full_lengther_next 0.6.2 → 0.9.8
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.
- checksums.yaml +7 -0
- data/.gitignore +9 -0
- data/.rspec +2 -0
- data/.travis.yml +5 -0
- data/CODE_OF_CONDUCT.md +49 -0
- data/Gemfile +4 -0
- data/LICENSE.txt +21 -0
- data/{README.rdoc → README.md} +0 -0
- data/Rakefile +6 -37
- data/bin/console +14 -0
- data/bin/download_fln_dbs.rb +2 -7
- data/bin/full_lengther_next +85 -6
- data/bin/make_user_db.rb +13 -5
- data/bin/setup +8 -0
- data/full_lengther_next.gemspec +42 -0
- data/lib/full_lengther_next.rb +2 -10
- data/lib/full_lengther_next/artifacts.rb +74 -0
- data/lib/full_lengther_next/{classes/blast_functions.rb → blast_functions.rb} +0 -0
- data/lib/full_lengther_next/{classes/cdhit.rb → cdhit.rb} +0 -0
- data/lib/full_lengther_next/{classes/chimeric_seqs.rb → chimeric_seqs.rb} +0 -0
- data/lib/full_lengther_next/{classes/common_functions.rb → common_functions.rb} +0 -0
- data/lib/full_lengther_next/{classes/exonerate_result.rb → exonerate_result.rb} +0 -0
- data/lib/full_lengther_next/{classes/fl_analysis.rb → fl_analysis.rb} +0 -0
- data/lib/full_lengther_next/{classes/fl_string_utils.rb → fl_string_utils.rb} +0 -0
- data/lib/full_lengther_next/fln_stats.rb +613 -0
- data/lib/full_lengther_next/go_methods.rb +42 -0
- data/lib/full_lengther_next/{classes/handle_db.rb → handle_db.rb} +0 -0
- data/lib/full_lengther_next/mapping.rb +296 -0
- data/lib/full_lengther_next/{classes/my_worker.rb → my_worker.rb} +71 -9
- data/lib/full_lengther_next/{classes/my_worker_EST.rb → my_worker_EST.rb} +0 -0
- data/lib/full_lengther_next/{classes/my_worker_manager_EST.rb → my_worker_manager_EST.rb} +0 -0
- data/lib/full_lengther_next/{classes/my_worker_manager_fln.rb → my_worker_manager_fln.rb} +181 -16
- data/lib/full_lengther_next/{classes/nc_rna.rb → nc_rna.rb} +0 -0
- data/lib/full_lengther_next/{classes/orf.rb → orf.rb} +0 -0
- data/lib/full_lengther_next/{classes/reptrans.rb → reptrans.rb} +9 -5
- data/lib/full_lengther_next/{classes/sequence.rb → sequence.rb} +26 -1
- data/lib/full_lengther_next/{classes/test_code.rb → test_code.rb} +1 -1
- data/lib/full_lengther_next/{classes/types.rb → types.rb} +3 -2
- data/lib/full_lengther_next/{classes/une_los_hit.rb → une_los_hit.rb} +0 -0
- data/lib/full_lengther_next/version.rb +3 -0
- data/lib/full_lengther_next/{classes/warnings.rb → warnings.rb} +0 -0
- data/report_templates/general_summary.erb +140 -0
- data/report_templates/mapping_summary.erb +98 -0
- data/report_templates/reptrans_summary.erb +32 -0
- metadata +112 -134
- data/.gemtest +0 -0
- data/History.txt +0 -32
- data/Manifest.txt +0 -44
- data/PostInstall.txt +0 -6
- data/bin/plot_fln.rb +0 -270
- data/bin/plot_taxonomy.rb +0 -70
- data/lib/expresscanvas.zip +0 -0
- data/lib/full_lengther_next/classes/artifacts.rb +0 -66
- data/lib/full_lengther_next/classes/fln_stats.rb +0 -641
- data/script/console +0 -10
- data/script/destroy +0 -14
- data/script/generate +0 -14
- data/test/test_full_lengther_next.rb +0 -11
- data/test/test_helper.rb +0 -3
data/script/console
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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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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"
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data/script/destroy
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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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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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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)
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data/script/generate
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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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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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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)
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data/test/test_helper.rb
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