bio-gff3 0.8.7 → 0.9.0
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.
- data/.travis.yml +12 -0
- data/Gemfile +4 -4
- data/Gemfile.lock +34 -20
- data/README.rdoc +22 -13
- data/Rakefile +24 -23
- data/VERSION +1 -1
- data/bin/gff3-fetch +15 -11
- data/bio-gff3.gemspec +30 -39
- data/lib/bio/db/gff/block/gffblockparser.rb +3 -4
- data/lib/bio/db/gff/digest/gfflrucache.rb +2 -1
- data/lib/bio/db/gff/digest/gffnocache.rb +2 -1
- data/lib/bio/db/gff/digest/gffparser.rb +5 -3
- data/lib/bio/db/gff/gffcomponent.rb +6 -5
- data/lib/bio/db/gff/gffsequence.rb +1 -1
- data/lib/bio/db/gff/gffvalidate.rb +2 -1
- data/spec/gff3_fileiterator_spec.rb +3 -4
- data/test/data/gff/m_hapla.WS232.annotations.part.gff3 +3725 -0
- data/test/data/gff/m_hapla.WS232.genomic.part.fa +3187 -0
- data/test/data/regression/test_ext_gff3.rtest +1 -5
- data/test/data/regression/test_gff3.rtest +1 -5
- data/test/data/regression/test_latest_wormbase_ext_gff3.ref +7885 -0
- data/test/data/regression/test_latest_wormbase_ext_gff3.rtest +280 -0
- data/test/data/regression/test_lrucache_ext_gff3.rtest +1 -3
- data/test/data/regression/test_lrucache_gff3.rtest +1 -3
- data/test/data/regression/test_nocache_ext_gff3.rtest +1 -3
- data/test/data/regression/test_nocache_gff3.rtest +1 -3
- data/test/helper.rb +1 -0
- data/test/{regressiontest.rb → regressiontest2.rb} +5 -5
- data/test/test_bio-gff3.rb +35 -10
- metadata +35 -36
data/.travis.yml
ADDED
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language: ruby
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rvm:
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- 1.8.7
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- 1.9.2
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- 1.9.3
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# - jruby-19mode # JRuby in 1.9 mode
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- rbx-19mode
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# - jruby-18mode # JRuby in 1.8 mode
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# - rbx-18mode
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# uncomment this line if your project needs to run something other than `rake`:
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# script: bundle exec rspec spec
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data/Gemfile
CHANGED
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# Include everything needed to run rake, tests, features, etc.
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group :development do
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gem "shoulda", ">= 0"
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gem "bundler", "~> 1.
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gem "jeweler", "~> 1.
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gem "
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gem "
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gem "bundler", "~> 1.1.5"
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gem "jeweler", "~> 1.8.3"
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gem "rspec", ">= 2.10.0"
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gem "regressiontest"
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end
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data/Gemfile.lock
CHANGED
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GEM
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remote: http://rubygems.org/
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specs:
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activesupport (3.2.7)
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i18n (~> 0.6)
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multi_json (~> 1.0)
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bio (1.4.2)
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bio-logger (1.0.0)
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log4r (>= 1.1.9)
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diff-lcs (1.1.
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diff-lcs (1.1.3)
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git (1.2.5)
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i18n (0.6.0)
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jeweler (1.8.4)
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bundler (~> 1.0)
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git (>= 1.2.5)
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rake
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rspec
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rdoc
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json (1.7.4)
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log4r (1.1.10)
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multi_json (1.3.6)
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rake (0.9.2.2)
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rdoc (3.12)
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json (~> 1.4)
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regressiontest (0.0.1)
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rspec (2.10.0)
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rspec-core (~> 2.10.0)
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rspec-expectations (~> 2.10.0)
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rspec-mocks (~> 2.10.0)
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rspec-core (2.10.1)
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rspec-expectations (2.10.0)
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diff-lcs (~> 1.1.3)
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rspec-mocks (2.10.1)
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shoulda (3.1.1)
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shoulda-context (~> 1.0)
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shoulda-matchers (~> 1.2)
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shoulda-context (1.0.0)
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shoulda-matchers (1.2.0)
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activesupport (>= 3.0.0)
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PLATFORMS
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ruby
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DEPENDENCIES
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bio (>= 1.3.1)
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bio-logger (> 0.8.0)
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bundler (~> 1.
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jeweler (~> 1.
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bundler (~> 1.1.5)
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jeweler (~> 1.8.3)
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log4r (> 1.1.6)
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-
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rspec (>= 2.
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regressiontest
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rspec (>= 2.10.0)
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shoulda
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data/README.rdoc
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{<img
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src="https://secure.travis-ci.org/pjotrp/bioruby-gff3-plugin.png"
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/>}[http://travis-ci.org/#!/pjotrp/bioruby-gff3-plugin]
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bio-gff3 is listed at http://biogems.info
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= bio-gff3
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GFF3 parser, aimed at parsing big data GFF3 to return sequences of any type,
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You can use this plugin in two ways. First as a standalone program,
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second as a plugin library to BioRuby.
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Note: a really fast GFF3 parser is in the
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Note: a really fast GFF3 parser, and way more flexible, is in the
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works. See https://github.com/mamarjan/gff3-pltools.
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== Install and run gff3-fetch
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-------------------------------------------------------------------------------
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Copyright (C) 2010,2011 Pjotr Prins <pjotr.prins@thebird.nl>
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= Command line usage (CLI)
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Fetch and assemble GFF3 types (e.g. ORF, mRNA, CDS) + print in FASTA format.
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Fetch and assemble GFF3 types (ORF, mRNA, CDS) + print in FASTA format.
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gff3-fetch [options] type [filename.fa] filename.gff3
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Where (NYI == Not Yet Implemented):
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Multiple GFF3 files can be used. With external FASTA files, always the last
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one before the GFF3 filename is matched.
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one before the GFF3 filename is matched. Make sure the FASTA file
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comes before the GFF3 file on the command line.
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Note that above switches are only partially implemented at this stage.
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feature support is projected Feb. 2011.
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Note that above switches are only partially implemented at this stage.
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Examples:
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Cache real user sys gff3 version
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------------------------------------------------------------
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in preparation
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https://github.com/pjotrp/biolib_hpc/tree/master/modules/gff3
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in preparation
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------------------------------------------------------------
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where
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ruby 1.9.2p136 (2010-12-25 revision 30365) [x86_64-linux]
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on an 8 CPU, 2.6 GHz (6MB cache), 16 GB RAM machine.
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Note: the new parser by Marjan is magnitudes faster, and way more
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flexible. See https://github.com/mamarjan/gff3-pltools
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== Cite
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If you use this software, please cite
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http://dx.doi.org/10.1093/bioinformatics/bts080
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or
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http://dx.doi.org/10.1093/bioinformatics/btq475
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== Copyright
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Copyright (C) 2010
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Copyright (C) 2010-2012 Pjotr Prins <pjotr.prins@thebird.nl>
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data/Rakefile
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require 'rubygems'
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require 'bundler'
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begin
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Bundler.setup(:default, :development)
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rescue Bundler::BundlerError => e
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$stderr.puts e.message
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$stderr.puts "Run `bundle install` to install missing gems"
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exit e.status_code
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end
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require 'rake'
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require 'rake/testtask'
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Rake::TestTask.new(:test) do |test|
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test.libs << 'lib' << 'test'
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test.pattern = 'test/**/test_*.rb'
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# test.pattern = 'test/**/test_*.rb' # breaks in 1.9.3
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test.test_files = Dir.glob("test/**/test_*.rb")
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test.verbose = true
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Kernel.system('rspec spec/*.rb')
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end
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#end
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# Rcov::RcovTask.new do |test|
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# test.libs << 'test'
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# test.pattern = 'test/**/test_*.rb'
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# test.verbose = true
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# end
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task :default => :test
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# require 'rake/rdoctask'
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# Rake::RDocTask.new do |rdoc|
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# version = File.exist?('VERSION') ? File.read('VERSION') : ""
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end
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# rdoc.rdoc_dir = 'rdoc'
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# rdoc.title = "bio-gff3 #{version}"
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# rdoc.rdoc_files.include('README*')
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# rdoc.rdoc_files.include('lib/**/*.rb')
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# end
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data/VERSION
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0.
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0.9.0
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data/bin/gff3-fetch
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#! /usr/bin/ruby
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#! /usr/bin/env ruby
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#
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# Author:: Pjotr Prins
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# Copyright:: August 2010
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# License:: Ruby License
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COPYRIGHT = "Copyright (C) 2010-2012 Pjotr Prins <pjotr.prins@thebird.nl>"
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USAGE = <<EOM
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Fetch and assemble GFF3 types (
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Fetch and assemble GFF3 types (ORF, mRNA, CDS) + print in FASTA format.
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gff3-fetch [options] type [filename.fa] filename.gff3
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Where (NYI == Not Yet Implemented):
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Multiple GFF3 files can be used. With external FASTA files, always the last
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one before the GFF3 filename is matched.
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one before the GFF3 filename is matched. Make sure the FASTA file
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comes before the GFF3 file on the command line.
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Note that above switches are only partially implemented at this stage.
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feature support is projected Feb. 2011.
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Note that above switches are only partially implemented at this stage.
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Examples:
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@@ -126,11 +125,15 @@ on an 8 CPU, 2.6 GHz (6MB cache), 16 GB RAM machine.
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If you use this software, please cite
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http://dx.doi.org/10.1093/bioinformatics/bts080
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or
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http://dx.doi.org/10.1093/bioinformatics/btq475
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== Copyright
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#{COPYRIGHT}
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EOM
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require 'ostruct'
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require 'bio/output/gfffastawriter'
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$stderr.print "
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$stderr.print "gff3-fetch (biogem Ruby #{RUBY_VERSION}) "+GFF3_VERSION+" "+COPYRIGHT+"\n\n"
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if ARGV.size == 0
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print USAGE
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options.parser = :line
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opts2 = OptionParser.new() { |opts|
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opts.on_tail("-h", "--help", "Show help and examples") {
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print(opts)
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print USAGE
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}
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opts = opts2
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opts.parse!(ARGV)
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Bio::Log::CLI.configure('bio-gff3')
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data/bio-gff3.gemspec
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s.name =
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s.name = "bio-gff3"
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s.version = "0.9.0"
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s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
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s.authors = [
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s.date =
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s.description =
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}
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s.email = %q{pjotr.prins@thebird.nl}
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s.executables = [%q{gff3-fetch}]
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s.authors = ["Pjotr Prins"]
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s.date = "2012-08-20"
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s.description = "GFF3 (genome browser) information and digest mRNA and CDS sequences.\nOptions for low memory use and caching of records.\nSupport for external FASTA files.\n"
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s.email = "pjotr.prins@thebird.nl"
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s.executables = ["gff3-fetch"]
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s.extra_rdoc_files = [
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"LICENSE.txt",
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"README.rdoc"
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]
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s.files = [
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+
".travis.yml",
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"Gemfile",
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"Gemfile.lock",
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24
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"LICENSE.txt",
|
@@ -59,6 +57,8 @@ Support for external FASTA files.
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"test/data/gff/MhA1_Contig1133.gff3",
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"test/data/gff/MhA1_Contig125.fa",
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"test/data/gff/MhA1_Contig125.gff3",
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+
"test/data/gff/m_hapla.WS232.annotations.part.gff3",
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+
"test/data/gff/m_hapla.WS232.genomic.part.fa",
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"test/data/gff/standard.gff3",
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"test/data/gff/test-cds.gff3",
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"test/data/gff/test-ext-fasta.fa",
|
@@ -66,30 +66,21 @@ Support for external FASTA files.
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"test/data/gff/test.gff3",
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"test/data/regression/test_ext_gff3.rtest",
|
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"test/data/regression/test_gff3.rtest",
|
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+
"test/data/regression/test_latest_wormbase_ext_gff3.ref",
|
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+
"test/data/regression/test_latest_wormbase_ext_gff3.rtest",
|
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"test/data/regression/test_lrucache_ext_gff3.rtest",
|
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"test/data/regression/test_lrucache_gff3.rtest",
|
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"test/data/regression/test_nocache_ext_gff3.rtest",
|
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|
"test/data/regression/test_nocache_gff3.rtest",
|
73
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|
"test/helper.rb",
|
74
|
-
"test/
|
75
|
-
"test/test_bio-gff3.rb"
|
76
|
-
]
|
77
|
-
s.homepage = %q{https://github.com/pjotrp/bioruby-gff3-plugin}
|
78
|
-
s.licenses = [%q{MIT}]
|
79
|
-
s.require_paths = [%q{lib}]
|
80
|
-
s.rubygems_version = %q{1.8.6}
|
81
|
-
s.summary = %q{GFF3 parser for big data}
|
82
|
-
s.test_files = [
|
83
|
-
"spec/gff3_assemble2_spec.rb",
|
84
|
-
"spec/gff3_assemble3_spec.rb",
|
85
|
-
"spec/gff3_assemble_spec.rb",
|
86
|
-
"spec/gff3_fileiterator_spec.rb",
|
87
|
-
"spec/gffdb_spec.rb",
|
88
|
-
"spec/gffparserec.rb",
|
89
|
-
"test/helper.rb",
|
90
|
-
"test/regressiontest.rb",
|
76
|
+
"test/regressiontest2.rb",
|
91
77
|
"test/test_bio-gff3.rb"
|
92
78
|
]
|
79
|
+
s.homepage = "https://github.com/pjotrp/bioruby-gff3-plugin"
|
80
|
+
s.licenses = ["MIT"]
|
81
|
+
s.require_paths = ["lib"]
|
82
|
+
s.rubygems_version = "1.8.10"
|
83
|
+
s.summary = "GFF3 parser for big data"
|
93
84
|
|
94
85
|
if s.respond_to? :specification_version then
|
95
86
|
s.specification_version = 3
|
@@ -99,29 +90,29 @@ Support for external FASTA files.
|
|
99
90
|
s.add_runtime_dependency(%q<log4r>, ["> 1.1.6"])
|
100
91
|
s.add_runtime_dependency(%q<bio-logger>, ["> 0.8.0"])
|
101
92
|
s.add_development_dependency(%q<shoulda>, [">= 0"])
|
102
|
-
s.add_development_dependency(%q<bundler>, ["~> 1.
|
103
|
-
s.add_development_dependency(%q<jeweler>, ["~> 1.
|
104
|
-
s.add_development_dependency(%q<
|
105
|
-
s.add_development_dependency(%q<
|
93
|
+
s.add_development_dependency(%q<bundler>, ["~> 1.1.5"])
|
94
|
+
s.add_development_dependency(%q<jeweler>, ["~> 1.8.3"])
|
95
|
+
s.add_development_dependency(%q<rspec>, [">= 2.10.0"])
|
96
|
+
s.add_development_dependency(%q<regressiontest>, [">= 0"])
|
106
97
|
else
|
107
98
|
s.add_dependency(%q<bio>, [">= 1.3.1"])
|
108
99
|
s.add_dependency(%q<log4r>, ["> 1.1.6"])
|
109
100
|
s.add_dependency(%q<bio-logger>, ["> 0.8.0"])
|
110
101
|
s.add_dependency(%q<shoulda>, [">= 0"])
|
111
|
-
s.add_dependency(%q<bundler>, ["~> 1.
|
112
|
-
s.add_dependency(%q<jeweler>, ["~> 1.
|
113
|
-
s.add_dependency(%q<
|
114
|
-
s.add_dependency(%q<
|
102
|
+
s.add_dependency(%q<bundler>, ["~> 1.1.5"])
|
103
|
+
s.add_dependency(%q<jeweler>, ["~> 1.8.3"])
|
104
|
+
s.add_dependency(%q<rspec>, [">= 2.10.0"])
|
105
|
+
s.add_dependency(%q<regressiontest>, [">= 0"])
|
115
106
|
end
|
116
107
|
else
|
117
108
|
s.add_dependency(%q<bio>, [">= 1.3.1"])
|
118
109
|
s.add_dependency(%q<log4r>, ["> 1.1.6"])
|
119
110
|
s.add_dependency(%q<bio-logger>, ["> 0.8.0"])
|
120
111
|
s.add_dependency(%q<shoulda>, [">= 0"])
|
121
|
-
s.add_dependency(%q<bundler>, ["~> 1.
|
122
|
-
s.add_dependency(%q<jeweler>, ["~> 1.
|
123
|
-
s.add_dependency(%q<
|
124
|
-
s.add_dependency(%q<
|
112
|
+
s.add_dependency(%q<bundler>, ["~> 1.1.5"])
|
113
|
+
s.add_dependency(%q<jeweler>, ["~> 1.8.3"])
|
114
|
+
s.add_dependency(%q<rspec>, [">= 2.10.0"])
|
115
|
+
s.add_dependency(%q<regressiontest>, [">= 0"])
|
125
116
|
end
|
126
117
|
end
|
127
118
|
|
@@ -69,23 +69,22 @@ module Bio
|
|
69
69
|
|
70
70
|
def each_seq(gfftype)
|
71
71
|
parse(gfftype) { | id, seq | yield id,seq }
|
72
|
-
|
73
72
|
end
|
74
73
|
|
75
74
|
def each_gene_seq
|
76
75
|
each_seq('gene') { | id, seq | yield id,seq }
|
77
76
|
end
|
77
|
+
|
78
78
|
def each_mRNA_seq
|
79
79
|
each_seq('mrna') { | id, seq | yield id,seq }
|
80
|
-
|
81
80
|
end
|
81
|
+
|
82
82
|
def each_exon_seq
|
83
83
|
each_seq('exon') { | id, seq | yield id,seq }
|
84
|
-
|
85
84
|
end
|
85
|
+
|
86
86
|
def each_CDS_seq
|
87
87
|
each_seq('cds') { | id, seq | yield id,seq }
|
88
|
-
|
89
88
|
end
|
90
89
|
end
|
91
90
|
end
|