genevalidator 1.6.12 → 2.1.3

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Files changed (91) hide show
  1. checksums.yaml +5 -5
  2. data/.gitignore +30 -1
  3. data/.ruby-version +1 -0
  4. data/.travis.yml +13 -12
  5. data/Gemfile +4 -1
  6. data/Gemfile.lock +135 -0
  7. data/README.md +104 -122
  8. data/Rakefile +377 -5
  9. data/aux/gv_results.slim +155 -0
  10. data/aux/html_files/css/gv.compiled.min.css +8 -0
  11. data/aux/{files → html_files}/css/src/bootstrap.min.css +0 -0
  12. data/aux/{files → html_files}/css/src/font-awesome.min.css +0 -0
  13. data/aux/{files → html_files}/css/src/style.css +0 -0
  14. data/aux/{files → html_files}/fonts/FontAwesome.otf +0 -0
  15. data/aux/{files → html_files}/fonts/fontawesome-webfont.eot +0 -0
  16. data/aux/{files → html_files}/fonts/fontawesome-webfont.svg +0 -0
  17. data/aux/{files → html_files}/fonts/fontawesome-webfont.ttf +0 -0
  18. data/aux/{files → html_files}/fonts/fontawesome-webfont.woff +0 -0
  19. data/aux/{files → html_files}/img/gene.png +0 -0
  20. data/aux/html_files/js/gv.compiled.min.js +1 -0
  21. data/aux/{files → html_files}/js/src/bootstrap.min.js +0 -0
  22. data/aux/{files → html_files}/js/src/d3.v3.min.js +0 -0
  23. data/aux/{files → html_files}/js/src/jquery-2.1.1.min.js +0 -0
  24. data/aux/{files → html_files}/js/src/jquery.tablesorter.min.js +0 -0
  25. data/aux/{files → html_files}/js/src/plots.js +1 -1
  26. data/aux/{files → html_files}/js/src/script.js +0 -0
  27. data/aux/{files → html_files}/json/.gitkeep +0 -0
  28. data/bin/genevalidator +393 -56
  29. data/exemplar_data/README.md +60 -0
  30. data/{data/mrna_data.fasta → exemplar_data/mrna_data.fa} +1 -1
  31. data/{data/protein_data.fasta → exemplar_data/protein_data.fa} +0 -0
  32. data/genevalidator.gemspec +35 -20
  33. data/install.sh +92 -0
  34. data/lib/genevalidator.rb +171 -56
  35. data/lib/genevalidator/arg_validation.rb +26 -55
  36. data/lib/genevalidator/blast.rb +44 -99
  37. data/lib/genevalidator/clusterization.rb +18 -22
  38. data/lib/genevalidator/exceptions.rb +17 -17
  39. data/lib/genevalidator/ext/array.rb +21 -4
  40. data/lib/genevalidator/get_raw_sequences.rb +32 -31
  41. data/lib/genevalidator/hsp.rb +31 -2
  42. data/lib/genevalidator/json_to_gv_results.rb +38 -122
  43. data/lib/genevalidator/output.rb +158 -172
  44. data/lib/genevalidator/output_files.rb +134 -0
  45. data/lib/genevalidator/pool.rb +2 -5
  46. data/lib/genevalidator/query.rb +1 -1
  47. data/lib/genevalidator/tabular_parser.rb +8 -29
  48. data/lib/genevalidator/validation.rb +48 -90
  49. data/lib/genevalidator/validation_alignment.rb +64 -75
  50. data/lib/genevalidator/validation_blast_reading_frame.rb +13 -9
  51. data/lib/genevalidator/validation_duplication.rb +85 -84
  52. data/lib/genevalidator/validation_gene_merge.rb +46 -35
  53. data/lib/genevalidator/validation_length_cluster.rb +18 -15
  54. data/lib/genevalidator/validation_length_rank.rb +19 -15
  55. data/lib/genevalidator/validation_maker_qi.rb +13 -12
  56. data/lib/genevalidator/validation_open_reading_frame.rb +16 -13
  57. data/lib/genevalidator/validation_report.rb +1 -1
  58. data/lib/genevalidator/validation_test.rb +1 -1
  59. data/lib/genevalidator/version.rb +1 -1
  60. data/test/overall.rb +1 -1
  61. data/test/test_all_validations.rb +36 -24
  62. data/test/test_blast.rb +39 -24
  63. data/test/test_clusterization_2d.rb +4 -4
  64. data/test/test_helper.rb +2 -2
  65. data/test/test_query.rb +16 -20
  66. data/test/test_validation_open_reading_frame.rb +122 -122
  67. data/test/test_validations.rb +12 -10
  68. metadata +94 -79
  69. data/aux/files/css/genevalidator.compiled.min.css +0 -16
  70. data/aux/files/js/genevalidator.compiled.min.js +0 -28
  71. data/aux/json_footer.erb +0 -8
  72. data/aux/json_header.erb +0 -19
  73. data/aux/json_query.erb +0 -15
  74. data/aux/template_footer.erb +0 -8
  75. data/aux/template_header.erb +0 -19
  76. data/aux/template_query.erb +0 -14
  77. data/data/README.md +0 -57
  78. data/data/mrna_data.fasta.blast_tabular +0 -3567
  79. data/data/mrna_data.fasta.blast_tabular.raw_seq +0 -53998
  80. data/data/mrna_data.fasta.blast_tabular.raw_seq.idx +0 -5440
  81. data/data/mrna_data.fasta.blast_xml +0 -39800
  82. data/data/mrna_data.fasta.blast_xml.raw_seq +0 -2554
  83. data/data/mrna_data.fasta.blast_xml.raw_seq.idx +0 -3127
  84. data/data/mrna_data.fasta.json +0 -1
  85. data/data/protein_data.fasta.blast_tabular +0 -3278
  86. data/data/protein_data.fasta.blast_tabular.raw_seq +0 -61295
  87. data/data/protein_data.fasta.blast_tabular.raw_seq.idx +0 -4438
  88. data/data/protein_data.fasta.blast_xml +0 -26228
  89. data/data/protein_data.fasta.blast_xml.raw_seq +0 -9803
  90. data/data/protein_data.fasta.blast_xml.raw_seq.idx +0 -1777
  91. data/data/protein_data.fasta.json +0 -1

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