAGACCCCCTGAGTGCCCTCCCTGTCCAGACCTCACCCACGAT
48
+ CCAAGACCCCCTGAGTGCCCTCCCTGTCCAGACCTCGCCCACAATCCAAGACCCCCGAGT
49
+ ACCCTCCCTGTCAAGGCCTCGCCCACGATCCAAGACCCCCGAGTGCCCGCCCTGTCCAGA
50
+ CCTCGCCCACGATCCAAGACCCCCGAGTGCCCTCCCTGTCCAGACCTCGCCCACGATCCA
51
+ AGACCCCCGAGTGCCCTCCCTGTCCAGACCTCGCCCACGATCCAAGACCCCCGAGTGCCC
52
+ TCCCTGTCCAGACCTCGCCCACGATCCAAGACCCCCGAGTGCCCTCCCTGTCCAGACCTC
53
+ GCCCATGATCCAAGACCCCCGAGTGCCCTCCCTGTCCAGACCTCGCCCACGATCCAAGAC
54
+ CCCCTGAGTGCCCTCCCTGTCCAGACCTCGCCCACGATCCAAGACCCCCTGAGTGCCCTC
55
+ CCTGTCCAGGCTTCCACCACGATCGCTCTGGGGGTGCTGCTCTCGTGCCTTGGAGTGCTG
56
+ AGTGCCACCAGGACCCCTGACCCAGACAACCTCTGTGTCTGGCACTGGGGCCCAGCAGGA
57
+ AAACAGTGAGGCTTCCTTGTTTACCTGCTGTGGCCCAGGAGGGCCGTGGGTGGCATCACG
58
+ CCCCAGGCTGCAGGCCAGACAGCTCTGTCACCTGGCACGTGGCTTCAGGCCTCCCTCTGT
59
+ GGCCGTCCTTGCCAGCAGATCTGGACCTCCAGGGCCTGGGTGACCACAGGGGGCGATGCT
60
+ GACAGGGAAGGAGTCCTGCCAGGTTTCTGTGACCTATGGGTCTGCCTGCCTGACCCCCCA
61
+ AGACCGGACACCTGAGGGCAGACGGCCATACTGACTCATCCCCTCCCACGGCCTGGGCCA
62
+ GGGCAGGTGTCACAAGTGTTTGCTAACTGAGCAATCATCTGTGCTAACCCTCCCCACACC
63
+ CTGGCTGCCAAGGCCCTGGAGGTGCAGCCCTGGTCCTGGGCTTCAGCTCCATCCAAGGGG
64
+ AGCCTGGAGCCCCTGCCAGTCCATTCTGTCTGCTGGTGGGTGCCCCTGGCCTGGGTCCCA
65
+ TATGCCTGACCTGGGCTGCCACGGGCCTGGAGCCACGCGGGCAGCCAGTGCCCACGTTCC
66
+ CCAGCAGTTGTGCTGGGCCGGGTCCCGGCCACCTGGACTGTGTAGGAGCTGGGATCAGCT
67
+ CGGGTGACTCAGAAAAGGCTTCAGGCAGCCTTCTGGGGACTTGACCCCAGGCCTGTGAGA
68
+ GTCCCTGCCTTGGGCAGGATACGGTGTCCCTCACACACACCCTCAGGCACCAGCACTGGG
69
+ AGTGGGATGGCCTTGGGCACCTTGTGAGCTGGGGCAGGTCTTGGGGCTGGGCTGGACTGA
70
+ GCCACCTGCCTTCTGCCCCTGCAGGCGCGCCTCAAGTTCCCCATCGACTACCCATACTCT
71
+ CCACCAGCCTTTCGGTTCCTGACCAAGATGTGGCACCCTAACATCTACGAGGTGAGCGCG
72
+ GCCCCCACGGGCCTCAAGTCCTCATCCTCCGGGACCCAGGGTGCTGGGAGCCTCACGTCC
73
+ TCATCCTTCCGGGACCCGGGGCGCTGGGAGCCTCACGTCCTCGTCCTCCGGGACCCGGGG
74
+ CGCTGGGAGCCTCACGTCCTCGTCCTTCCGGGACCCGAGGCGCTGGGAGCCTCATGTCCT
75
+ CGTCCTTCCGGGACCCGGGGCGCTGGGAGCCTCACGTCCTCGTCCTCCACGTCCTCATCC
76
+ TCCGGGACCTGGGGCACTGGGAGCCCGTGCTGACCTCTGACCTGTTCTGACCTGTCTTCT
77
+ TCTTGTGCAGACGGGGGACGTGTGTATCTCCATCCTCCACCCGCCGGTGGACGACCCCCA
78
+ GAGCGGGGAGCTGCCCTCAGAGAGGTGGAACCCCACGCAGAACGTCAGGTAAGCCGGCCC
79
+ AACCCCCTGTGTCCACCCAGAACATCAGGTAGGCCGGGCTCCGTCCCGTATCCACCCAGA
80
+ CCATCAGGTAGGCCGGGCTCCCCCACAGGCTGTGGCGCCAAGGCCTGATTCGGGACCTGC
81
+ CAGCTGGCGGTCCTGGGCCTCGCTGTACCTGCACGGTAGGTGCTTTCACGGGGCCTGCGG
82
+ CACCGTGTGTCGGTGCAGACTCCCACCAGGACCCCAGGCCGGCCCCACCGTCTGGAACCA
83
+ CCTAGAGGTGTCCCGCCATCCTCAGTCCTGGGGCCTTCTCCTTACCCAGCCGTCTCTGGG
84
+ TTGGTCACCTCGTGCCACGTGTGCCGCCTGGGCCTCGTCCCCAGGTACAAGCACTGGGCC
85
+ GTGTTGCCCGTGTGTCCTGGAGTGTAGTCTAGGCAGGACGTGCGGGTGTGAGGGCAGCCC
86
+ CGGGTCTGACGGAGGGGTCTGCACCTTGCTGCCCTCCCTGGTCTTGGCGTGGGAGGGAGG
87
+ AGACTGATGCAGGTCCAGCCCCTGCTGTTCTGGGGGCCTGAGACAGAAGCAGAGGCCATG
88
+ AGGCCAGGTGAAGGTCACCTGCTGGGTGGGTCCAGGCGTCCCCGTGACCCTCAGGGCCAG
89
+ AGAAGAGCCGGAAGGCTGGGGTGCCCCGGGCCGCCCCACTCCGACCCACTCTCCCCACAG
90
+ GACCATTCTCCTGAGTGTGATCTCCCTCCTGAACGAGCCCAACACCTTCTCGCCCGCAAA
91
+ CGTGGACGCCTCCGTGATGTACAGGAAGTGGAAAGAGAGCAAGGGGAAGGATCGGGAGTA
92
+ CACAGACATCATCCGGTGAGGGCGGGCGGGGGCGTCACGGGAGGAGAGACTCAGATCCGG
93
+ CCTGCACCCCGGCCCCTGGTCCCACGGCCGCCCAGCCCCACCTTCCTGGTGAGGGTGGCG
94
+ GAGCTTCCTGGTGCCCATTTACAGGGTGCCAGTCACAGATGGAGGCCGGGCCGAGTGGCG
95
+ GAGGGTCCAGCCAGGTTCAAGCCCAGCTTCTTGCCCCTTTTCCTCTTTTTTTTTGTTTGA
96
+ GACAGAGTCTCTCTCTGTCACCCAGGCTGGAGTGCAGTGGCGCGATCTCGGCTCACTGCA
97
+ AGCTCCGCCTCCCGGGTTCACGCCATTCTCCTGCCTCAGCCTCCCAAGTAGCTGGGACTA
98
+ CAGGCGCCCGTCACCACGCCCGGCTAATTTTTTGTATTTTTAGTAGAGACGGGGTTTCAG
99
+ CGTGTTAGCCAGGATGGTCTCGATCTCCTGACCTCGTGATCCATCTGCCTCGGCCTCCCA
100
+ AAGTGCAGGGATTACAGGCGTGAGCCACCGCGGCCGGCCTTTTTTTTTTTTTTTTTTTTT
101
+ GGAGACAGAGTTATACTCTCTTGCCTAGGCTGCAGTGCAGTGGTGCGATCTCGGCTCACT
102
+ GCAGCCTCCACTACTCGGGTTGGAGCAGTTCTCCCCCTTCATCCTGCCAAGCAGCTGGGA
103
+ TTACAGGTGCCCACTACCACGCCGAGCTAATTTTTGTAATTTTTAGTAGAGGTGGGATTT
104
+ CACCATCTTAGCCAGGCTGGTCTCAAACTCCTGACCTCAGGTGATCCACCCGCCTCGGCC
105
+ TCCCAAAGTGCTGGGATGACAGGCGTGAGCCACTGCACCTGGCCTGGTGGTTAGTGTTTT
106
+ CATAGATTCTTCCAGGCTTTTCAGTTTAACGCATGTCTGTGCTTTAATGAAGAAATGGGG
107
+ TCGTGCTGTGTGTGCCCAGTGACTGACTGTTAGGGAACATGTGTCTGTGCCTTAATGAAG
108
+ AAATGGGGTCGTGCTGTGTGTGCCCAGTGACTGACTGTTAGGGAACATGTGTCTGTGCTT
109
+ TAATGAAAAAATGGGGTCGTGCTGTGTGTGCCCAGTGACTGACTGTTAGTCAGGGGTGTT
110
+ GGCCTTACTCATGTCTGGAGTGCGTCCCTGCAGGCTCTTGGCCTGGTGAGCTCTGGGTAC
111
+ AGCTGTGCAGTCGCCTACCGGCGCCTTCTGTACCTGCAGTCCACTTAGCTTGCGTGGCTG
112
+ TGTGTGGTGACCCACGGCTCTCCCTCTCCTCCCATCGCCCTCATGCCCCAGAGCTGAGCC
113
+ CCACAGCCCCTTCTCTTGGGTGCCTGTGTTCACATGAATGTGTAAACACGTGCGTGTCTG
114
+ TGTACAAAGACAAGGCTTTCTTTACGGGTTGACGGCCTTAATGGTTCCTGCTCTTCCTGT
115
+ TACATAGAGGCCCTTCCTATCCATTTTTTTTTTTTCTCAGAGTGATATTGCATAGATTTC
116
+ CTCACAGAGGCCTCACCTATTTTTGTTGGTATTTTGTATAAACAGAATCTTAAAAACAAC
117
+ TTTTAAAATATTGCACACATAATGCATGTGTCTTCCTCGCCCCAGGACCCAGGAGCATCC
118
+ AGGGCACCTTCCATCCTGCACTCGCTGGTACCTGGTGTCGTGGGGTCATCTCGGGGCAGC
119
+ ATCCTGGTGCTGGGCGGTCTCGGCTCTGAGCAGCCATGGTGGGCGGGCCCCGTGCGGCCT
120
+ CCTGGGAAGTGGCCTGCAAGCACCTGCTGGCCTCTGGAGGTCACAGGGTAGCTGCCCTGG
121
+ CCGTCCCTCTGGTGCAGATGTCCTCGGTGGCCCCGGTCCGGTCGTGTCACCTGGCCCAGG
122
+ TGGCTGGCTCCTTGGCCCGGTTCTTCCCGGCCACCTCCCTGAGGCACCACCTCCTTGAGA
123
+ TCCCAGCACAGAAATAAAAGCCACACTATTTTTATCCCTCAAAACTCCCTGTGGGCCAAC
124
+ ACACATGTGCCATGTGGACTCTGCTGTGGTCGCCGTTTCTGCCTGTTTTTTCATCTGTGT
125
+ GCGTGTTGGCCTCGTGGCAGCCCAAGTCCCGCTGAGCTGTGTCGGGCAGGCTGCCGTGGA
126
+ GCCCGGCTTGGTCAGGGATGTTGGTCTTGCTGAACAGGACCTCCAGACCGTCCTCCAGCT
127
+ CATGCTGGCGGTGTGCCGGCGGCACCTCCACGGTGCAGGTCAGTTCCCACCCTGGCCCTC
128
+ CCCTGCGTCTCCCCACAGCCGCCACCTCTGCGGTGCCGTCCCCGGGGCACCGTCACCCCC
129
+ CCAGCCCGTCCACCCTGGCCCTCCCCTGCGTCTCCCCACTGCTGCCACCCGTGCAGTGCC
130
+ GTCCCCGGGGCACTGTCAGTCACCCCCCCAGCCCATCGGAGAGCTTGGAAAGCAAAGCTT
131
+ GGCGTCCGCTGGGTCCCGCCACCCAGGGACGTCCCTGAGGCCAGACGCCTGCCCTCCACG
132
+ CGTCATGCATCCCCATAAAAAGCACTGGGCTTGTGGGCTGGGCTTGGGGCTGTCTGTCTG
133
+ CTCCCTGGTGCCCTCCCATGCGGGCACTGTGGGACCCGCACACCCTGGTAGCAGCCAGCC
134
+ CCAGAGCCCAGAGCCGTGCCTGGTCGGTGATAGGGGCTCGAGCCCATTGCCTGCGGCTGC
135
+ AGCCTCGTTCCTGTTTTCTGTCAAATGGGGTCAGCGTGCCGCCTGGCCCTGCTGTGCCAC
136
+ CCCCGGAAGCCCCTTTGCTTCCAGTCCTGGGGGGACATTCTTGACGCGTGTCCTGGAGGT
137
+ GGAGCCGGGGGCAGGTTCCTCGTAGGTCCTGGTGTGCGCGGTGCAGCCCCTCATAGGGCC
138
+ GGGTGTACACGGTGCCCTCCAGGAAGTTTGAGCTAACTTGTCCTCCCTTCCTGCCAGAGG
139
+ CTGGGATGGCCAGGCCCCCCAGGTTTAGAATCCGGAGGCCGGGGTGGCCAGGCCCCCAGG
140
+ TTTAGAATCCGGAGGCCGGGGTGGCCAGGCCCCCCACGTTTAGAATCCGGAGGCCGGGGT
141
+ GGCCAGGCCCCCCAGGTTTAGAATCCGGAGGCCGGGGTGGCCAGGCCCCCCACGTTTAGA
142
+ ATCCGGAGGCCGGGGTGGCCAGGCCCCCCGGGTTTAGAATCCGGAGGCCGGGGTGGCCAG
143
+ GCCCCCCGGGTTTAGAATCCGGAGGCCGGGGTGGCCAGGCCCCCCGGGTTTAGAATCCGG
144
+ AGGCCGGGGTGGCCAGGCCCCCCGGTTTAGAATCCGGAGGCCGGGGTGGCCAGGCCCCCC
145
+ GGGTTTAGAATCCGGAGGCCGGGGTGGCCAGGCCCCCCGGGTTTAGAATCCGGAGGCCGG
146
+ GGTGGCCAGGCCCCCCGGGTTTAGAATCCGGAGGCCGGGGTGGCCAGGCCCCCCGGGTTT
147
+ AGAATCCGGAGGCCGGGGTGGCCAGGCCCCCCGGGTTTAGAATCCGGAGGCCGGGGTGGC
148
+ CAGGCCCCCCGGGTTTAGAATCCGGAGGCCGGGGTGGCCAGGCCCCCCGGGTTTAGAATC
149
+ CGGAGGCCGGGGTGGCCAGGCCCCCCGGGTTTAGAATCCGGAGGCCGGGGTGGCCAGGCC
150
+ CCCCGGGTTTAGAATCCGGAGGCCGGGGTGGCCAGGCCCCCCGGGTTTAGAATCCGGAGG
151
+ CCGGGGTGGCCAGGCCCCCCACGTTTAGAATCCGGAGGCCGGGGTGGCCAGGCCCCCGGG
152
+ TTTAGAATCCGGAGGCTGGGATGGCCAGGCCCCCGGGTTTAGAATCCAGAGGCTGGGATG
153
+ GCCAGGCCCCCCGGTTTAGAATCCGGAGGCCGGGGTGGCCAGGCCCCCGGGTTTAGAATC
154
+ CTGCTGAGGCCACGGAGAGGCTCAGGCCGTTTTTGCGTTTCCCATCTCACCTGTGCTGGT
155
+ TCCCGTCTCCAGGGATGGTCCTGCCTCCTGTCCTTGGGCCCTCCCAGCTGCTTCCTTTGC
156
+ TCCTGCGCTGAGGAAGGCTTTTGCCCCCCAGTGGGGCAGCATGGGCCCTCCCTGTTGCCG
157
+ GCATCGTTATTTTCTCCCAGCTCCTGATGGGTCCCTTGGGTTGTGCTTCGGGGCGGGGCA
158
+ GGCGGGTGTGACTGCACTGCGCCCGTCCAGCCTCCCACCCGCACCTCCTGCCCTTCCCGA
159
+ GCCCCCTCCTCTGTCATTTCTCCCCCTGGAGTTCCTCACGCACAGGGCTTTGTCCTAAGT
160
+ GGTCGCCACACGCCGTTTTAAGAGAAACCTGAGCGTTGGGGTGAGCGTCGGACCTGGGGG
161
+ AGGGGGGCCGGGCAGGGGCCGAGTCCAGGCACGTGGGTGGCGCCCTCACCCACCCTGTCC
162
+ CCCCAGGAAGCAGGTCCTGGGGACCAAGGTGGACGCGGAGCGTGACGGCGTGAAGGTGCC
163
+ CACCACGCTGGCCGAGTACTGCGTGAAGACCAAGGCGCCGGCGCCCGACGAGGGCTCAGA
164
+ CCTCTTCTACGACGACTACTACGAGGACGGCGAGGTGGAGGAGGAGGCCGACAGCTGCTT
165
+ CGGGGACGATGAGGATGACTCTGGCACGGAGGAGTCCTGACACCACCAGAATAAACTTGC
166
+ CGAGTTTACCTCACTAGGGCCGGACCCGTGGCTCCTTAGACGACAGACTACCTCACGGAG
167
+ GTTTTGTGCTGGTCCCCGTCTCCTCTGGTTGTTTCGTTTTGGCTTTTTCTCCCTCCCCAT
168
+ GTCTGTTCTGGGTTTTCACGTGCTTCAGAGAAGAGGGGCTGCCCCACCGCCACTCACGTC
169
+ ACTCGGGGCTCGGTGGACGGGCCCAGGGTGGGAGCGGCCGGCCCACCTGTCCCCTCGGGA
170
+ GGGGAGCTGAGCCCGACTTCTACCGGGGTCCCCCAGCTTCCGGACTGGCCGCACCCCGGA
171
+ GGAGCCACGGGGGCGCTGCTGGGAACGTGGGCGGGGGGCCGTTTCCTGACACTACCAGCC
172
+ TGGGAGGCCCAGGTGTAGCGGTCCGAGGGGCCCGGTCCTGCCTGTCAGCTCCAGGTCCTG
173
+ GAGCCACGTCCAGCACAGAGTGGACGGATTCACCGTGGCCGACTCTTTTCCCTGCTTTGG
174
+ TTTGTTTGAAATCTAAATAAAACTACTTTATG
data/test/data/seq_ub2r1_transcript.fa ADDED
@@ -0,0 +1,26 @@
1
+ >UB2R1_transcript
2
+ GGCAAGCGCCGGTGGGGCGGCGGCGCCAGAGCTGCTGGAGCGCTCGGGGTCCCCGGGCGG
3
+ CGGCGGCGGCGCAGAGGAGGAGGCAGGCGGCGGCCCCGGTGGCTCCCCCCCGGACGGTGC
4
+ GCGGCCCGGCCCGTCTCGCGAACTCGCGGTGGTCGCGCGGCCCCGCGCTGCTCCGACCCC
5
+ GGGCCCCTCCGCCGCCGCCATGGCTCGGCCGCTAGTGCCCAGCTCGCAGAAGGCGCTGCT
6
+ GCTGGAGCTCAAGGGGCTGCAGGAAGAGCCGGTCGAGGGATTCCGCGTGACACTGGTGGA
7
+ CGAGGGCGATCTATACAACTGGGAGGTGGCCATCTTCGGGCCCCCCAACACCTACTACGA
8
+ GGGCGGCTACTTCAAGGCGCGCCTCAAGTTCCCCATCGACTACCCATACTCTCCACCAGC
9
+ CTTTCGGTTCCTGACCAAGATGTGGCACCCTAACATCTACGAGACGGGGGACGTGTGTAT
10
+ CTCCATCCTCCACCCGCCGGTGGACGACCCCCAGAGCGGGGAGCTGCCCTCAGAGAGGTG
11
+ GAACCCCACGCAGAACGTCAGGACCATTCTCCTGAGTGTGATCTCCCTCCTGAACGAGCC
12
+ CAACACCTTCTCGCCCGCAAACGTGGACGCCTCCGTGATGTACAGGAAGTGGAAAGAGAG
13
+ CAAGGGGAAGGATCGGGAGTACACAGACATCATCCGGAAGCAGGTCCTGGGGACCAAGGT
14
+ GGACGCGGAGCGTGACGGCGTGAAGGTGCCCACCACGCTGGCCGAGTACTGCGTGAAGAC
15
+ CAAGGCGCCGGCGCCCGACGAGGGCTCAGACCTCTTCTACGACGACTACTACGAGGACGG
16
+ CGAGGTGGAGGAGGAGGCCGACAGCTGCTTCGGGGACGATGAGGATGACTCTGGCACGGA
17
+ GGAGTCCTGACACCACCAGAATAAACTTGCCGAGTTTACCTCACTAGGGCCGGACCCGTG
18
+ GCTCCTTAGACGACAGACTACCTCACGGAGGTTTTGTGCTGGTCCCCGTCTCCTCTGGTT
19
+ GTTTCGTTTTGGCTTTTTCTCCCTCCCCATGTCTGTTCTGGGTTTTCACGTGCTTCAGAG
20
+ AAGAGGGGCTGCCCCACCGCCACTCACGTCACTCGGGGCTCGGTGGACGGGCCCAGGGTG
21
+ GGAGCGGCCGGCCCACCTGTCCCCTCGGGAGGGGAGCTGAGCCCGACTTCTACCGGGGTC
22
+ CCCCAGCTTCCGGACTGGCCGCACCCCGGAGGAGCCACGGGGGCGCTGCTGGGAACGTGG
23
+ GCGGGGGGCCGTTTCCTGACACTACCAGCCTGGGAGGCCCAGGTGTAGCGGTCCGAGGGG
24
+ CCCGGTCCTGCCTGTCAGCTCCAGGTCCTGGAGCCACGTCCAGCACAGAGTGGACGGATT
25
+ CACCGTGGCCGACTCTTTTCCCTGCTTTGGTTTGTTTGAAATCTAAATAAAACTACTTTA
26
+ TG
data/test/data/seq_y.fa ADDED
@@ -0,0 +1,2 @@
1
+ >Y dna:chromosome chromosome:NCBI36:Y:2709497:2709542:1
2
+ TAGTTATAGATTAAAAGAAGTTAAGGCCGGGCGCGGTGGCTCACGC
data/test/default/test_connection.rb ADDED
@@ -0,0 +1,60 @@
1
+ #
2
+ # = test/unit/test_connection.rb - Unit test for Ensembl::Core
3
+ #
4
+ # Copyright:: Copyright (C) 2009
5
+ # Jan Aerts <http://jandot.myopenid.com>
6
+ # Francesco Strozzi <francesco.strozzi@gmail.com>
7
+ # License:: Ruby's
8
+ #
9
+ # $Id:
10
+
11
+ require File.expand_path File.join(File.dirname(__FILE__),"../helper.rb")
12
+
13
+
14
+ class TestConnection < Test::Unit::TestCase
15
+
16
+ def test_remote_core_connection
17
+ assert_nothing_raised do
18
+ Ensembl::Core::DBConnection.connect('Homo sapiens',56)
19
+ end
20
+ end
21
+
22
+ # This is to check if the overwrite of the default parameters is possible,
23
+ # so you can specify an Ensembl database on a host that is different from the official Ensembl website.
24
+
25
+ def test_local_core_connection
26
+
27
+ # Change username, password, host and port in order to test the connection with a different Ensembl db server
28
+ assert_nothing_raised do
29
+ Ensembl::Core::DBConnection.connect('Homo sapiens',56,:username => "anonymous",:host => "ensembldb.ensembl.org", :port => 5306)
30
+ end
31
+ end
32
+
33
+ def test_remote_variation_connection
34
+ assert_nothing_raised do
35
+ Ensembl::Variation::DBConnection.connect('Homo sapiens',56)
36
+ end
37
+ end
38
+
39
+ def test_local_variation_connection
40
+
41
+ # Change username, password, host and port in order to test the connection with a different Ensembl db server
42
+ assert_nothing_raised do
43
+ Ensembl::Variation::DBConnection.connect('Bos taurus',56,:username => "anonymous",:host => "ensembldb.ensembl.org", :port => 5306)
44
+ end
45
+ end
46
+
47
+ def test_connection_ensembl_genomes
48
+ assert_nothing_raised do
49
+ Ensembl::Core::DBConnection.ensemblgenomes_connect('Staphylococcus aureus MRSA252',7)
50
+ end
51
+ end
52
+
53
+ def test_manual_connection_ensembl_genomes
54
+ assert_nothing_raised do
55
+ Ensembl::Core::DBConnection.connect("Bacillus collection",7, :host => "mysql.ebi.ac.uk", :port => 4157)
56
+ end
57
+ end
58
+
59
+ end
60
+