RubyGems - bio-ensembl - Versions diffs - 1.1.0 - Mend

bio-ensembl 1.1.0

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 (81) hide show

data/.document +5 -0
data/Gemfile +20 -0
data/Gemfile.lock +40 -0
data/LICENSE.txt +20 -0
data/README.rdoc +19 -0
data/Rakefile +71 -0
data/VERSION +1 -0
data/bin/ensembl +40 -0
data/bin/variation_effect_predictor +106 -0
data/bio-ensembl.gemspec +190 -0
data/lib/bio-ensembl.rb +65 -0
data/lib/bio-ensembl/core/activerecord.rb +1812 -0
data/lib/bio-ensembl/core/collection.rb +64 -0
data/lib/bio-ensembl/core/project.rb +262 -0
data/lib/bio-ensembl/core/slice.rb +657 -0
data/lib/bio-ensembl/core/transcript.rb +409 -0
data/lib/bio-ensembl/core/transform.rb +95 -0
data/lib/bio-ensembl/db_connection.rb +205 -0
data/lib/bio-ensembl/variation/activerecord.rb +536 -0
data/lib/bio-ensembl/variation/variation_feature.rb +376 -0
data/lib/bio-ensembl/variation/variation_feature62.rb +444 -0
data/samples/ensembl_genomes_example.rb +60 -0
data/samples/examples_perl_tutorial.rb +125 -0
data/samples/small_example_ruby_api.rb +34 -0
data/samples/variation_effect_predictor_data.txt +4 -0
data/samples/variation_example.rb +67 -0
data/test/data/seq_c6qbl.fa +10 -0
data/test/data/seq_cso19_coding.fa +16 -0
data/test/data/seq_cso19_transcript.fa +28 -0
data/test/data/seq_drd3_gene.fa +838 -0
data/test/data/seq_drd3_transcript.fa +22 -0
data/test/data/seq_drd4_transcript.fa +24 -0
data/test/data/seq_forward_composite.fa +1669 -0
data/test/data/seq_par_boundary.fa +169 -0
data/test/data/seq_rnd3_transcript.fa +47 -0
data/test/data/seq_ub2r1_coding.fa +13 -0
data/test/data/seq_ub2r1_gene.fa +174 -0
data/test/data/seq_ub2r1_transcript.fa +26 -0
data/test/data/seq_y.fa +2 -0
data/test/default/test_connection.rb +60 -0
data/test/default/test_releases.rb +130 -0
data/test/ensembl_genomes/test_collection.rb +122 -0
data/test/ensembl_genomes/test_gene.rb +46 -0
data/test/ensembl_genomes/test_slice.rb +65 -0
data/test/ensembl_genomes/test_variation.rb +38 -0
data/test/helper.rb +18 -0
data/test/release_50/core/test_project.rb +210 -0
data/test/release_50/core/test_project_human.rb +52 -0
data/test/release_50/core/test_relationships.rb +72 -0
data/test/release_50/core/test_sequence.rb +170 -0
data/test/release_50/core/test_slice.rb +116 -0
data/test/release_50/core/test_transcript.rb +125 -0
data/test/release_50/core/test_transform.rb +217 -0
data/test/release_50/variation/test_activerecord.rb +138 -0
data/test/release_50/variation/test_variation.rb +79 -0
data/test/release_53/core/test_gene.rb +61 -0
data/test/release_53/core/test_project.rb +91 -0
data/test/release_53/core/test_project_human.rb +61 -0
data/test/release_53/core/test_slice.rb +42 -0
data/test/release_53/core/test_transform.rb +57 -0
data/test/release_53/variation/test_activerecord.rb +137 -0
data/test/release_53/variation/test_variation.rb +66 -0
data/test/release_56/core/test_gene.rb +61 -0
data/test/release_56/core/test_project.rb +91 -0
data/test/release_56/core/test_slice.rb +49 -0
data/test/release_56/core/test_transform.rb +57 -0
data/test/release_56/variation/test_activerecord.rb +141 -0
data/test/release_56/variation/test_consequence.rb +131 -0
data/test/release_56/variation/test_variation.rb +63 -0
data/test/release_60/core/test_gene.rb +61 -0
data/test/release_60/core/test_project_human.rb +34 -0
data/test/release_60/core/test_slice.rb +42 -0
data/test/release_60/core/test_transcript.rb +120 -0
data/test/release_60/core/test_transform.rb +57 -0
data/test/release_60/variation/test_activerecord.rb +216 -0
data/test/release_60/variation/test_consequence.rb +153 -0
data/test/release_60/variation/test_variation.rb +64 -0
data/test/release_62/core/test_gene.rb +42 -0
data/test/release_62/variation/test_activerecord.rb +86 -0
data/test/release_62/variation/test_consequence.rb +191 -0
metadata +287 -0

data/test/data/seq_par_boundary.fa ADDED

@@ -0,0 +1,169 @@
+>Y dna:chromosome chromosome:NCBI36:Y:2705106:2715105:1
+TCCAAATGATGCTCTGCCATAAGAAGAAATTCACACCCTGAATAGCACAGCAGGATGCGA
+ATAGCAATGCCAGCCAAAGACATTGCAAACAAGCCGGTAAAACTAAGTGATTGTTAGCTG
+TTTAAAAAAATAATAATAACTGGTGTTAACAACAAAGTGAAACTTAACTTCTGAAGATGA
+GGCTACCTTCACAGAGAGGATAAGAAAGGAAGAACTGAGTAAAAGTAGTTAGATATTGCT
+GGATTTTGACATTTTAAGGTTAAGTGTTCCTGCTAAAAATAAAAATTGAACATATAACTC
+CTGAACTAGTGGATGAAAATGAAGAATGAAGAATAAAATTAAATACAAAAAAAATGAAGA
+GTAAAATTAAATACCAAAATTAGCCAAGTGTTGTGGTGAATGCCTGTAGTCCCAGCTACT
+CAGGAGGCTGAGGTGGGAGGATCACTTGAGCCCCAGAGGTGGAGGTTGCAGTGAGCTGAG
+ATTGCGCCACTGCACTTCCGCCTGGGTGGCAGAGCCAGGCTTTGTCTCAAAAATAAAAAA
+AAATAATAAATTAAAAACCTGAATACTAAATGGAAGTTAAGAAGGAAGGAATTAAAAAAG
+AAGAAAAGTAAAATAAAATAGTAGGAATAGTGAATCCTTAGTTATGTTAGATGTTCAGTG
+ATTTAATAAATCTGTAAAAAGACGGAGATGAGATGATGCAATTTAAAATGTTTCGGCTGG
+GCGCAGTGGCTCACGCCTGTAATCCCAGCACTGTAGGAAGCCGAGGCGGGTGGATCACGA
+GGTCAGGAGATCGAGACCATCCTGGCTAACACGGTGAAACCCCATCTCTACTAAAAATAC
+AAATAAAATGTTTCATGCTATTTACGAGAGAAGCATTTGCAACAAAATGCCAAAGAGAAG
+GTGAAAATAGCTGGAAAAAAAATGCGCAAAGCAAATAACCAATAGAAAGAAAGCCAAGTT
+GGGCTAGCAAAATCAGACAAAATAACCTTCGAGGTGCAAACAACTTTGAGGCCCAAATAG
+AGGTTCTTCCCACTAAAAGAATGATTCCCTGAATGATAATGGAATCTTGACCCAGCCTGC
+ACCTCAGGTTAAGTTAAAAGTGGAAATTTAAAGATCTAAGTGTGAGATTTTAAAAAGCAT
+TTCCCCAGAAATACCAGGATCTGTAGATGGAAATGTTATTAAGAATAAAGATGTGGAGCT
+GGGCGTGGTGGCTCACGCCTGTAATCCCAGAACTTTGGGAGGCTGAGACTGGCTGATTTC
+TTGAGCCCAGGAGTTTGAGACTAGCCTGGACAACATAGTGAGACCCCATCTTTACAAAAA
+AATTAAAAAAAATTAGTGGACATGGTGGCATGCACCTCTAGTCCCAGTTACTCAGGAGGC
+TGAGGTGGGAGGATCACCTGTGCCCAGGCTGAGGCTGCAGTGAGCCATGATCACGCCACT
+GCACTCCAGCCTGCGTGACAGAGCAAGACCCTGTCTCAAAAGAAAAGAAAAAAAAAGAAG
+AAAGAAATGAAAACCGTAGCTCAGAGACAGAGAAACTGAGCAATGCATAGGTTCAGAAGG
+GTTTGAAACAGACTGAATTGTGTCTTGGCATATGAGAGAGGTCGCAGCTATAAAACAATG
+AGAGAAGAAACCAAATTCCACATAGGCAGGACTGAGACAATTGGCTGTTCTTGTGGATGA
+TACGTGATCAAATCTCAACCTCATGCGATACTTTTTTTTTTTTTTTTGAGATGGAGTCTC
+GCTCTGTCACCCAGGCTGCAGTGCAGTGGTGTGATCTCACCTCCCCGCAAACTTCTCCTC
+CCGGGTTCAAGTAATTCTCGTGCCTCAGCTGGGACTACAGGCATGTGCCACCACGCCTGG
+CTAATTTTTGCATTTTTTTAGTAGAGACGGGGTTTCACCAAGTTGGCCAGGCTGGTCTCG
+AACTCCTGACCTCAGGTGATCTGTCCACCTCGGTGTCCCAAAGTGCTGGGATTACAGGTG
+TGAACCACCACACCCAGCCTCATGTAATACTTAAAAATGAACTACAGGTGGATTACAAAC
+CTGAATATAAAAGAAAACTTTTTTTTTTGAAAAATAGAGGGAAATGTCTTATAACCTCAG
+AGTTAGGAGGTTTTTCTTAGATACAATACAAAAAGCATAACCACGCCCATAGTCCCAGCT
+ACTCAGGAGGCTGAGGCATAAGAATCACTTGAGCTCGAGAGGTGGAGGTTGCAGTGAGCC
+GAGATCCTGCCATTGCACTCCAGCTGAGGCTACAGAGTGAGAGTATAAAAAAAAAAAAAA
+AAAAGCATAACCTTTAAAAATGGGTTAGCCTATGTCTACATTTAAATAATAATAATAATA
+ATAATGTTCCAACTTCAGGCTCTGAAAAAAGTCAAAAGATGAGCTGTCAACTAGAAGAGG
+CTCCTTACTGCTCATACCACCAGGGAAAGTTTAATATGCAAAATGCAGTCATCCTTCAGA
+ATTCATGGGGGATTAGTTTTAAGACGCCTTCTTCCCCGCAGACACCAAAATCCACAGCTG
+CTGAAGTCTCTGATATAAAACGTGCAGTACTTGCATATAATGCAAGTATATGTTCCTGTA
+TATTTTTATTTATTTATTTGGAGACAGAATCTCACTCTGTTGCCCAGGCTGGAGTGCAGT
+GGCGTGATCTTGGCTCACTGTAACCTCCACCTCCCGGGTTCAAGAGATTCTCCTGACTCA
+ACCTCCCAAGTAGCTGGGATTACAGGTATGCGCCACCACCCCCAGCTAATTTTTGTATTT
+TTGGTAGAGACGGGTTTTAACCATGTTGTCCAGGCTGGTTTCGAACTCCTGACCTCACAT
+AATCTGCCCACCTTGGCCTCCCAAAGTGCTGGGATTACAGGGATGAGCCACCGTGTCCAG
+CCTCTGGTATACTTTAAATTATCTCTAGGTTACTCATAACTCCTGATACGCTGTAAATGC
+TATGCAAATAGTTGTTATACTATATTATTTTTTATTTGTATTACTTTTTATTGGATTGCT
+ATATTTTATTTTTTGAAATATTTTCAATACAAGACTGGTTGGATCTATAGATGCAGAAAT
+TCTGGTTATAGAGCACAAACTGTGTATAGATAGCTCCTACCAAAACAGACGGATGGTGAA
+AAAAAGAAAAGAAAAGAAAAGAAAAAGAAAATGGAGGAGAGAGACTATGAGGCGACTAAA
+AGAAGAGGGATATGATCATTCCATTCGCTGACAAGAAAAATTCAAAGAAGAGGGAATTAT
+GCAATTGACCAGCTGATGTGTGTTAGAAATGCTCAGGGTCACACATATTCATTGAAAGCC
+AATTTAAGCCACTATTTAAATTTAAACCGATTTAAACAATTGGGCTTTTTTTTTTTTTTC
+TAAAAAAAAAAAAAAGTCAATTAGGCCAGGCGAGGTGGCTCACACCTGTCATCCCGGCAC
+TTTGGGAGGCCGAGGTGGGTGGATCACAAGGTCAGGAGTTTGAGACCAGCCTGGCCAACA
+TGGTGAAACCCTGTTTCTACTAAAAATACAAAAGTTAGCTGGGCATGGTGGTGTGTGCCT
+GAGGCTGTGAGACTGAGGCAGGAGAATCACTTGAACCCAGGAGGCGGAGGTTGCAGGGAG
+CGGAGATCATGCCACTGCACTCCAGCTTGGGCGACAGACCAAGACTCTGTCTCAAAAAAA
+AAAAAGAAGAAGTATATTGGTTCCGTCTGGAAAGGTGGAGCACTTGAAGCAAAGGCAGGA
+AGACTGGAAGCAGGGAGAGGGTTTTCAGGTCACAAACAGGTGAGAGACAAAACAGTTGCC
+TTCTTTTGAGTTTCTGATTAGCCTTTCCAAAGGAGGCGATCAGATACGAATCTGCCTCAG
+GGAGCAGAGGGGGGACTTTGAATAGAATGGGAGGCAGGTTGGCCCTAAGCAGTTCCCAGC
+TGGACTTTTCCCTTTAGCTTAGTGACTTGGGGGTCCCGAGATTTATGTTCCCTTCACAGT
+GTATGAGTGAGAGCACTTGGAAACTGAGAGTGGAAGTGTCGCAGGCCAGGTCTCACTAAC
+ACAGGCCCCCACAACACCTGTTTCAGTATTGACTGAGTGGTTAAATATTAAAAGCCAGTG
+CTGTTATACAAAGGCTGGAATGTAACAAAAGCCCACCGAGAGTTTTTCCCAGGACTTTCC
+CGGGCCTTAAAGCATGACAAAATAATGAATGAATTCTTAACAGGACCCATTTAGGATTAA
+ACAAGTTTTACTGGGGGTCTGCAGAAACTCCCCAGGCCTCCACAAACAAGTTTATTGGGG
+CTTTGAAGGAACTCTGCAAACCTCCTGGATTTAGCAGGAGACAACATGAGGGTAATCACC
+CCGGCACCTGGACCCATTAGATTAAGTCAATTTACTGAGGCTCCTGAGGAAGATCCTCAG
+GACTCAGACCTTAGTTATAGATTAAAAGAAGTTAAGGCCGGGCGCGGTGGCTCACGCCTG
+TAATCCCAGCACTTTGGGAGGCCAAGATGGGCGGATCACGAGGTCAGGAGATCGAGACCA
+TCTTGGCTAACACCGCGAAACCCCGTCTCTACTAAAAATACAAAAAAATCAGCCGGGCGT
+AGTGGCGGGCGCCTATAGTGCCAGCTACGCCGGAGGCTGAGGCAGGAGAGTGGCGTGAAC
+CCGGGAGGCGGCGCTTGCAGTGAGCTGAGATTGCGCCACTGCACTCCAGCCTGGGCGACA
+GAGCGAGACTCCGCCTCAAAAAAAAAAAAAAAAAAAAAAAAGTTAATCATTTATGTCGTT
+ACATAAATGGGCACTTACACATAGACGTATAGCTCAGAAGGTATATAAGCTCTATAAAAC
+TTTATCATTTTGAGTGGGTCTGGTAATATTATCTACATGCCTTCTCCCTGTAACCACTTG
+TAGAAATAAAAACTCTCTTCCTTCTCAGTTCATCTGCATCTCATTATTGGGCCACAAAAA
+AATAGCAGCCTGACCCTCAATTTGCTCAGGAAAGACAAGGGGACTTGGGAACACTCCTTA
+CACTTCAAAGAGAAGGCTCAAGGCCATTAAGAAAGACCTGTTGGGGTGCCATCCTTCCAT
+CTGGCTTAGTTAGTTCTTAAAAAGATTTACATATACCTCAAAAAACAGAGGGGAAAATAC
+TAGTTTTCTAAAGGTAGTACTCTAATGAAAAGTAGGAGGAAGGATTACTTTCTTACCTGA
+CAACAAGGAAAACTCAAATTACATAGATTTTAGACTTACAAAAATTTTCTGGACAGATAT
+GAAGAACATTATTAAACTAACAAACAGCAATCCAGAACTTTTTTTGTTGTTGTTTTTGCT
+AAACGTATTTGTAGTTCTGTTAATTTCCTTACTGTAATCTACCAACTTTATGTGATCTCT
+GTCTAAAAAGCAGAACTTTCTGGTCATTTCTAAAGAGCATAGAGATTTTAAGGAACATCA
+GCAATATTCAAATTTAAGAAAACTGATTATAACTTAGAAATTCTGAGGAAGAAGAGTAAT
+GAGGGGTAACTTGTTCTAGCAGAAAATCAAGTATATTTTTATAACCACTTTAATTATTTT
+AACTACATACCTTCATTCTGTGGTTAAAATTTAAGACACTAACAGTTCCAAATTTTGGTG
+AGCATGTATAGCAACGGAAAGCTCAGACATTGCTGTGGCAGTGTGAAATAGCACAAAAAC
+CCTGGAAAATTCTTGGAAAGGTACACACAAAATTAACTGAGCTGAAAATTTCACTCCTAG
+ATGTTGGCCCAGGTACATTAAAAACAGATGTCCACTTAGAGACTTGAGCTCAACTGTTGA
+TAGCAGCTTTATTAATAAAAGCCTCAAGCTCAAAATAGCCCAGTGTTCACCACCAACAGT
+GTACATAAACTGTGGTAAATTCATGCAAATTTCAACCTGAATGAAAGAAGCCAGATGCCC
+TTCAGAATACAGCTCCGTTGATATAAAGCCTTGAACTCAGCCGGGCGTGGTGGCTCACGC
+CTGTCATCCCAGCACTTTGAGAGGTCGAGGTGGGCAGATCACGAGGTCAGGAGATCGAGA
+CCATCCTGGCTAACACGGTGAAACCCTGGCTGTACTAAAAATACAAAAAATTATCCAGGC
+GTGGTGGCGGGCGCCTGTAGTCCCAGCTACTAGGGAGGCTGAGGCAGGAGAATGGCGTGA
+ACCGGGAGGCGGAGCTTGTGGTGAGCCTAGATTGGGCCACTGTACTCCATCCTGAGTGAC
+AGAGCAAGACTCTGTCTCAAAAAAAAAAAAAAAAGATCTCTCAATTGCATGATAGAAATC
+ATGCAATTGACAGAGGAATTGCAAAAGGGCACAGGAAATTTTAAGGGTTGAAGGAATGAT
+GTAAATAGCTTGTAACCTAGTTGGGGTGATAGTTACTCAGGCATATGCATTTGCCAAAGT
+TCATGCATCTATAAATAAAAGATCTGTGCACAATATCTCATGAAGATTTTTACTCTTGAC
+ATTATTACATAGTCCAATATGAAATAAAATATTAATTAAATTTCTTGAAATACTAGAACT
+CTGATAACTACCTTTTGTTTCTACACCTTGTAGAAACAAATCTTTGTGGAACAGATTTGG
+AACAAATATGGAAAATTAATGTATTTCACATCAGTAAAATCGTGACATTGGGAAAAACAT
+TACCCACTTCAATGCCTAATGAAATAATGTCTAATCAATCATGAATATCTACATTACTCT
+TCACTAAGATATTTTTTAGATGGAGCAATTACTTTCAGGTTAATAATAGCAAATATTTAG
+TTAATTCTTCACTAATGCTGATGTCTGTTCTAAGTATTTCTTTTTTTCTTTTCTTTTCTT
+TTTTTTTTTTTTTTTTTGTTGAGATGGAGTCTTGCTCTGTCGCCCAGGCTGGAGTGCAGT
+GGCGCCATCTTGGCTCACTGCAAGCTCCATCTACTGGATTCAAGCCCTCTCCTGCCTCAG
+CCTCCCAAGTAGCTGGGACTACAGGCGCCCGCCACCAAGCCTGGCTAATTTTTTGTATTT
+TTAGTAGAGACGGGGTTTCACCATGTTAGCTAGGATGATCTCAATCTCCTGACCTCGTGA
+TCCACCCACCTTGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACTGCTCCCAGCC
+TGTTCTAAGTATTTCTTATATACACTCACTTATTTAATGCTTGTGTACCTTAATTCATGT
+AGCCTTCACATCTCTTCATGGGTTGGTTTTATTAGTAAATAGCATTTCAACTAACAAAAT
+TATTACAGAATTGAAAAAACTGAGACTCAGACAGCGAAGTAAATTGTTCAAGCTCAAGCC
+TGTAAGTGGCACTCAAGTGAGCCAAAGCTGAAGGGTTTACCTTCCAGAGCCTGTGTTCTT
+TATTCAGTACCAAGCTCCCTCTTAATGTATTTTAAGTGTTGGCATTTTAAAATATAGCAA
+ACATCCATTGGCAGCCAAAGCACACTTGATACTTATAGTTAGAATTTGTTTGTTTATTGA
+TGTTTGTTTAAACATCACAAAAATACAAAAATGCTTCATTTCAGTAATTCCTAAGTAAAC
+CATACATAAAGTATCAATTCCTCTCCTGGGAGTGTGCTTCACAGAAATTCTTATAAATGT
+TCTCCATTGTACATGTATAAGAATGTATAAAAAAGCACTGTTTGTAATAATTGAAACCAG
+TAAGTGTCCATTCATTTGTCCAACAAAAATAGAATGAAATACGCACAACAATTTTTTCTT
+AAAAATTCTAGTTTGGGCAGCATATACACTAAAATTAGAATGGTATGGAGAAGAATAACA
+CTGTCCCTGGGCCAGGAGGGTATTCAAATGTGAAGTCTTTCATATTTTTGGGAGTAGAAT
+TGTGGCTACCCTCTAGTAGGGTCAGGTGAAGAGATGAGTATTGTTATTCAAAAATTATAA
+TATTTCATCTAGATAGAAGCAATTAGTTCAGATCTATTGTAAAGCATGTTGAATATAGGT
+AATAAGAATGTATTGTATGCTTGAAAATTGCTAAGAGAATACAATTTAAATGTTCCCAGT
+GCAAAAGGAAAGGGAAGTATATGAGGTAGTAGATACATTAGCTTGATTTAGTCTTTCCAA
+AATGTATACATGCATGATGTCATAATTTTTAATAATCTGAAAACCACCAAAATGTATTAA
+GCAAAAGAAGCTCCACATAATATTTTGTATTTATATTTATTCACATTGTTAAGGAAAAAT
+GGTATTCAGTGATACTTGTTCAAACTTGATAAGGAAGACTATTCACGACCAACAGCACAG
+CAATGAGGTCTTGCACTGGGGGAGAGATTGGCCTTAGCTCCACATACACAGCTGGGTAGG
+TGGGGATTTATAGCCAAGGAGCAGGGAGTAGGGTCAATGGATGGACAATCACTAAGAGAA
+GACATCATAGATAAGGAGGATTCTTGCTGAAGACAGGCTAGGCTGATCAGACATCACCTA
+GAGGGTGGTGGAGGATGAGAAACCTGATCAGATATTGAGGGTGATCGATCAAGTGTTGAG
+TGTGATCAGATATGCGGTGGGGGTACAGTCTGGCTAACCTGGCTTAGGAGAGTTCTTTGC
+CAAAACTGAGTTTGGCAAGGAAGTGCACAGGCGAGTCTAGGAGAAGGTTCAGAAACCTGA
+CTAAAGTTTGGTCAAACAGAGAATCTGTGTCAGAGGTTCAAGAAAAGGAAAATTAATGTA
+TGGTAATGAAGGTCAGAATGGGTGTTATTTTTGGGAGAGTGAAAAGAGTGGTTTTAAATA
+TTACAAAGTAGTTTTGAGTCAGTGTTTAAAAGGTAATGGGCAATATACAGTTCTCATTTG
+GCATAAAGCTCAGATTAAGTAATATTGTCTCTGGAATAAAGCTTTTTTTAAACCCTGAAC
+TTTGAGAAACATGACATCCATCTCTAATATACACTCTTTTAGTGTTTGAGTTTTATTATT
+TAAGGTAATGTCTCTGAAAAGTTTTGAAATATTGGAAAGCTGACTTTGATACATACCATT
+AATTTTGACTTTTGATTTATTTTTATTGTAGAAAAATTTATTTGTAATTTATACTTTAAA
+CTGTGGTTTACAGTTATTTGTAAACTTCTAGTTTCCTGCTTTAGCTTATGTGCAAATTTT
+ATGAAGTCTTGGCATTACATTTTTATTTAAATCCCATCAAATTAAACCAGTTGGGTCACC
+AGCCCCCGCCCTTCCATCTCCATAATCTGGGTAGTCGGCGTTCTCAACATTCCTGTTGAG
+AATGAAAATTCTGTATTTTTCATTCCACAGGCTTAAAAGTTAATAGGCCATGGAAACAAG
+TAGATTGCCATTTTAAAAGATAGTTTTCAGAAGAAAGGCAAAATGATAAGTTTCATAGAG
+ATACAAAAATGACAAGGAATTAAATATTTTGTTTTACCAGAGGCATTTTATAACTAGTTG
+AAAGGAAATGTCAACCGTTTGGATTTATATGGAGTAAAGGAACTGAATTGCAAGTGGAGG
+TAAAACTGGTTTTTTCCACAGCGTGAAGGGGAGAGAAAGAAACAAGTTTGATCCTGCTTA
+CATATCCATTCCTTAGTTACCTGCAATTTATAGACACGTACAAAGTAGCTGAAAGACCAA
+TGAATACACGGTCTAGAGAGGACTGCTTAACACGCTGCATATAGAAGTGTGATTTTTTTT
+GGTACAATTTTCAAGTGTGTTTCTCATTAGAGCATTTAAAGTAAGCCACAGTGTCCGTTT
+GTATCAAGTTAGTACTCTGACGGCCACAAACATAGGCAGGCTCACTTCTGGATGTCTTAT
+TTCTTTGCATGTTAATCGTGTTGACACAACTTGTCTTGAAATTAAGTTTAAAATGAAATA
+CCAGTAAAACTGAAATGAATAAGGCCTTTATTAGCCAGAGAAAAGAAAACAATATTGAAA
+CTAAACATAAGAAAGTGAGGGCTGTAAGTTATCGTAAAAAGGAGCATCTAGGTAGGTCTT
+TGTAGCCAATGTTACCCGATTGTCCTACAGCTTTGTCCAGTGGCTGTAGCGGTCCCGTTG
+CTGCGGTGAGCTGGCTGCGTTGATGGGCGGTAAGTGGCCT

data/test/data/seq_rnd3_transcript.fa ADDED

@@ -0,0 +1,47 @@
+>ENSG00000115963|ENST00000263895
+CAGTCGGCTCGGAATTGGACTTGGGAGGCGCGGTGAGGAGTCAGGCTTAAAACTTGTTGG
+AGGGGAGTAACCAGCCTGCTCCTCTCGCTCTCCTCCTCGTCTGCGCCGCGTTTCAGAGAG
+AAAATTCCTGTTCCAAGAGAAAATAAGGCAACATCAATGAAGGAGAGAAGAGCCAGCCAG
+AAATTATCCAGCAAATCTATCATGGATCCTAATCAGAACGTGAAATGCAAGATAGTTGTG
+GTGGGAGACAGTCAGTGTGGAAAAACTGCGCTGCTCCATGTCTTCGCCAAGGACTGCTTC
+CCCGAGAATTACGTTCCTACAGTGTTTGAGAATTACACGGCCAGTTTTGAAATCGACACA
+CAAAGAATAGAGTTGAGCCTGTGGGACACTTCGGGTTCTCCTTACTATGACAATGTCCGC
+CCCCTCTCTTACCCTGATTCGGATGCTGTGCTGATTTGCTTTGACATCAGTAGACCAGAG
+ACCCTGGACAGTGTCCTCAAAAAGTGGAAAGGTGAAATCCAGGAATTTTGTCCAAATACC
+AAAATGCTCTTGGTCGGCTGCAAGTCTGATCTGCGGACAGATGTTAGTACATTAGTAGAG
+CTCTCCAATCACAGGCAGACGCCAGTGTCCTATGACCAGGGGGCAAATATGGCCAAACAG
+ATTGGAGCAGCTACTTATATCGAATGCTCAGCTTTACAGTCGGAAAATAGCGTCAGAGAC
+ATTTTTCACGTTGCCACCTTGGCATGTGTAAATAAGACAAATAAAAACGTTAAGCGGAAC
+AAATCACAGAGAGCCACAAAGCGGATTTCACACATGCCTAGCAGACCAGAACTCTCGGCA
+GTTGCTACGGACTTACGAAAGGACAAAGCGAAGAGCTGCACTGTGATGTGAATCTTTCAT
+TATCTTTAATGAAGACAAAGGAATCTAGTGTAAAAAACAACAGCAAACAAAAAGGTGAAG
+TCTAAATGAAGTGCACAGCCAAAGTCATGTATACCAGAGGCTTAGGAGGCGTTTGAGAGG
+ATACTCATCTTTTTGGAATCCTGACCTTAGGTTCGGCATGTAGACCAAGTGATGAGAAGT
+GAATACATGGAAGAGTTTTTAAGTGTGACTTGAAAAATATGCCAAAAAATGAGAGATACA
+AATGAGCTAGAGGAAGATGAGGGGGGATGCGAGTACCTCCAAGAAGAAAAATCACACTCT
+GAATGGTGCTTGCATTTTTGGGTTTTTTTTTTTTGTTATAATCTATTCATGGATCTCCAC
+TTTGATTTAATTTTTAAATGTTTTAATCTCCTTTACAAAAAGTATACGTTAATATACCGT
+CCTCAAGGGGGAACTGGCACTGTGACCTTAGCATTTAGTTTTCTAGAGGATGTGATCTAA
+TTTCTTTCTAGCTCATCATTAAAAAGGAAATTGTATCAGGACCCATGGGATATATCCAGA
+GGCAAACTTTATGAGGCTTTGAAATCTTGCCTTCCTGAAGATAGCTGAGTAGGATGGTTC
+TAAGGAAAGCCTTTGCAATCTTGCAAGATTTGTAGACCAGCACTACAAAGATCGCATAGA
+TCAAATAGGAAAAAAAATGTCGATTTTTATTCAGTCTGATGGTTCTGTTCTTCATTGTGA
+TTGTCATTAAAAAGTGGTAAATTGCTCAATGTAATATTTTTGTGCGCTGTTTAGAAGTTG
+TGTGATTTTTTGCCATCGTTGATAAAAATGCAAAGTCAAATAAAAGGTGTCTTGGTTTGA
+TGTCATAGAATGATCCAAGGAGAGAAAAAAGGTAGTTACTGTTTTCACCAGAAAAGGTAA
+TGAGTGAAGGAAAGAATAGTAGCAGAAAGCACAGTTTGTGAGTAAAGCTGTCTGGAATTA
+AGTTACCAAAAATACAAAGCAAAAGGACTATTATTTTGGGTTGAAGCTCCAAAACTGACA
+GCATCTGATAATCTGTTGGTTTATTTCACTTTTCATTAAATGAACATTGATGAGAGAAGA
+TGCCACTTACCCAAGCTTTAGAGAATCCCTAGTGGAAGATTATATGATAAACTTTCAGTC
+CTGACATAACACTAGGGCATTTCTAGAGTGTCATTGCTAAAACCTCACTGAACAGATGCA
+GCCAAGGTCTGTGTTCAGCACTTGGTCTCTGTTGTTACGTAAAATAATAAGCATTTAAAA
+TAGTTTACAGATATTTTTGACCAGTTCCTTTTAGAGATTCTTTCAGAGAAGAAACCAGAT
+CTGACCTGTTTATTGTTGGCGCTTGTTGAAAACGAGCTTTCTTTCCCATGATAGTGCTTC
+GTTTTTGAAGTGTTGAAGCTGTGCTCCCCTTAAATCGTGGCAGGAGAGATTAAGGTAATT
+ACAACACTCAGTTCTATGTCTTACAAGCACTTTGTCTTGTCTCTGCAAGAAAATTCGATT
+CCAGTCATTTCCCATAAAATACAGACATTTTACCAACATAATATGCTTTGATTGATGCAG
+CATTATGCTTTGGGCAGTATTACAAAATAGCTGGCGAGTGCTTTCTGTATTTAAATATTG
+TAAAAAGAAAATAAGTTATAACTGTTATAAAGCAGAACTTTTGTTGCATTTTTTAAACTG
+TTGAAGTCACTGTGTATGTTTGTTTGGTCAATGTTTCCGCAGTATTTATTAAAACATACT
+TTTTTTTTCTTCAAATAAAAAAGTAACCATGTCTTTGTCTAAA

data/test/data/seq_ub2r1_coding.fa ADDED

@@ -0,0 +1,13 @@
+>UB2R1_coding
+ATGGCTCGGCCGCTAGTGCCCAGCTCGCAGAAGGCGCTGCTGCTGGAGCTCAAGGGGCTG
+CAGGAAGAGCCGGTCGAGGGATTCCGCGTGACACTGGTGGACGAGGGCGATCTATACAAC
+TGGGAGGTGGCCATCTTCGGGCCCCCCAACACCTACTACGAGGGCGGCTACTTCAAGGCG
+CGCCTCAAGTTCCCCATCGACTACCCATACTCTCCACCAGCCTTTCGGTTCCTGACCAAG
+ATGTGGCACCCTAACATCTACGAGACGGGGGACGTGTGTATCTCCATCCTCCACCCGCCG
+GTGGACGACCCCCAGAGCGGGGAGCTGCCCTCAGAGAGGTGGAACCCCACGCAGAACGTC
+AGGACCATTCTCCTGAGTGTGATCTCCCTCCTGAACGAGCCCAACACCTTCTCGCCCGCA
+AACGTGGACGCCTCCGTGATGTACAGGAAGTGGAAAGAGAGCAAGGGGAAGGATCGGGAG
+TACACAGACATCATCCGGAAGCAGGTCCTGGGGACCAAGGTGGACGCGGAGCGTGACGGC
+GTGAAGGTGCCCACCACGCTGGCCGAGTACTGCGTGAAGACCAAGGCGCCGGCGCCCGAC
+GAGGGCTCAGACCTCTTCTACGACGACTACTACGAGGACGGCGAGGTGGAGGAGGAGGCC
+GACAGCTGCTTCGGGGACGATGAGGATGACTCTGGCACGGAGGAGTCCTGA

data/test/data/seq_ub2r1_gene.fa ADDED

@@ -0,0 +1,174 @@
+>UB2R1_gene
+GGCAAGCGCCGGTGGGGCGGCGGCGCCAGAGCTGCTGGAGCGCTCGGGGTCCCCGGGCGG
+CGGCGGCGGCGCAGAGGAGGAGGCAGGCGGCGGCCCCGGTGGCTCCCCCCCGGACGGTGC
+GCGGCCCGGCCCGTCTCGCGAACTCGCGGTGGTCGCGCGGCCCCGCGCTGCTCCGACCCC
+GGGCCCCTCCGCCGCCGCCATGGCTCGGCCGCTAGTGCCCAGCTCGCAGAAGGCGCTGCT
+GCTGGAGCTCAAGGGGCTGCAGGAAGAGCCGGTCGAGGGATTCCGCGTGACACTGGTGGA
+CGAGGGCGATCTATACAACTGGGAGGTGGCCATCTTCGGGCCCCCCAACACCTACTACGA
+GGGCGGCTACTTCAAGGTGAGCGCGGCGACCCCCGCCCGGGTCCCGGAGCCCACGAGCGA
+CCTCGGGCGCCGGGAACCAGCTCCCTGCCCCGCGGTCCTAGCGCTGTTGCTGGGCGGGCC
+CCGAAGCCTCCTGGCTTGGGCTCGTTTCCCTTCTATGGCCACGTTCCCCCACCCAGCTCT
+GCCCGGCCCCCTCCTCGGACCGTCTCGGGGACCTTCAGCCTCTGCTGCAGTCCTCGAAAA
+TCCCCAGTTCCCTTCAAGGCATCGTCCGGTCCCCTGTTAGGCTCTTGGCCCCCGGAGGGG
+TGGCCGGGGGCCCTCCCTGTAGCATCTGGGCGTGGGGCTCTTGCCCACCTCCTCCTTGGC
+GGGGGCTGGACCCCGGCTGCCTCCCCCTCCGCCCCTGCGAGAAAGAGGGAGCGGAGCCCA
+GGCCGCGCCGGCCTTTCAGCTGCCCTCCCCGCCCTCCCCGGAGGAGACAAAGAGGCCCCC
+CCAGACCCCGTAGCTGCTATTGTTGGGGAGCTGGGCCCGTGAGCGGGGGAGCGAGGCCAG
+CCTGGGGGTGGCTGGCGCGGCCACTCGCTCAGTCTCCAACAAAGGCCCGGATGAGCCTTG
+GCAGCCAGGACCCGCCTGGAAAGCGGCCACCCTTGCCAGTAGCAGCCGGCCAGGCGCCCT
+GGGCTCCATCCCCTGCTTTATGTAACCTGCGCCCTCGGGAAGGCCGAAGTAGGGGCGTGC
+CTCCCACCTGCTCCCTGCAGCTCTCTCCAGGCCTCCCGGCTCGGGCCCGCGTCCCGGACC
+CCGACCTCAGAAGCTCCGGGCTCGCTCATCCCAGCTGGTCTTGGCCTTTCTCAGAGTCCA
+CTGAACAGGTGGCTTCTTGGGACCCAAACCCCGAGTTCTGGGCCGTTTCTTCTGCCCTCT
+GGCGGTTTAATTCCAAGCAGTTTCTGGATGTTTTTGTTGTTGTTGGGAGCGGGGAGGCTG
+TTTCTGTCTCATGTGAAAAGGACTCAGGCCAAAACCAGGGCAGTTTTCTTGATCTCACGA
+TCCAGACGTGACCTTTGACTTCTTTTAGCGTTCAGGGACCTCGTTCTTGGGGCCAGAGGG
+ACAAAGCGAGGGGCCCTGTGTGAGCGGTGGGGAACGAGCACCCTGTCCAGGAATCTCCCC
+CTCCCACCGTCACTTCCTGCCAAGAGCCTGGACACGACACGACACTGCAGGGCCCGGCCC
+GCTCTGCCCCGGCCAGCTGCGGGCGTGGGGCCGAGGGACCGATGCCTCCCGCACGATATG
+TGTCTGCTCTCCGAGCTAATTAGTGTCTGAACCGCACCCGCTCAGCGGCTGTGAGGGCAG
+CAGCCTGGTCTGCTGGGGGCGATTCCTGAGCAGAGAGTGGGACGCCCGTGGGTTCTGCAT
+CTGGAATCCTGCGTCCCCACACAGGGAACAGAGTTTGGGTCTCGAGGTTGCCAAATGGTT
+TTAGCAGCTCCTCCGCCAGCCCCTTCTGTCTGCTTGGGGGAGCAGCTGGCTGAGGAGCCG
+CAGCCCCACCTCGAAGCCAGGCCTGTGAGGCGGCTGCTGTTCTGGAAGGAGGGGATGGGG
+GTTTCTGGCTGCTGTGCCCACCAGACCGGTTGCCAGGGATTGTGGGCAGAGCTTCCTGGG
+CCAGCATTAGGGGATAATCCGGTTTTCCGGATTTCCCAGGGAGGGGGCCTCTAGACATCT
+GCCACAGGGTCAGTCCTCAGAAGCCAGTGTTGAGACGGGGGTGCTGCCACCCACGAGGAC
+TCTCCCTTCCCGCTGTGCCTGGGAGGGAGTTGGGGGAGCGTGGAAATACAGAACCTGCTG
+AGTGCCCAGGGCCGCTGCTGCCCAGCCACTGCCTGCAGCTGCTGTTCCTTCAGGAGCCAA
+AGTGAGCCCTGGGGCAGGGGCCGCCAGAGAGAGCCCTCCACAGCCGACTTGCTGTCTGCC
+CTTGGCAGGGCGCTTTCCTTTTCTGAGCCTGGGTTTGCTCCGGGGAAAAGACATTCTTAG
+AGGTGCCCAAAATAAGAGGCTCATTGGGACTTGGTGGGGTTTGGTACAGATGAGGCCTTG
+GCTGTTGTCAAGGATTGCCGCCTGAAACCCAGCACCAGGCTTGGGGGGCCTGAAGTCTTG
+GGGAACCGCAGGACAGTTCTGAGACTGAAGTTCCAGCCTTGCTCTGTGGCCGCGGCCAAG
+TCACTTGCCTTACGGGGCACCAGTGAGTTCCCTGTCAAACAGAGGACACCCCCCAAGACA
+CCCCGCGTGCCCTCCCTGTCCAGGAGGGGCCCGTCCACGATCCAAGACCCCCAAAGTGCC
+CTGCCTGTCCGGGAGGGGCCTCGCCCACAATCCAAGACCCCCGAGTACCCTCCCTGTCCA
+GACCTCGCCCACGATCCAAGACCCCCTGAGTGCCCTCCCTGTCCAGACCTCACCCACGAT
+CCAAGACCCCCTGAGTGCCCTCCCTGTCCAGACCTCGCCCACAATCCAAGACCCCCGAGT
+ACCCTCCCTGTCAAGGCCTCGCCCACGATCCAAGACCCCCGAGTGCCCGCCCTGTCCAGA
+CCTCGCCCACGATCCAAGACCCCCGAGTGCCCTCCCTGTCCAGACCTCGCCCACGATCCA
+AGACCCCCGAGTGCCCTCCCTGTCCAGACCTCGCCCACGATCCAAGACCCCCGAGTGCCC
+TCCCTGTCCAGACCTCGCCCACGATCCAAGACCCCCGAGTGCCCTCCCTGTCCAGACCTC
+GCCCATGATCCAAGACCCCCGAGTGCCCTCCCTGTCCAGACCTCGCCCACGATCCAAGAC
+CCCCTGAGTGCCCTCCCTGTCCAGACCTCGCCCACGATCCAAGACCCCCTGAGTGCCCTC
+CCTGTCCAGGCTTCCACCACGATCGCTCTGGGGGTGCTGCTCTCGTGCCTTGGAGTGCTG
+AGTGCCACCAGGACCCCTGACCCAGACAACCTCTGTGTCTGGCACTGGGGCCCAGCAGGA
+AAACAGTGAGGCTTCCTTGTTTACCTGCTGTGGCCCAGGAGGGCCGTGGGTGGCATCACG
+CCCCAGGCTGCAGGCCAGACAGCTCTGTCACCTGGCACGTGGCTTCAGGCCTCCCTCTGT
+GGCCGTCCTTGCCAGCAGATCTGGACCTCCAGGGCCTGGGTGACCACAGGGGGCGATGCT
+GACAGGGAAGGAGTCCTGCCAGGTTTCTGTGACCTATGGGTCTGCCTGCCTGACCCCCCA
+AGACCGGACACCTGAGGGCAGACGGCCATACTGACTCATCCCCTCCCACGGCCTGGGCCA
+GGGCAGGTGTCACAAGTGTTTGCTAACTGAGCAATCATCTGTGCTAACCCTCCCCACACC
+CTGGCTGCCAAGGCCCTGGAGGTGCAGCCCTGGTCCTGGGCTTCAGCTCCATCCAAGGGG
+AGCCTGGAGCCCCTGCCAGTCCATTCTGTCTGCTGGTGGGTGCCCCTGGCCTGGGTCCCA
+TATGCCTGACCTGGGCTGCCACGGGCCTGGAGCCACGCGGGCAGCCAGTGCCCACGTTCC
+CCAGCAGTTGTGCTGGGCCGGGTCCCGGCCACCTGGACTGTGTAGGAGCTGGGATCAGCT
+CGGGTGACTCAGAAAAGGCTTCAGGCAGCCTTCTGGGGACTTGACCCCAGGCCTGTGAGA
+GTCCCTGCCTTGGGCAGGATACGGTGTCCCTCACACACACCCTCAGGCACCAGCACTGGG
+AGTGGGATGGCCTTGGGCACCTTGTGAGCTGGGGCAGGTCTTGGGGCTGGGCTGGACTGA
+GCCACCTGCCTTCTGCCCCTGCAGGCGCGCCTCAAGTTCCCCATCGACTACCCATACTCT
+CCACCAGCCTTTCGGTTCCTGACCAAGATGTGGCACCCTAACATCTACGAGGTGAGCGCG
+GCCCCCACGGGCCTCAAGTCCTCATCCTCCGGGACCCAGGGTGCTGGGAGCCTCACGTCC
+TCATCCTTCCGGGACCCGGGGCGCTGGGAGCCTCACGTCCTCGTCCTCCGGGACCCGGGG
+CGCTGGGAGCCTCACGTCCTCGTCCTTCCGGGACCCGAGGCGCTGGGAGCCTCATGTCCT
+CGTCCTTCCGGGACCCGGGGCGCTGGGAGCCTCACGTCCTCGTCCTCCACGTCCTCATCC
+TCCGGGACCTGGGGCACTGGGAGCCCGTGCTGACCTCTGACCTGTTCTGACCTGTCTTCT
+TCTTGTGCAGACGGGGGACGTGTGTATCTCCATCCTCCACCCGCCGGTGGACGACCCCCA
+GAGCGGGGAGCTGCCCTCAGAGAGGTGGAACCCCACGCAGAACGTCAGGTAAGCCGGCCC
+AACCCCCTGTGTCCACCCAGAACATCAGGTAGGCCGGGCTCCGTCCCGTATCCACCCAGA
+CCATCAGGTAGGCCGGGCTCCCCCACAGGCTGTGGCGCCAAGGCCTGATTCGGGACCTGC
+CAGCTGGCGGTCCTGGGCCTCGCTGTACCTGCACGGTAGGTGCTTTCACGGGGCCTGCGG
+CACCGTGTGTCGGTGCAGACTCCCACCAGGACCCCAGGCCGGCCCCACCGTCTGGAACCA
+CCTAGAGGTGTCCCGCCATCCTCAGTCCTGGGGCCTTCTCCTTACCCAGCCGTCTCTGGG
+TTGGTCACCTCGTGCCACGTGTGCCGCCTGGGCCTCGTCCCCAGGTACAAGCACTGGGCC
+GTGTTGCCCGTGTGTCCTGGAGTGTAGTCTAGGCAGGACGTGCGGGTGTGAGGGCAGCCC
+CGGGTCTGACGGAGGGGTCTGCACCTTGCTGCCCTCCCTGGTCTTGGCGTGGGAGGGAGG
+AGACTGATGCAGGTCCAGCCCCTGCTGTTCTGGGGGCCTGAGACAGAAGCAGAGGCCATG
+AGGCCAGGTGAAGGTCACCTGCTGGGTGGGTCCAGGCGTCCCCGTGACCCTCAGGGCCAG
+AGAAGAGCCGGAAGGCTGGGGTGCCCCGGGCCGCCCCACTCCGACCCACTCTCCCCACAG
+GACCATTCTCCTGAGTGTGATCTCCCTCCTGAACGAGCCCAACACCTTCTCGCCCGCAAA
+CGTGGACGCCTCCGTGATGTACAGGAAGTGGAAAGAGAGCAAGGGGAAGGATCGGGAGTA
+CACAGACATCATCCGGTGAGGGCGGGCGGGGGCGTCACGGGAGGAGAGACTCAGATCCGG
+CCTGCACCCCGGCCCCTGGTCCCACGGCCGCCCAGCCCCACCTTCCTGGTGAGGGTGGCG
+GAGCTTCCTGGTGCCCATTTACAGGGTGCCAGTCACAGATGGAGGCCGGGCCGAGTGGCG
+GAGGGTCCAGCCAGGTTCAAGCCCAGCTTCTTGCCCCTTTTCCTCTTTTTTTTTGTTTGA
+GACAGAGTCTCTCTCTGTCACCCAGGCTGGAGTGCAGTGGCGCGATCTCGGCTCACTGCA
+AGCTCCGCCTCCCGGGTTCACGCCATTCTCCTGCCTCAGCCTCCCAAGTAGCTGGGACTA
+CAGGCGCCCGTCACCACGCCCGGCTAATTTTTTGTATTTTTAGTAGAGACGGGGTTTCAG
+CGTGTTAGCCAGGATGGTCTCGATCTCCTGACCTCGTGATCCATCTGCCTCGGCCTCCCA
+AAGTGCAGGGATTACAGGCGTGAGCCACCGCGGCCGGCCTTTTTTTTTTTTTTTTTTTTT
+GGAGACAGAGTTATACTCTCTTGCCTAGGCTGCAGTGCAGTGGTGCGATCTCGGCTCACT
+GCAGCCTCCACTACTCGGGTTGGAGCAGTTCTCCCCCTTCATCCTGCCAAGCAGCTGGGA
+TTACAGGTGCCCACTACCACGCCGAGCTAATTTTTGTAATTTTTAGTAGAGGTGGGATTT
+CACCATCTTAGCCAGGCTGGTCTCAAACTCCTGACCTCAGGTGATCCACCCGCCTCGGCC
+TCCCAAAGTGCTGGGATGACAGGCGTGAGCCACTGCACCTGGCCTGGTGGTTAGTGTTTT
+CATAGATTCTTCCAGGCTTTTCAGTTTAACGCATGTCTGTGCTTTAATGAAGAAATGGGG
+TCGTGCTGTGTGTGCCCAGTGACTGACTGTTAGGGAACATGTGTCTGTGCCTTAATGAAG
+AAATGGGGTCGTGCTGTGTGTGCCCAGTGACTGACTGTTAGGGAACATGTGTCTGTGCTT
+TAATGAAAAAATGGGGTCGTGCTGTGTGTGCCCAGTGACTGACTGTTAGTCAGGGGTGTT
+GGCCTTACTCATGTCTGGAGTGCGTCCCTGCAGGCTCTTGGCCTGGTGAGCTCTGGGTAC
+AGCTGTGCAGTCGCCTACCGGCGCCTTCTGTACCTGCAGTCCACTTAGCTTGCGTGGCTG
+TGTGTGGTGACCCACGGCTCTCCCTCTCCTCCCATCGCCCTCATGCCCCAGAGCTGAGCC
+CCACAGCCCCTTCTCTTGGGTGCCTGTGTTCACATGAATGTGTAAACACGTGCGTGTCTG
+TGTACAAAGACAAGGCTTTCTTTACGGGTTGACGGCCTTAATGGTTCCTGCTCTTCCTGT
+TACATAGAGGCCCTTCCTATCCATTTTTTTTTTTTCTCAGAGTGATATTGCATAGATTTC
+CTCACAGAGGCCTCACCTATTTTTGTTGGTATTTTGTATAAACAGAATCTTAAAAACAAC
+TTTTAAAATATTGCACACATAATGCATGTGTCTTCCTCGCCCCAGGACCCAGGAGCATCC
+AGGGCACCTTCCATCCTGCACTCGCTGGTACCTGGTGTCGTGGGGTCATCTCGGGGCAGC
+ATCCTGGTGCTGGGCGGTCTCGGCTCTGAGCAGCCATGGTGGGCGGGCCCCGTGCGGCCT
+CCTGGGAAGTGGCCTGCAAGCACCTGCTGGCCTCTGGAGGTCACAGGGTAGCTGCCCTGG
+CCGTCCCTCTGGTGCAGATGTCCTCGGTGGCCCCGGTCCGGTCGTGTCACCTGGCCCAGG
+TGGCTGGCTCCTTGGCCCGGTTCTTCCCGGCCACCTCCCTGAGGCACCACCTCCTTGAGA
+TCCCAGCACAGAAATAAAAGCCACACTATTTTTATCCCTCAAAACTCCCTGTGGGCCAAC
+ACACATGTGCCATGTGGACTCTGCTGTGGTCGCCGTTTCTGCCTGTTTTTTCATCTGTGT
+GCGTGTTGGCCTCGTGGCAGCCCAAGTCCCGCTGAGCTGTGTCGGGCAGGCTGCCGTGGA
+GCCCGGCTTGGTCAGGGATGTTGGTCTTGCTGAACAGGACCTCCAGACCGTCCTCCAGCT
+CATGCTGGCGGTGTGCCGGCGGCACCTCCACGGTGCAGGTCAGTTCCCACCCTGGCCCTC
+CCCTGCGTCTCCCCACAGCCGCCACCTCTGCGGTGCCGTCCCCGGGGCACCGTCACCCCC
+CCAGCCCGTCCACCCTGGCCCTCCCCTGCGTCTCCCCACTGCTGCCACCCGTGCAGTGCC
+GTCCCCGGGGCACTGTCAGTCACCCCCCCAGCCCATCGGAGAGCTTGGAAAGCAAAGCTT
+GGCGTCCGCTGGGTCCCGCCACCCAGGGACGTCCCTGAGGCCAGACGCCTGCCCTCCACG
+CGTCATGCATCCCCATAAAAAGCACTGGGCTTGTGGGCTGGGCTTGGGGCTGTCTGTCTG
+CTCCCTGGTGCCCTCCCATGCGGGCACTGTGGGACCCGCACACCCTGGTAGCAGCCAGCC
+CCAGAGCCCAGAGCCGTGCCTGGTCGGTGATAGGGGCTCGAGCCCATTGCCTGCGGCTGC
+AGCCTCGTTCCTGTTTTCTGTCAAATGGGGTCAGCGTGCCGCCTGGCCCTGCTGTGCCAC
+CCCCGGAAGCCCCTTTGCTTCCAGTCCTGGGGGGACATTCTTGACGCGTGTCCTGGAGGT
+GGAGCCGGGGGCAGGTTCCTCGTAGGTCCTGGTGTGCGCGGTGCAGCCCCTCATAGGGCC
+GGGTGTACACGGTGCCCTCCAGGAAGTTTGAGCTAACTTGTCCTCCCTTCCTGCCAGAGG
+CTGGGATGGCCAGGCCCCCCAGGTTTAGAATCCGGAGGCCGGGGTGGCCAGGCCCCCAGG
+TTTAGAATCCGGAGGCCGGGGTGGCCAGGCCCCCCACGTTTAGAATCCGGAGGCCGGGGT
+GGCCAGGCCCCCCAGGTTTAGAATCCGGAGGCCGGGGTGGCCAGGCCCCCCACGTTTAGA
+ATCCGGAGGCCGGGGTGGCCAGGCCCCCCGGGTTTAGAATCCGGAGGCCGGGGTGGCCAG
+GCCCCCCGGGTTTAGAATCCGGAGGCCGGGGTGGCCAGGCCCCCCGGGTTTAGAATCCGG
+AGGCCGGGGTGGCCAGGCCCCCCGGTTTAGAATCCGGAGGCCGGGGTGGCCAGGCCCCCC
+GGGTTTAGAATCCGGAGGCCGGGGTGGCCAGGCCCCCCGGGTTTAGAATCCGGAGGCCGG
+GGTGGCCAGGCCCCCCGGGTTTAGAATCCGGAGGCCGGGGTGGCCAGGCCCCCCGGGTTT
+AGAATCCGGAGGCCGGGGTGGCCAGGCCCCCCGGGTTTAGAATCCGGAGGCCGGGGTGGC
+CAGGCCCCCCGGGTTTAGAATCCGGAGGCCGGGGTGGCCAGGCCCCCCGGGTTTAGAATC
+CGGAGGCCGGGGTGGCCAGGCCCCCCGGGTTTAGAATCCGGAGGCCGGGGTGGCCAGGCC
+CCCCGGGTTTAGAATCCGGAGGCCGGGGTGGCCAGGCCCCCCGGGTTTAGAATCCGGAGG
+CCGGGGTGGCCAGGCCCCCCACGTTTAGAATCCGGAGGCCGGGGTGGCCAGGCCCCCGGG
+TTTAGAATCCGGAGGCTGGGATGGCCAGGCCCCCGGGTTTAGAATCCAGAGGCTGGGATG
+GCCAGGCCCCCCGGTTTAGAATCCGGAGGCCGGGGTGGCCAGGCCCCCGGGTTTAGAATC
+CTGCTGAGGCCACGGAGAGGCTCAGGCCGTTTTTGCGTTTCCCATCTCACCTGTGCTGGT
+TCCCGTCTCCAGGGATGGTCCTGCCTCCTGTCCTTGGGCCCTCCCAGCTGCTTCCTTTGC
+TCCTGCGCTGAGGAAGGCTTTTGCCCCCCAGTGGGGCAGCATGGGCCCTCCCTGTTGCCG
+GCATCGTTATTTTCTCCCAGCTCCTGATGGGTCCCTTGGGTTGTGCTTCGGGGCGGGGCA
+GGCGGGTGTGACTGCACTGCGCCCGTCCAGCCTCCCACCCGCACCTCCTGCCCTTCCCGA
+GCCCCCTCCTCTGTCATTTCTCCCCCTGGAGTTCCTCACGCACAGGGCTTTGTCCTAAGT
+GGTCGCCACACGCCGTTTTAAGAGAAACCTGAGCGTTGGGGTGAGCGTCGGACCTGGGGG
+AGGGGGGCCGGGCAGGGGCCGAGTCCAGGCACGTGGGTGGCGCCCTCACCCACCCTGTCC
+CCCCAGGAAGCAGGTCCTGGGGACCAAGGTGGACGCGGAGCGTGACGGCGTGAAGGTGCC
+CACCACGCTGGCCGAGTACTGCGTGAAGACCAAGGCGCCGGCGCCCGACGAGGGCTCAGA
+CCTCTTCTACGACGACTACTACGAGGACGGCGAGGTGGAGGAGGAGGCCGACAGCTGCTT
+CGGGGACGATGAGGATGACTCTGGCACGGAGGAGTCCTGACACCACCAGAATAAACTTGC
+CGAGTTTACCTCACTAGGGCCGGACCCGTGGCTCCTTAGACGACAGACTACCTCACGGAG
+GTTTTGTGCTGGTCCCCGTCTCCTCTGGTTGTTTCGTTTTGGCTTTTTCTCCCTCCCCAT
+GTCTGTTCTGGGTTTTCACGTGCTTCAGAGAAGAGGGGCTGCCCCACCGCCACTCACGTC
+ACTCGGGGCTCGGTGGACGGGCCCAGGGTGGGAGCGGCCGGCCCACCTGTCCCCTCGGGA
+GGGGAGCTGAGCCCGACTTCTACCGGGGTCCCCCAGCTTCCGGACTGGCCGCACCCCGGA
+GGAGCCACGGGGGCGCTGCTGGGAACGTGGGCGGGGGGCCGTTTCCTGACACTACCAGCC
+TGGGAGGCCCAGGTGTAGCGGTCCGAGGGGCCCGGTCCTGCCTGTCAGCTCCAGGTCCTG
+GAGCCACGTCCAGCACAGAGTGGACGGATTCACCGTGGCCGACTCTTTTCCCTGCTTTGG
+TTTGTTTGAAATCTAAATAAAACTACTTTATG

data/test/data/seq_ub2r1_transcript.fa ADDED

@@ -0,0 +1,26 @@
+>UB2R1_transcript
+GGCAAGCGCCGGTGGGGCGGCGGCGCCAGAGCTGCTGGAGCGCTCGGGGTCCCCGGGCGG
+CGGCGGCGGCGCAGAGGAGGAGGCAGGCGGCGGCCCCGGTGGCTCCCCCCCGGACGGTGC
+GCGGCCCGGCCCGTCTCGCGAACTCGCGGTGGTCGCGCGGCCCCGCGCTGCTCCGACCCC
+GGGCCCCTCCGCCGCCGCCATGGCTCGGCCGCTAGTGCCCAGCTCGCAGAAGGCGCTGCT
+GCTGGAGCTCAAGGGGCTGCAGGAAGAGCCGGTCGAGGGATTCCGCGTGACACTGGTGGA
+CGAGGGCGATCTATACAACTGGGAGGTGGCCATCTTCGGGCCCCCCAACACCTACTACGA
+GGGCGGCTACTTCAAGGCGCGCCTCAAGTTCCCCATCGACTACCCATACTCTCCACCAGC
+CTTTCGGTTCCTGACCAAGATGTGGCACCCTAACATCTACGAGACGGGGGACGTGTGTAT
+CTCCATCCTCCACCCGCCGGTGGACGACCCCCAGAGCGGGGAGCTGCCCTCAGAGAGGTG
+GAACCCCACGCAGAACGTCAGGACCATTCTCCTGAGTGTGATCTCCCTCCTGAACGAGCC
+CAACACCTTCTCGCCCGCAAACGTGGACGCCTCCGTGATGTACAGGAAGTGGAAAGAGAG
+CAAGGGGAAGGATCGGGAGTACACAGACATCATCCGGAAGCAGGTCCTGGGGACCAAGGT
+GGACGCGGAGCGTGACGGCGTGAAGGTGCCCACCACGCTGGCCGAGTACTGCGTGAAGAC
+CAAGGCGCCGGCGCCCGACGAGGGCTCAGACCTCTTCTACGACGACTACTACGAGGACGG
+CGAGGTGGAGGAGGAGGCCGACAGCTGCTTCGGGGACGATGAGGATGACTCTGGCACGGA
+GGAGTCCTGACACCACCAGAATAAACTTGCCGAGTTTACCTCACTAGGGCCGGACCCGTG
+GCTCCTTAGACGACAGACTACCTCACGGAGGTTTTGTGCTGGTCCCCGTCTCCTCTGGTT
+GTTTCGTTTTGGCTTTTTCTCCCTCCCCATGTCTGTTCTGGGTTTTCACGTGCTTCAGAG
+AAGAGGGGCTGCCCCACCGCCACTCACGTCACTCGGGGCTCGGTGGACGGGCCCAGGGTG
+GGAGCGGCCGGCCCACCTGTCCCCTCGGGAGGGGAGCTGAGCCCGACTTCTACCGGGGTC
+CCCCAGCTTCCGGACTGGCCGCACCCCGGAGGAGCCACGGGGGCGCTGCTGGGAACGTGG
+GCGGGGGGCCGTTTCCTGACACTACCAGCCTGGGAGGCCCAGGTGTAGCGGTCCGAGGGG
+CCCGGTCCTGCCTGTCAGCTCCAGGTCCTGGAGCCACGTCCAGCACAGAGTGGACGGATT
+CACCGTGGCCGACTCTTTTCCCTGCTTTGGTTTGTTTGAAATCTAAATAAAACTACTTTA
+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 @@
+#
+# = test/unit/test_connection.rb - Unit test for Ensembl::Core
+#
+# Copyright::   Copyright (C) 2009
+#               Jan Aerts <http://jandot.myopenid.com>
+#               Francesco Strozzi <francesco.strozzi@gmail.com>
+# License::     Ruby's
+#
+# $Id:
+require File.expand_path File.join(File.dirname(__FILE__),"../helper.rb")
+class TestConnection < Test::Unit::TestCase
+  def test_remote_core_connection
+    assert_nothing_raised do
+      Ensembl::Core::DBConnection.connect('Homo sapiens',56)
+    end
+  end
+  # This is to check if the overwrite of the default parameters is possible,
+  # so you can specify an Ensembl database on a host that is different from the official Ensembl website.
+  def test_local_core_connection
+    # Change username, password, host and port in order to test the connection with a different Ensembl db server
+    assert_nothing_raised do
+      Ensembl::Core::DBConnection.connect('Homo sapiens',56,:username => "anonymous",:host => "ensembldb.ensembl.org", :port => 5306)
+    end
+  end
+  def test_remote_variation_connection
+    assert_nothing_raised do
+      Ensembl::Variation::DBConnection.connect('Homo sapiens',56)
+    end
+  end
+  def test_local_variation_connection
+    # Change username, password, host and port in order to test the connection with a different Ensembl db server
+    assert_nothing_raised do
+      Ensembl::Variation::DBConnection.connect('Bos taurus',56,:username => "anonymous",:host => "ensembldb.ensembl.org", :port => 5306)
+    end
+  end
+  def test_connection_ensembl_genomes
+    assert_nothing_raised do
+      Ensembl::Core::DBConnection.ensemblgenomes_connect('Staphylococcus aureus MRSA252',7)
+    end
+  end
+  def test_manual_connection_ensembl_genomes
+    assert_nothing_raised do
+      Ensembl::Core::DBConnection.connect("Bacillus collection",7, :host => "mysql.ebi.ac.uk", :port => 4157)
+    end
+  end
+end