biointerchange 1.0.1 → 1.0.2

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 (54) hide show
  1. checksums.yaml +4 -4
  2. data/.travis.yml +2 -4
  3. data/Gemfile +2 -3
  4. data/README.md +36 -22
  5. data/VERSION +1 -1
  6. data/examples/Felis_catus.gvf.gz +0 -0
  7. data/examples/Felis_catus_incl_consequences.vcf.gz +0 -0
  8. data/generators/rdfxml.rb +1 -1
  9. data/generators/tsv2rubyclass.rb +31 -0
  10. data/lib/biointerchange/core.rb +17 -5
  11. data/lib/biointerchange/genomics/gff3_rdf_ntriples.rb +591 -137
  12. data/lib/biointerchange/genomics/gff3_reader.rb +16 -3
  13. data/lib/biointerchange/genomics/gvf_reader.rb +1 -1
  14. data/lib/biointerchange/genomics/vcf_feature.rb +46 -0
  15. data/lib/biointerchange/genomics/vcf_feature_set.rb +14 -0
  16. data/lib/biointerchange/genomics/vcf_reader.rb +238 -0
  17. data/lib/biointerchange/gfvo.rb +689 -553
  18. data/lib/biointerchange/life_science_registry.rb +3595 -0
  19. data/lib/biointerchange/textmining/text_mining_rdf_ntriples.rb +33 -35
  20. data/lib/biointerchange/writer.rb +11 -16
  21. data/make.sh +4 -0
  22. data/spec/exceptions_spec.rb +1 -7
  23. data/spec/gff3_rdfwriter_spec.rb +2 -16
  24. data/spec/gvf_rdfwriter_spec.rb +2 -19
  25. data/spec/phylogenetics_spec.rb +1 -13
  26. data/spec/text_mining_pdfx_xml_reader_spec.rb +1 -13
  27. data/spec/text_mining_pubannos_json_reader_spec.rb +1 -14
  28. data/spec/text_mining_rdfwriter_spec.rb +8 -19
  29. data/test.sh +4 -0
  30. data/web/about.html +10 -14
  31. data/web/api.html +11 -13
  32. data/web/bootstrap/css/bootstrap-theme.css +347 -0
  33. data/web/bootstrap/css/bootstrap-theme.css.map +1 -0
  34. data/web/bootstrap/css/bootstrap-theme.min.css +7 -0
  35. data/web/bootstrap/css/bootstrap.css +4764 -4603
  36. data/web/bootstrap/css/bootstrap.css.map +1 -0
  37. data/web/bootstrap/css/bootstrap.min.css +6 -8
  38. data/web/bootstrap/fonts/glyphicons-halflings-regular.eot +0 -0
  39. data/web/bootstrap/fonts/glyphicons-halflings-regular.svg +229 -0
  40. data/web/bootstrap/fonts/glyphicons-halflings-regular.ttf +0 -0
  41. data/web/bootstrap/fonts/glyphicons-halflings-regular.woff +0 -0
  42. data/web/bootstrap/js/bootstrap.js +1372 -1448
  43. data/web/bootstrap/js/bootstrap.min.js +5 -5
  44. data/web/cli.html +14 -28
  45. data/web/index.html +15 -33
  46. data/web/ontologies.html +1089 -945
  47. data/web/webservices.html +12 -14
  48. metadata +24 -27
  49. data/lib/biointerchange/gff3o.rb +0 -525
  50. data/lib/biointerchange/gvf1o.rb +0 -1354
  51. data/web/bootstrap/css/bootstrap-responsive.css +0 -1040
  52. data/web/bootstrap/css/bootstrap-responsive.min.css +0 -9
  53. data/web/bootstrap/img/glyphicons-halflings-white.png +0 -0
  54. data/web/bootstrap/img/glyphicons-halflings.png +0 -0

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