full_lengther_next 0.6.2 → 0.9.8

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Files changed (59) hide show
  1. checksums.yaml +7 -0
  2. data/.gitignore +9 -0
  3. data/.rspec +2 -0
  4. data/.travis.yml +5 -0
  5. data/CODE_OF_CONDUCT.md +49 -0
  6. data/Gemfile +4 -0
  7. data/LICENSE.txt +21 -0
  8. data/{README.rdoc → README.md} +0 -0
  9. data/Rakefile +6 -37
  10. data/bin/console +14 -0
  11. data/bin/download_fln_dbs.rb +2 -7
  12. data/bin/full_lengther_next +85 -6
  13. data/bin/make_user_db.rb +13 -5
  14. data/bin/setup +8 -0
  15. data/full_lengther_next.gemspec +42 -0
  16. data/lib/full_lengther_next.rb +2 -10
  17. data/lib/full_lengther_next/artifacts.rb +74 -0
  18. data/lib/full_lengther_next/{classes/blast_functions.rb → blast_functions.rb} +0 -0
  19. data/lib/full_lengther_next/{classes/cdhit.rb → cdhit.rb} +0 -0
  20. data/lib/full_lengther_next/{classes/chimeric_seqs.rb → chimeric_seqs.rb} +0 -0
  21. data/lib/full_lengther_next/{classes/common_functions.rb → common_functions.rb} +0 -0
  22. data/lib/full_lengther_next/{classes/exonerate_result.rb → exonerate_result.rb} +0 -0
  23. data/lib/full_lengther_next/{classes/fl_analysis.rb → fl_analysis.rb} +0 -0
  24. data/lib/full_lengther_next/{classes/fl_string_utils.rb → fl_string_utils.rb} +0 -0
  25. data/lib/full_lengther_next/fln_stats.rb +613 -0
  26. data/lib/full_lengther_next/go_methods.rb +42 -0
  27. data/lib/full_lengther_next/{classes/handle_db.rb → handle_db.rb} +0 -0
  28. data/lib/full_lengther_next/mapping.rb +296 -0
  29. data/lib/full_lengther_next/{classes/my_worker.rb → my_worker.rb} +71 -9
  30. data/lib/full_lengther_next/{classes/my_worker_EST.rb → my_worker_EST.rb} +0 -0
  31. data/lib/full_lengther_next/{classes/my_worker_manager_EST.rb → my_worker_manager_EST.rb} +0 -0
  32. data/lib/full_lengther_next/{classes/my_worker_manager_fln.rb → my_worker_manager_fln.rb} +181 -16
  33. data/lib/full_lengther_next/{classes/nc_rna.rb → nc_rna.rb} +0 -0
  34. data/lib/full_lengther_next/{classes/orf.rb → orf.rb} +0 -0
  35. data/lib/full_lengther_next/{classes/reptrans.rb → reptrans.rb} +9 -5
  36. data/lib/full_lengther_next/{classes/sequence.rb → sequence.rb} +26 -1
  37. data/lib/full_lengther_next/{classes/test_code.rb → test_code.rb} +1 -1
  38. data/lib/full_lengther_next/{classes/types.rb → types.rb} +3 -2
  39. data/lib/full_lengther_next/{classes/une_los_hit.rb → une_los_hit.rb} +0 -0
  40. data/lib/full_lengther_next/version.rb +3 -0
  41. data/lib/full_lengther_next/{classes/warnings.rb → warnings.rb} +0 -0
  42. data/report_templates/general_summary.erb +140 -0
  43. data/report_templates/mapping_summary.erb +98 -0
  44. data/report_templates/reptrans_summary.erb +32 -0
  45. metadata +112 -134
  46. data/.gemtest +0 -0
  47. data/History.txt +0 -32
  48. data/Manifest.txt +0 -44
  49. data/PostInstall.txt +0 -6
  50. data/bin/plot_fln.rb +0 -270
  51. data/bin/plot_taxonomy.rb +0 -70
  52. data/lib/expresscanvas.zip +0 -0
  53. data/lib/full_lengther_next/classes/artifacts.rb +0 -66
  54. data/lib/full_lengther_next/classes/fln_stats.rb +0 -641
  55. data/script/console +0 -10
  56. data/script/destroy +0 -14
  57. data/script/generate +0 -14
  58. data/test/test_full_lengther_next.rb +0 -11
  59. data/test/test_helper.rb +0 -3
data/script/console DELETED
@@ -1,10 +0,0 @@
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- #!/usr/bin/env ruby
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- # File: script/console
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- irb = RUBY_PLATFORM =~ /(:?mswin|mingw)/ ? 'irb.bat' : 'irb'
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-
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- libs = " -r irb/completion"
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- # Perhaps use a console_lib to store any extra methods I may want available in the cosole
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- # libs << " -r #{File.dirname(__FILE__) + '/../lib/console_lib/console_logger.rb'}"
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- libs << " -r #{File.dirname(__FILE__) + '/../lib/full_lengther_next.rb'}"
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- puts "Loading full_lengther_next gem"
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- exec "#{irb} #{libs} --simple-prompt"
data/script/destroy DELETED
@@ -1,14 +0,0 @@
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- #!/usr/bin/env ruby
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- APP_ROOT = File.expand_path(File.join(File.dirname(__FILE__), '..'))
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-
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- begin
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- require 'rubigen'
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- rescue LoadError
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- require 'rubygems'
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- require 'rubigen'
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- end
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- require 'rubigen/scripts/destroy'
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-
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- ARGV.shift if ['--help', '-h'].include?(ARGV[0])
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- RubiGen::Base.use_component_sources! [:rubygems, :newgem, :newgem_theme, :test_unit]
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- RubiGen::Scripts::Destroy.new.run(ARGV)
data/script/generate DELETED
@@ -1,14 +0,0 @@
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- #!/usr/bin/env ruby
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- APP_ROOT = File.expand_path(File.join(File.dirname(__FILE__), '..'))
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-
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- begin
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- require 'rubigen'
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- rescue LoadError
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- require 'rubygems'
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- require 'rubigen'
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- end
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- require 'rubigen/scripts/generate'
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-
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- ARGV.shift if ['--help', '-h'].include?(ARGV[0])
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- RubiGen::Base.use_component_sources! [:rubygems, :newgem, :newgem_theme, :test_unit]
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- RubiGen::Scripts::Generate.new.run(ARGV)
data/test/test_full_lengther_next.rb DELETED
@@ -1,11 +0,0 @@
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- require File.dirname(__FILE__) + '/test_helper.rb'
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-
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- class TestFullLengtherNext < Test::Unit::TestCase
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-
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- def setup
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- end
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-
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- def test_truth
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- assert true
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- end
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- end
data/test/test_helper.rb DELETED
@@ -1,3 +0,0 @@
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- require 'stringio'
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- require 'test/unit'
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- require File.dirname(__FILE__) + '/../lib/full_lengther_next'