ruby-ensembl-api 0.9.6 → 1.0

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Files changed (62) hide show
  1. data/TUTORIAL.rdoc +1 -1
  2. data/bin/variation_effect_predictor +106 -0
  3. data/lib/ensembl.rb +2 -2
  4. data/lib/ensembl/core/activerecord.rb +119 -225
  5. data/lib/ensembl/core/collection.rb +14 -10
  6. data/lib/ensembl/core/project.rb +6 -8
  7. data/lib/ensembl/core/slice.rb +87 -123
  8. data/lib/ensembl/core/transcript.rb +49 -65
  9. data/lib/ensembl/core/transform.rb +6 -8
  10. data/lib/ensembl/db_connection.rb +56 -72
  11. data/lib/ensembl/variation/activerecord.rb +138 -8
  12. data/lib/ensembl/variation/variation.rb +284 -46
  13. data/samples/ensembl_genomes_example.rb +60 -0
  14. data/samples/examples_perl_tutorial.rb +125 -0
  15. data/samples/small_example_ruby_api.rb +34 -0
  16. data/samples/variation_example.rb +67 -0
  17. data/test/unit/{release_56 → release_60}/core/test_gene.rb +6 -6
  18. data/test/unit/release_60/core/test_project_human.rb +38 -0
  19. data/test/unit/{release_56 → release_60}/core/test_slice.rb +1 -8
  20. data/test/unit/release_60/core/test_transcript.rb +126 -0
  21. data/test/unit/{release_53 → release_60}/core/test_transform.rb +21 -21
  22. data/test/unit/release_60/variation/test_activerecord.rb +213 -0
  23. data/test/unit/release_60/variation/test_consequence.rb +158 -0
  24. data/test/unit/{release_56 → release_60}/variation/test_variation.rb +18 -17
  25. data/test/unit/test_connection.rb +2 -2
  26. data/test/unit/test_releases.rb +8 -8
  27. metadata +27 -43
  28. data/test/unit/data/seq_c6qbl.fa +0 -10
  29. data/test/unit/data/seq_cso19_coding.fa +0 -16
  30. data/test/unit/data/seq_cso19_transcript.fa +0 -28
  31. data/test/unit/data/seq_drd3_gene.fa +0 -838
  32. data/test/unit/data/seq_drd3_transcript.fa +0 -22
  33. data/test/unit/data/seq_drd4_transcript.fa +0 -24
  34. data/test/unit/data/seq_forward_composite.fa +0 -1669
  35. data/test/unit/data/seq_par_boundary.fa +0 -169
  36. data/test/unit/data/seq_rnd3_transcript.fa +0 -47
  37. data/test/unit/data/seq_ub2r1_coding.fa +0 -13
  38. data/test/unit/data/seq_ub2r1_gene.fa +0 -174
  39. data/test/unit/data/seq_ub2r1_transcript.fa +0 -26
  40. data/test/unit/data/seq_y.fa +0 -2
  41. data/test/unit/ensembl_genomes/test_collection.rb +0 -51
  42. data/test/unit/ensembl_genomes/test_gene.rb +0 -52
  43. data/test/unit/ensembl_genomes/test_slice.rb +0 -71
  44. data/test/unit/ensembl_genomes/test_variation.rb +0 -17
  45. data/test/unit/release_50/core/test_project.rb +0 -215
  46. data/test/unit/release_50/core/test_project_human.rb +0 -58
  47. data/test/unit/release_50/core/test_relationships.rb +0 -66
  48. data/test/unit/release_50/core/test_sequence.rb +0 -175
  49. data/test/unit/release_50/core/test_slice.rb +0 -121
  50. data/test/unit/release_50/core/test_transcript.rb +0 -108
  51. data/test/unit/release_50/core/test_transform.rb +0 -223
  52. data/test/unit/release_50/variation/test_activerecord.rb +0 -143
  53. data/test/unit/release_50/variation/test_variation.rb +0 -84
  54. data/test/unit/release_53/core/test_gene.rb +0 -66
  55. data/test/unit/release_53/core/test_project.rb +0 -96
  56. data/test/unit/release_53/core/test_project_human.rb +0 -65
  57. data/test/unit/release_53/core/test_slice.rb +0 -47
  58. data/test/unit/release_53/variation/test_activerecord.rb +0 -145
  59. data/test/unit/release_53/variation/test_variation.rb +0 -71
  60. data/test/unit/release_56/core/test_project.rb +0 -96
  61. data/test/unit/release_56/core/test_transform.rb +0 -63
  62. data/test/unit/release_56/variation/test_activerecord.rb +0 -142
data/test/unit/data/seq_par_boundary.fa DELETED
@@ -1,169 +0,0 @@
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/unit/data/seq_rnd3_transcript.fa DELETED
@@ -1,47 +0,0 @@
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/unit/data/seq_ub2r1_coding.fa DELETED
@@ -1,13 +0,0 @@
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/unit/data/seq_ub2r1_gene.fa DELETED
@@ -1,174 +0,0 @@
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/unit/data/seq_ub2r1_transcript.fa DELETED
@@ -1,26 +0,0 @@
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/unit/data/seq_y.fa DELETED
@@ -1,2 +0,0 @@
1
- >Y dna:chromosome chromosome:NCBI36:Y:2709497:2709542:1
2
- TAGTTATAGATTAAAAGAAGTTAAGGCCGGGCGCGGTGGCTCACGC
data/test/unit/ensembl_genomes/test_collection.rb DELETED
@@ -1,51 +0,0 @@
1
- #
2
- # = test/unit/release_53/ensembl_genomes/test_collection.rb - Unit test for Ensembl::Core
3
- #
4
- # Copyright:: Copyright (C) 2009
5
- # Francesco Strozzi <francesco.strozzi@gmail.com>
6
- # License:: Ruby's
7
- #
8
- # $Id:
9
-
10
- require 'pathname'
11
- libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 4, 'lib')).cleanpath.to_s
12
- $:.unshift(libpath) unless $:.include?(libpath)
13
-
14
- require 'test/unit'
15
- require 'lib/ensembl'
16
-
17
- include Ensembl::Core
18
-
19
-
20
- class TestCollection < Test::Unit::TestCase
21
-
22
- def teardown
23
- DBConnection.remove_connection
24
- end
25
-
26
- def test_check_collection
27
- DBConnection.ensemblgenomes_connect('bacillus_collection',3)
28
- assert_equal(true,Collection.check)
29
- DBConnection.connect('homo_sapiens',56)
30
- assert_equal(false,Collection.check)
31
- end
32
-
33
- def test_check_species
34
- DBConnection.ensemblgenomes_connect('bacillus_collection',3)
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- assert_equal(["Bacillus subtilis","Bacillus amyloliquefaciens","Bacillus anthracis Ames","Bacillus anthracis Ames ancestor","Bacillus anthracis Sterne","Bacillus cereus ATCC 10987","Bacillus cereus ATCC 14579","Bacillus cereus NVH 391-98","Bacillus cereus ZK","Bacillus clausii","Bacillus halodurans","Bacillus licheniformis Goettingen","Bacillus licheniformis Novozymes","Bacillus pumilus SAFR-032","Bacillus thuringiensis Al Hakam","Bacillus thuringiensis konkukian 97-27","Bacillus weihenstephanensis","Bacillus cereus AH820","Bacillus cereus AH187","Bacillus cereus Q1","Bacillus cereus G9842","Bacillus cereus B4264"],Collection.species)
36
- end
37
-
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- def test_get_species_id
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- DBConnection.ensemblgenomes_connect('bacillus_collection',3)
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- assert_equal(9,Collection.get_species_id("Bacillus cereus ZK"))
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- assert_nil(Collection.get_species_id("Dummy specie"))
42
- end
43
-
44
- def test_connection_with_a_species
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- assert_nothing_raised do
46
- DBConnection.ensemblgenomes_connect('Bacillus_licheniformis_Goettingen',3)
47
- end
48
- assert_equal('bacillus licheniformis goettingen', Ensembl::SESSION.collection_species)
49
- end
50
-
51
- end