reubypathdb 0.1.0
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- data/.document +5 -0
- data/.gitignore +21 -0
- data/LICENSE +20 -0
- data/README.rdoc +17 -0
- data/Rakefile +53 -0
- data/VERSION +1 -0
- data/lib/eupathdb_gene_information_table.rb +103 -0
- data/test/data/eupathGeneInformation.txt +278 -0
- data/test/helper.rb +9 -0
- data/test/test_eupathdb_gene_information_table.rb +60 -0
- metadata +91 -0
data/.document
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data/.gitignore
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data/LICENSE
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Copyright (c) 2009 Ben J Woodcroft
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Permission is hereby granted, free of charge, to any person obtaining
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a copy of this software and associated documentation files (the
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"Software"), to deal in the Software without restriction, including
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without limitation the rights to use, copy, modify, merge, publish,
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distribute, sublicense, and/or sell copies of the Software, and to
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permit persons to whom the Software is furnished to do so, subject to
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the following conditions:
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The above copyright notice and this permission notice shall be
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included in all copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
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MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
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LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
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OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
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WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
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data/README.rdoc
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= eupathdb
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Description goes here.
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== Note on Patches/Pull Requests
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* Fork the project.
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* Make your feature addition or bug fix.
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* Add tests for it. This is important so I don't break it in a
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future version unintentionally.
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* Commit, do not mess with rakefile, version, or history.
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(if you want to have your own version, that is fine but bump version in a commit by itself I can ignore when I pull)
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* Send me a pull request. Bonus points for topic branches.
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== Copyright
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Copyright (c) 2010 Ben J Woodcroft. See LICENSE for details.
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data/Rakefile
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require 'rubygems'
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require 'rake'
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begin
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require 'jeweler'
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Jeweler::Tasks.new do |gem|
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gem.name = "reubypathdb"
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gem.summary = %Q{Classes to help parsing EuPathDB data files}
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gem.description = %Q{Classes to help parsing EuPathDB data files}
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gem.email = "donttrustben near gmail.com"
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gem.homepage = "http://github.com/wwood/reubypathdb"
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gem.authors = ["Ben J Woodcroft"]
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gem.add_development_dependency "thoughtbot-shoulda", ">= 0"
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# gem is a Gem::Specification... see http://www.rubygems.org/read/chapter/20 for additional settings
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end
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Jeweler::GemcutterTasks.new
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rescue LoadError
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puts "Jeweler (or a dependency) not available. Install it with: gem install jeweler"
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end
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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.verbose = true
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end
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begin
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require 'rcov/rcovtask'
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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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rescue LoadError
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task :rcov do
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abort "RCov is not available. In order to run rcov, you must: sudo gem install spicycode-rcov"
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end
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end
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task :test => :check_dependencies
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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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rdoc.rdoc_dir = 'rdoc'
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rdoc.title = "reubypathdb #{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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0.1.0
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class EuPathDBGeneInformationTable
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include Enumerable
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def initialize(io)
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@io = io
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end
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def each
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while g = next_gene
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yield g
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end
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end
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# Returns a EuPathDBGeneInformation object with all the data you could
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# possibly want.
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def next_gene
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info = EuPathDBGeneInformation.new
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# first, read the table, which should start with the ID column
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line = @io.readline.strip
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while line == ''
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return nil if @io.eof?
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line = @io.readline.strip
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end
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while line != ''
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if matches = line.match(/^(.*?)\: (.*)$/)
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info.add_information(matches[1], matches[2])
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else
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raise Exception, "EuPathDBGeneInformationTable Couldn't parse this line: #{line}"
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end
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line = @io.readline.strip
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end
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# now read each of the tables, which should start with the
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# 'TABLE: <name>' entry
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line = @io.readline.strip
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table_name = nil
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headers = nil
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data = []
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while line != '------------------------------------------------------------'
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if line == ''
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# add it to the stack unless we are just starting out
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info.add_table(table_name, headers, data) unless table_name.nil?
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# reset things
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table_name = nil
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headers = nil
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data = []
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elsif matches = line.match(/^TABLE\: (.*)$/)
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# name of a table
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table_name = matches[1]
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elsif line.match(/^\[.*\]/)
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# headings of the table
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headers = line.split("\t").collect do |header|
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header.gsub(/^\[/,'').gsub(/\]$/,'')
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end
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else
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# a proper data row
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data.push line.split("\t")
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end
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line = @io.readline.strip
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end
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# return the object that has been created
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return info
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end
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end
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class EuPathDBGeneInformation
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def info
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@info
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end
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def get_info(key)
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@info[key]
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end
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alias_method :[], :get_info
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def get_table(table_name)
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@tables[table_name]
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end
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def add_information(key, value)
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@info ||= {}
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@info[key] = value
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"Added info #{key}, now is #{@info[key]}"
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end
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def add_table(name, headers, data)
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@tables ||= {}
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@tables[name] = []
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data.each do |row|
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final = {}
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row.each_with_index do |cell, i|
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final[headers[i]] = cell
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end
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@tables[name].push final
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end
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end
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end
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ID: TGME49_000010
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Gene Group: TG_9133
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Data Source: T.gondii ME49 contigs from Genbank
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Genomic Sequence ID: TGME49_chrXII
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Chromosome: XII
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Genomic Location: TGME49_chrXII: 2,230,843 - 2,234,577 (-)
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Gene Strand: reverse
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Gene Type: protein coding
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# Exons: 2
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Transcript Length: 3391
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CDS Length: 1242
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Product Description: hypothetical protein
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Protein Length: 413
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# TM Domains: 0
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Molecular Weight: 45197
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Isoelectric Point: 7.92
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EC Numbers: null
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Ortholog count: 3
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Paralog count: 2
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Temporary Ortholog Group: OG3_85809
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Total SNPs All Strains: 5
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Nonsynonymous SNPs All Strains: 1
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Synonymous SNPs All Strains: 0
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Nonsyn/Syn SNP Ratio All Strains: 0
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SignalP Scores: null
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SignalP Peptide: null
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Annotated GO Function: null
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Annotated GO Process: null
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Annotated GO Component: null
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Predicted GO Function: null
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Predicted GO Process: null
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Predicted GO Component: null
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TypeIII / TypeI fold-change: -11.6288769802844
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TypeIII / TypeII fold-change: -7.03490049704923
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TypeII / TypeI fold-change: -1.65302650480445
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Organism: Toxoplasma gondii ME49
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Release4 IDs: 1.m00014
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= Release4 Protein?: Yes
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Predicted Protein Sequence: MHSRNCVGGSFYDGAVCCSPPSRAFGNMHNLVLVLLAFLSSWEDNETRRGDVVEQQNPFRLAIHGKTERDRDGNCTQHGVRSNDFRFVDEGDMSAEVGRGLALQKHVRVPLQASIARRLSDRESEKRSQGSDNGNGTTPPLPPRRTPSPRPSGASGVVQQGAAGVGTPTMLGTGGQHLSDQGATGSVAPSVQSSSSSAVSVEGALPLIQFFGSRSSSPEVPLCHACHTVEAAVGVLQSIRHRRRAGAREAAERIAALESQHALLVSSSTQGEHSQGARPSDILVSHRALQRARREATRQEETLRGEEASLEAFIRVASEKREREGQRSLEVLRQRVENQTAELAVLRVEAALERQREMVELERRRGDLLALALVAEDDEEYLRLSAEEEAVQRQIEQLAEETRRPRRGRRKPA
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Predicted RNA/mRNA Sequence (introns spliced out): TCTCACGTGAACCGGCCCCAACTGAGGAACACATACGACGGTGGAACCAGGGTGCAGTCGGCACGTCGCTAGGGTTCGTTATTCTGCACCACTGTCTGATTTGGCTGTGCGCCCGAATCTGTGGAACACGTGCACTCGCGAATATTCATGAGAACACATTGTTTTGGAATCAACTAGCCAAATCCTTCCCTCTGCCACACATGCTGAAAGACGAGCTTGGGGGTGAAAGCTCTACTTCAACAAACGCACGGGCAGACGGTTCTCACATGTGCGACGTCGCTAGACGAGTTCGAAGTCGTAGACATCATACTTTTGGGTTGTGTGTGAAGTTAACAACTAACCACTAGATACGTGTTCTGAACAACCGGGAACACCGGACAGGCGCCCACTGCTTTCTGGATAACAAACGAATGGAGGAAGCTCAGCCGCACAGCTTCTTCTGGAGGACTGGGAGAGAAGTGGTCCGACAGAGGCTCAGCTTCGAAACGGTTTTGTGGGCTTTAGTTCTGAACTGAGCTTTTTTTGTTCGACTCATCACCCCAAAATCAAGACTCGGTTGATACATCAGCCGAAGTTGGGGCGGGCTGACGACACCTTAAACGTTCACAGAGACGAGAGAACCCGTTCTCCCGGTGTTGCAATTCATGCTGGGAATCCCCGATGTATGGGGATACAGCTTCAGAGCGAGCCACCACCACCAAGGTTGCCGTTGATGCGGCAGTGACGCGAAGTAGAAGAGCGAAAGAGTGTGCCAATACTTTTGTCTGTTTCACGTGTTTTAAATTGAAGCAACACCGTTCACTCATGCATTTCGCGCCACAGAAGCAGGTAGCAGAGAACCAAAGTTTATTCGCTAACAATTGAACAACACAAGGATACAATCGAGGATCATCGCCACGCAAGTTGGGATCACGGGCCGACTTCAAACAAACGAGGGGTGTACGTGCGAGGGCCCCTGTTCAGCGACGCGTAGTTCCTGCCATGTACACACTTCAGTACTCGTATGAATCCGTTCACGTTGCCGCTGTTTTGTGATTTAGCGTACAATTTTCAAACAGACGAAAGCTACAAATGCTGTACAGGGATAGACATGATGCGGTGTCTTTCCTATCTCTGTCTTGGGTCGGACCTATCCTTTCATTCGGCGTTGCTCTGCCAGCGTGTGACGTTTGAACAGCTGCCATGGAACGCATGAAGTTTGAGAATGGACGCATCCTTGTTTCACAGGGAGAGCTGAGTGAAGGAACTTGCTGCAGAAGTTCAGTCAATCGTCGCTCCTGCCTGCGAAGATTTGCGTATTTGCGCTACAAGTGTGACCAGCCTGCTAAACTGACTGGCGAGCTGTGGCGTTAACGTCGTGGCGAAACGCGTAGCTAAGGGCAGAGAGCCAACAAGCGTACTTTGAATATCAATTACGAGCTCGTTGTTCGTACTTCATCATTCTGGGTTCGCAGAAAAGGTGACGCTTACCCCGTCGTGTGGAGTTTAGTACCTTCAGGAAAGTCACCCTGAGGATGCATAGCCGGAACTGCGTCGGAGGATCGTTTTATGACGGGGCCGTGTGTTGTTCGCCTCCATCGCGTGCTTTCGGCAATATGCACAACCTAGTCCTGGTGTTGCTGGCGTTTCTGTCTTCGTGGGAAGACAACGAAACCAGGCGCGGCGATGTGGTGGAACAGCAGAATCCTTTTCGCCTAGCGATTCACGGCAAAACTGAGAGAGACCGTGACGGGAATTGCACACAACACGGCGTGAGATCAAATGATTTCCGTTTCGTGGATGAAGGTGACATGTCTGCTGAAGTAGGTCGTGGTCTGGCTTTACAGAAACATGTCCGAGTTCCGCTGCAGGCTTCGATTGCTCGGCGGCTTTCTGACAGGGAGTCGGAAAAGAGGAGCCAAGGTTCCGACAACGGAAACGGCACTACCCCACCTTTGCCACCACGGCGGACCCCGTCTCCGCGGCCTTCAGGAGCCAGTGGAGTTGTCCAACAAGGAGCTGCCGGTGTGGGCACGCCTACGATGTTGGGGACAGGTGGCCAACATCTCTCTGACCAGGGAGCTACAGGTTCAGTCGCACCATCAGTGCAATCTTCCTCATCTAGTGCTGTCAGTGTTGAGGGTGCATTGCCTCTAATCCAGTTTTTCGGAAGCCGTAGCAGTTCTCCTGAAGTCCCTCTATGTCATGCGTGCCACACTGTAGAGGCAGCTGTAGGCGTGCTTCAAAGCATAAGACACCGCAGACGGGCTGGCGCGCGTGAGGCAGCTGAGCGAATAGCGGCACTGGAGTCCCAACATGCTCTTCTTGTCAGTTCCTCCACCCAGGGAGAGCACAGTCAAGGTGCACGGCCAAGTGATATCCTTGTGAGTCACCGGGCGCTACAACGGGCGCGCCGAGAGGCCACCCGACAGGAAGAAACGCTACGGGGAGAAGAAGCCTCCCTGGAAGCGTTTATACGCGTGGCCTCTGAAAAGCGTGAAAGAGAAGGGCAGAGGTCTCTCGAGGTGCTCCGCCAGCGCGTGGAAAATCAGACTGCAGAACTTGCTGTGTTACGCGTCGAGGCAGCACTAGAGCGGCAACGTGAAATGGTGGAGCTCGAGAGGAGGCGCGGAGACTTACTGGCCCTGGCCTTAGTCGCAGAAGACGACGAAGAATATCTTCGGCTGAGTGCAGAAGAAGAAGCAGTCCAACGGCAAATCGAGCAATTGGCGGAGGAAACGAGGAGACCGCGCCGTGGCCGTAGAAAGCCCGCGTGATGCAGAAGTGAACAGTGATTCCAAGTGTCTTAAGCACAGTTATTTGAAAAAACAACAATGCATTCTGAATGCGAAACGGTGGTATCGGAGGTATAATGTAGGTAGGGGAACGGGGCACCCCCCGATCTTATTTTGTCAGTCCTGTTACGGAAAGGAAACTGCCTTGTCGGGAGCAGAGGTAAATCCCATTAGGCGCGAGGGTAGCAGAAACCCGCTTCGTGCTGCGTTATGCTTTTGATACTCGCACGCTATTTTGATTACCTCGCAAGCACCTTTGGCGACACTGTGAAAATGCTTTTCTGACAAAGCGATACACGATTGCGGATTTCCCAGTTGGTGTCGTGGTGCGCCTGTCGCCGAATCAAGAGGACATCCTAATTGCACTTCATATGTGAATCCGGCACATACGTTCGTTACCATTTTCTCAGCAACAGGCTTCTGGAGAAACCGAAACTGGTTTTCCAGTGTAGATGGCAATGTCACTCGTGGGGATAACGAAACCCTGAAGATTGCCCTGGCGGGTTCGAAAGTATACGTTCACAGGCGTCCACCGAACATATCCTATTCATGATGTGAACAGCCTATTGATGATGTCTCTACTGAACACACTAGTTGAAAGACACCTGCGAGAGCGG
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Coding Sequence: ATGCATAGCCGGAACTGCGTCGGAGGATCGTTTTATGACGGGGCCGTGTGTTGTTCGCCTCCATCGCGTGCTTTCGGCAATATGCACAACCTAGTCCTGGTGTTGCTGGCGTTTCTGTCTTCGTGGGAAGACAACGAAACCAGGCGCGGCGATGTGGTGGAACAGCAGAATCCTTTTCGCCTAGCGATTCACGGCAAAACTGAGAGAGACCGTGACGGGAATTGCACACAACACGGCGTGAGATCAAATGATTTCCGTTTCGTGGATGAAGGTGACATGTCTGCTGAAGTAGGTCGTGGTCTGGCTTTACAGAAACATGTCCGAGTTCCGCTGCAGGCTTCGATTGCTCGGCGGCTTTCTGACAGGGAGTCGGAAAAGAGGAGCCAAGGTTCCGACAACGGAAACGGCACTACCCCACCTTTGCCACCACGGCGGACCCCGTCTCCGCGGCCTTCAGGAGCCAGTGGAGTTGTCCAACAAGGAGCTGCCGGTGTGGGCACGCCTACGATGTTGGGGACAGGTGGCCAACATCTCTCTGACCAGGGAGCTACAGGTTCAGTCGCACCATCAGTGCAATCTTCCTCATCTAGTGCTGTCAGTGTTGAGGGTGCATTGCCTCTAATCCAGTTTTTCGGAAGCCGTAGCAGTTCTCCTGAAGTCCCTCTATGTCATGCGTGCCACACTGTAGAGGCAGCTGTAGGCGTGCTTCAAAGCATAAGACACCGCAGACGGGCTGGCGCGCGTGAGGCAGCTGAGCGAATAGCGGCACTGGAGTCCCAACATGCTCTTCTTGTCAGTTCCTCCACCCAGGGAGAGCACAGTCAAGGTGCACGGCCAAGTGATATCCTTGTGAGTCACCGGGCGCTACAACGGGCGCGCCGAGAGGCCACCCGACAGGAAGAAACGCTACGGGGAGAAGAAGCCTCCCTGGAAGCGTTTATACGCGTGGCCTCTGAAAAGCGTGAAAGAGAAGGGCAGAGGTCTCTCGAGGTGCTCCGCCAGCGCGTGGAAAATCAGACTGCAGAACTTGCTGTGTTACGCGTCGAGGCAGCACTAGAGCGGCAACGTGAAATGGTGGAGCTCGAGAGGAGGCGCGGAGACTTACTGGCCCTGGCCTTAGTCGCAGAAGACGACGAAGAATATCTTCGGCTGAGTGCAGAAGAAGAAGCAGTCCAACGGCAAATCGAGCAATTGGCGGAGGAAACGAGGAGACCGCGCCGTGGCCGTAGAAAGCCCGCGTGA
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42
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+
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43
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TABLE: SNPs Summary
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44
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[strain_a_query] [strain_b_query] [Strain A] [Strain B] [gene_source_id] [CDS SNP Density] [Non-synonymous] [Synonymous] [Nonsense] [Non-coding] [Total]
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45
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RH (type I) VEG (type III) RH VEG TGME49_000010 .81 1 0 0 4 5
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ME49 (type II) RH (type I) ME49 RH TGME49_000010 .81 1 0 0 4 5
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|
48
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TABLE: Gene Model
|
49
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[Type] [Start] [End]
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50
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exon 2230843 2232576
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intron 2232577 2232920
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exon 2232921 2234577
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53
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+
|
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TABLE: ME49 Microarray Expression Data
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55
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[ME49 Gene Model]
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56
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TGME49_000010
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57
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TGME49_045430
|
58
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+
|
59
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TABLE: Three archetypal T. gondii lineages - Percentiles
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60
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[Strain] [Percentile]
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61
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VEG 11.5
|
62
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CTG 23.2
|
63
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+
Prugniaud 71.9
|
64
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RH 78.7
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65
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GT1 78.2
|
66
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+
ME49 82.7
|
67
|
+
|
68
|
+
TABLE: InterPro Domains
|
69
|
+
[Name] [Primary ID] [Secondary ID] [Start Min] [End Min] [E-value]
|
70
|
+
|
71
|
+
TABLE: Transmembrane Domains
|
72
|
+
[Name] [Parent ID] [Start Min] [End Max] [Sequence] [Topology]
|
73
|
+
|
74
|
+
TABLE: Low Complexity Regions
|
75
|
+
[Name] [Parent ID] [Start Min] [End Max]
|
76
|
+
263625 89354 403 410
|
77
|
+
263623 89354 341 354
|
78
|
+
263622 89354 287 304
|
79
|
+
263620 89354 186 201
|
80
|
+
263619 89354 136 166
|
81
|
+
263621 89354 239 256
|
82
|
+
263624 89354 367 382
|
83
|
+
|
84
|
+
TABLE: Signal Peptide
|
85
|
+
[Name] [NN Conclusion Score] [NN D-Score] [HMM Signal Probabability] [Start Min] [End Max]
|
86
|
+
|
87
|
+
TABLE: BlastP Hits
|
88
|
+
[Feature ID] [Name] [Parent ID] [Score] [Start] [End] [Description] [Expect Value] [Percent Identity] [Percent Positive]
|
89
|
+
728519 TGME49_000010 89354 147 240 400 E() = 9.9e-6, 30% identity, gi|183598034|ref|ZP_02959527.1| hypothetical protein PROSTU_01390 [Providencia stuartii ATCC 25827]gi|188022813|gb|EDU60853.1| hypothetical protein PROSTU_01390 [Providencia stuartii ATCC 25827] 9.9e-6 0 0
|
90
|
+
|
91
|
+
TABLE: Gene Location
|
92
|
+
[Sequence Level] [Genomic Sequence] [Location] [start] [end] [is_reversed] [start_context] [end_context] [Feature ID]
|
93
|
+
Chromosome TGME49_chrXII 2230843 - 2234577 (-) 2230843 2234577 - 2225843 2239577 TGME49_000010
|
94
|
+
Scaffold DS984812 1393 - 5127 (+) 1393 5127 + -3607 10127 TGME49_000010
|
95
|
+
|
96
|
+
TABLE: Release 4 Genes
|
97
|
+
[Gene ID] [Product] [Sequence ID] [Location] [=Release5 protein?] [cyc_gene_id] [start] [end] [strand] [context_start] [context_end]
|
98
|
+
1.m00014 hypothetical protein TGG_995340 1393 - 5127 (+) Yes 1.M00014 1393 5127 + 0 10127
|
99
|
+
|
100
|
+
TABLE: Notes
|
101
|
+
[Note]
|
102
|
+
encoded by transcript TGME49_000010A
|
103
|
+
|
104
|
+
TABLE: User Comments
|
105
|
+
[Comment ID] [stable_id] [comment_target_id] [Headline] [PubMed ID(s)] [# Related Genes] [# Uploaded Files] [Made by] [Date]
|
106
|
+
|
107
|
+
TABLE: EC Number
|
108
|
+
[EC Number] [Source] [EC Description]
|
109
|
+
|
110
|
+
TABLE: Mass Spec.-based Expression Evidence
|
111
|
+
[Experiment Name] [Sequences] [Sequence Count] [Spectrum Count]
|
112
|
+
|
113
|
+
TABLE: GO Terms
|
114
|
+
[GO ID] [Ontology] [GO Term Name] [Source] [Evidence Code] [lowercase_evidence_code] [Is Not]
|
115
|
+
|
116
|
+
TABLE: Orthologs and Paralogs within ToxoDB
|
117
|
+
[Gene] [Species] [Product]
|
118
|
+
TGME49_087740 Toxoplasma gondii ME49 hypothetical protein
|
119
|
+
|
120
|
+
TABLE: Metabolic Pathways
|
121
|
+
[pathway_id] [Pathway] [activity]
|
122
|
+
|
123
|
+
TABLE: Strains summary
|
124
|
+
[Gene] [Strain] [Product] [Protein Length] [# Exons] [# TM] [Signal Peptide] [Proteomics?] [User Comment?]
|
125
|
+
TGME49_000010 ME49 hypothetical protein 413 2 0 No No Yes
|
126
|
+
|
127
|
+
TABLE: Toxoplasma Genome Sequencing Project Annotation
|
128
|
+
[TASK Annotation]
|
129
|
+
Unsure of gene model. There is difference between the manatee and the Gbrowse gene models.<br/><b>Reviewed by</b>: DS
|
130
|
+
|
131
|
+
TABLE: Antibody Reagents
|
132
|
+
[remark] [Reagent ID] [Reagent Type]
|
133
|
+
|
134
|
+
TABLE: External Links
|
135
|
+
[Database] [source_id] [link_url]
|
136
|
+
|
137
|
+
TABLE: Epitopes from IEDB
|
138
|
+
[Epitope] [Sequence] [Location on Protein] [Strain] [Confidence]
|
139
|
+
|
140
|
+
TABLE: Product
|
141
|
+
[Product]
|
142
|
+
hypothetical protein
|
143
|
+
|
144
|
+
|
145
|
+
------------------------------------------------------------
|
146
|
+
|
147
|
+
ID: TGME49_000110
|
148
|
+
Gene Group: TG_16806
|
149
|
+
Data Source: T.gondii ME49 contigs from Genbank
|
150
|
+
Genomic Sequence ID: TGME49_chrIX
|
151
|
+
Chromosome: IX
|
152
|
+
Genomic Location: TGME49_chrIX: 106,477 - 106,854 (+)
|
153
|
+
Gene Strand: forward
|
154
|
+
Gene Type: protein coding
|
155
|
+
# Exons: 1
|
156
|
+
Transcript Length: 378
|
157
|
+
CDS Length: 378
|
158
|
+
Product Description: hypothetical protein, conserved
|
159
|
+
Protein Length: 125
|
160
|
+
# TM Domains: 0
|
161
|
+
Molecular Weight: 13492
|
162
|
+
Isoelectric Point: 5.63
|
163
|
+
EC Numbers: null
|
164
|
+
Ortholog count: 1
|
165
|
+
Paralog count: 0
|
166
|
+
Temporary Ortholog Group: ORTH_16806.tmp
|
167
|
+
Total SNPs All Strains: 11
|
168
|
+
Nonsynonymous SNPs All Strains: 7
|
169
|
+
Synonymous SNPs All Strains: 4
|
170
|
+
Nonsyn/Syn SNP Ratio All Strains: 1.75
|
171
|
+
SignalP Scores: null
|
172
|
+
SignalP Peptide: null
|
173
|
+
Annotated GO Function: null
|
174
|
+
Annotated GO Process: null
|
175
|
+
Annotated GO Component: null
|
176
|
+
Predicted GO Function: null
|
177
|
+
Predicted GO Process: null
|
178
|
+
Predicted GO Component: null
|
179
|
+
TypeIII / TypeI fold-change: 1.01844018466976
|
180
|
+
TypeIII / TypeII fold-change: -2.02099469638244
|
181
|
+
TypeII / TypeI fold-change: 2.05826221180034
|
182
|
+
Organism: Toxoplasma gondii ME49
|
183
|
+
Release4 IDs: 2.m00067
|
184
|
+
= Release4 Protein?: Yes
|
185
|
+
Predicted Protein Sequence: MVLKENLRVKQVHQGEDPMDIGYQPGNVWSVGSEVDVSCCVFVERAVKPAEISGTVRECRHAPAGNSCNADCLSSPTVHVLIFLTTTTEGGVCQMAKAKYVGRRQEAICLQAALGEMLSEITNPL
|
186
|
+
Predicted RNA/mRNA Sequence (introns spliced out): ATGGTATTAAAAGAGAATTTGCGCGTGAAGCAGGTACACCAGGGGGAGGATCCCATGGATATTGGTTACCAGCCGGGGAATGTTTGGTCCGTCGGCTCGGAGGTGGATGTGAGCTGTTGTGTATTTGTGGAACGAGCGGTGAAGCCTGCCGAAATTAGCGGAACCGTCAGAGAATGCCGCCACGCGCCTGCGGGAAACAGTTGCAACGCCGATTGTTTGTCGTCACCGACTGTGCACGTCCTTATTTTCCTCACAACGACCACCGAGGGAGGTGTTTGCCAGATGGCGAAGGCGAAGTACGTTGGCCGCCGCCAAGAAGCGATCTGTCTGCAGGCCGCCCTCGGAGAAATGCTGAGCGAGATCACAAATCCGCTATGA
|
187
|
+
Coding Sequence: ATGGTATTAAAAGAGAATTTGCGCGTGAAGCAGGTACACCAGGGGGAGGATCCCATGGATATTGGTTACCAGCCGGGGAATGTTTGGTCCGTCGGCTCGGAGGTGGATGTGAGCTGTTGTGTATTTGTGGAACGAGCGGTGAAGCCTGCCGAAATTAGCGGAACCGTCAGAGAATGCCGCCACGCGCCTGCGGGAAACAGTTGCAACGCCGATTGTTTGTCGTCACCGACTGTGCACGTCCTTATTTTCCTCACAACGACCACCGAGGGAGGTGTTTGCCAGATGGCGAAGGCGAAGTACGTTGGCCGCCGCCAAGAAGCGATCTGTCTGCAGGCCGCCCTCGGAGAAATGCTGAGCGAGATCACAAATCCGCTATGA
|
188
|
+
|
189
|
+
TABLE: SNPs Summary
|
190
|
+
[strain_a_query] [strain_b_query] [Strain A] [Strain B] [gene_source_id] [CDS SNP Density] [Non-synonymous] [Synonymous] [Nonsense] [Non-coding] [Total]
|
191
|
+
454 Me49 454 Me49 TGME49_000110 29.1 7 4 1 0 11
|
192
|
+
|
193
|
+
TABLE: Gene Model
|
194
|
+
[Type] [Start] [End]
|
195
|
+
exon 106477 106854
|
196
|
+
|
197
|
+
TABLE: ME49 Microarray Expression Data
|
198
|
+
[ME49 Gene Model]
|
199
|
+
TGME49_000110
|
200
|
+
|
201
|
+
TABLE: Three archetypal T. gondii lineages - Percentiles
|
202
|
+
[Strain] [Percentile]
|
203
|
+
VEG 31
|
204
|
+
CTG 41
|
205
|
+
ME49 51.2
|
206
|
+
RH 32.7
|
207
|
+
GT1 37.8
|
208
|
+
Prugniaud 63.8
|
209
|
+
|
210
|
+
TABLE: InterPro Domains
|
211
|
+
[Name] [Primary ID] [Secondary ID] [Start Min] [End Min] [E-value]
|
212
|
+
|
213
|
+
TABLE: Transmembrane Domains
|
214
|
+
[Name] [Parent ID] [Start Min] [End Max] [Sequence] [Topology]
|
215
|
+
|
216
|
+
TABLE: Low Complexity Regions
|
217
|
+
[Name] [Parent ID] [Start Min] [End Max]
|
218
|
+
|
219
|
+
TABLE: Signal Peptide
|
220
|
+
[Name] [NN Conclusion Score] [NN D-Score] [HMM Signal Probabability] [Start Min] [End Max]
|
221
|
+
|
222
|
+
TABLE: BlastP Hits
|
223
|
+
[Feature ID] [Name] [Parent ID] [Score] [Start] [End] [Description] [Expect Value] [Percent Identity] [Percent Positive]
|
224
|
+
|
225
|
+
TABLE: Gene Location
|
226
|
+
[Sequence Level] [Genomic Sequence] [Location] [start] [end] [is_reversed] [start_context] [end_context] [Feature ID]
|
227
|
+
Chromosome TGME49_chrIX 106477 - 106854 (+) 106477 106854 + 101477 111854 TGME49_000110
|
228
|
+
Scaffold DS984780 3292 - 3669 (-) 3292 3669 - -1708 8669 TGME49_000110
|
229
|
+
|
230
|
+
TABLE: Release 4 Genes
|
231
|
+
[Gene ID] [Product] [Sequence ID] [Location] [=Release5 protein?] [cyc_gene_id] [start] [end] [strand] [context_start] [context_end]
|
232
|
+
2.m00067 conserved hypothetical protein IX 106377 - 106754 (+) Yes 2.M00067 106377 106754 + 101377 111754
|
233
|
+
|
234
|
+
TABLE: Notes
|
235
|
+
[Note]
|
236
|
+
encoded by transcript TGME49_000110A
|
237
|
+
|
238
|
+
TABLE: User Comments
|
239
|
+
[Comment ID] [stable_id] [comment_target_id] [Headline] [PubMed ID(s)] [# Related Genes] [# Uploaded Files] [Made by] [Date]
|
240
|
+
|
241
|
+
TABLE: EC Number
|
242
|
+
[EC Number] [Source] [EC Description]
|
243
|
+
|
244
|
+
TABLE: Mass Spec.-based Expression Evidence
|
245
|
+
[Experiment Name] [Sequences] [Sequence Count] [Spectrum Count]
|
246
|
+
|
247
|
+
TABLE: GO Terms
|
248
|
+
[GO ID] [Ontology] [GO Term Name] [Source] [Evidence Code] [lowercase_evidence_code] [Is Not]
|
249
|
+
|
250
|
+
TABLE: Orthologs and Paralogs within ToxoDB
|
251
|
+
[Gene] [Species] [Product] [is syntenic] [has comments]
|
252
|
+
|
253
|
+
TABLE: Metabolic Pathways
|
254
|
+
[pathway_id] [Pathway] [activity]
|
255
|
+
|
256
|
+
TABLE: Strains summary
|
257
|
+
[Gene] [Strain] [Product] [Protein Length] [# Exons] [# TM] [Signal Peptide] [Proteomics?] [User Comment?]
|
258
|
+
TGME49_000110 ME49 hypothetical protein, conserved 125 1 0 No No No
|
259
|
+
|
260
|
+
TABLE: Toxoplasma Genome Sequencing Project Annotation
|
261
|
+
[TASK Annotation]
|
262
|
+
|
263
|
+
TABLE: Antibody Reagents
|
264
|
+
[remark] [Reagent ID] [Reagent Type]
|
265
|
+
|
266
|
+
TABLE: External Links
|
267
|
+
[Database] [source_id] [link_url]
|
268
|
+
|
269
|
+
TABLE: Epitopes from IEDB
|
270
|
+
[Epitope] [Sequence] [Location on Protein] [Strain] [Confidence]
|
271
|
+
|
272
|
+
TABLE: Product
|
273
|
+
[Product]
|
274
|
+
hypothetical protein, conserved
|
275
|
+
|
276
|
+
|
277
|
+
------------------------------------------------------------
|
278
|
+
|
data/test/helper.rb
ADDED
@@ -0,0 +1,60 @@
|
|
1
|
+
|
2
|
+
require 'helper'
|
3
|
+
require 'eupathdb_gene_information_table'
|
4
|
+
|
5
|
+
class EuPathDBGeneInformationTableTest < Test::Unit::TestCase
|
6
|
+
def test_gene_splitting
|
7
|
+
eu = EuPathDBGeneInformationTable.new(File.open(File.join(File.dirname(__FILE__),'data','eupathGeneInformation.txt'),'r'))
|
8
|
+
genes = %w(TGME49_000010 TGME49_000110)
|
9
|
+
total = 0
|
10
|
+
eu.each_with_index do |info, i|
|
11
|
+
total += 1
|
12
|
+
assert_equal genes[i], info.get_info('ID')
|
13
|
+
end
|
14
|
+
assert_equal 2, total
|
15
|
+
end
|
16
|
+
|
17
|
+
def test_table
|
18
|
+
eu = EuPathDBGeneInformationTable.new(File.open(File.join(File.dirname(__FILE__),'data','eupathGeneInformation.txt'),'r'))
|
19
|
+
genes = [
|
20
|
+
{
|
21
|
+
'Type' => 'exon',
|
22
|
+
'Start' => '2230843',
|
23
|
+
'End' => '2232576'
|
24
|
+
},
|
25
|
+
{
|
26
|
+
'Type' => 'intron',
|
27
|
+
'Start' => '2232577',
|
28
|
+
'End' => '2232920'
|
29
|
+
},
|
30
|
+
{
|
31
|
+
'Type' => 'exon',
|
32
|
+
'Start' => '2232921',
|
33
|
+
'End' => '2234577'
|
34
|
+
},
|
35
|
+
]
|
36
|
+
assert_equal genes, eu.to_a[0].get_table('Gene Model')
|
37
|
+
end
|
38
|
+
|
39
|
+
def test_last_entry
|
40
|
+
eu = EuPathDBGeneInformationTable.new(File.open(File.join(File.dirname(__FILE__),'data','eupathGeneInformation.txt'),'r'))
|
41
|
+
a = eu.to_a
|
42
|
+
first = a[0]
|
43
|
+
last = a[1]
|
44
|
+
assert_equal [{'Product' => 'hypothetical protein, conserved'}],
|
45
|
+
last.get_table('Product')
|
46
|
+
assert_equal [{'Product' => 'hypothetical protein'}],
|
47
|
+
first.get_table('Product')
|
48
|
+
end
|
49
|
+
|
50
|
+
def test_alias_brackets
|
51
|
+
eu = EuPathDBGeneInformationTable.new(File.open(File.join(File.dirname(__FILE__),'data','eupathGeneInformation.txt'),'r'))
|
52
|
+
genes = %w(TGME49_000010 TGME49_000110)
|
53
|
+
total = 0
|
54
|
+
eu.each_with_index do |info, i|
|
55
|
+
total += 1
|
56
|
+
assert_equal genes[i], info['ID']
|
57
|
+
end
|
58
|
+
assert_equal 2, total
|
59
|
+
end
|
60
|
+
end
|
metadata
ADDED
@@ -0,0 +1,91 @@
|
|
1
|
+
--- !ruby/object:Gem::Specification
|
2
|
+
name: reubypathdb
|
3
|
+
version: !ruby/object:Gem::Version
|
4
|
+
hash: 27
|
5
|
+
prerelease: false
|
6
|
+
segments:
|
7
|
+
- 0
|
8
|
+
- 1
|
9
|
+
- 0
|
10
|
+
version: 0.1.0
|
11
|
+
platform: ruby
|
12
|
+
authors:
|
13
|
+
- Ben J Woodcroft
|
14
|
+
autorequire:
|
15
|
+
bindir: bin
|
16
|
+
cert_chain: []
|
17
|
+
|
18
|
+
date: 2010-11-01 00:00:00 +11:00
|
19
|
+
default_executable:
|
20
|
+
dependencies:
|
21
|
+
- !ruby/object:Gem::Dependency
|
22
|
+
name: thoughtbot-shoulda
|
23
|
+
prerelease: false
|
24
|
+
requirement: &id001 !ruby/object:Gem::Requirement
|
25
|
+
none: false
|
26
|
+
requirements:
|
27
|
+
- - ">="
|
28
|
+
- !ruby/object:Gem::Version
|
29
|
+
hash: 3
|
30
|
+
segments:
|
31
|
+
- 0
|
32
|
+
version: "0"
|
33
|
+
type: :development
|
34
|
+
version_requirements: *id001
|
35
|
+
description: Classes to help parsing EuPathDB data files
|
36
|
+
email: donttrustben near gmail.com
|
37
|
+
executables: []
|
38
|
+
|
39
|
+
extensions: []
|
40
|
+
|
41
|
+
extra_rdoc_files:
|
42
|
+
- LICENSE
|
43
|
+
- README.rdoc
|
44
|
+
files:
|
45
|
+
- .document
|
46
|
+
- .gitignore
|
47
|
+
- LICENSE
|
48
|
+
- README.rdoc
|
49
|
+
- Rakefile
|
50
|
+
- VERSION
|
51
|
+
- lib/eupathdb_gene_information_table.rb
|
52
|
+
- test/data/eupathGeneInformation.txt
|
53
|
+
- test/helper.rb
|
54
|
+
- test/test_eupathdb_gene_information_table.rb
|
55
|
+
has_rdoc: true
|
56
|
+
homepage: http://github.com/wwood/reubypathdb
|
57
|
+
licenses: []
|
58
|
+
|
59
|
+
post_install_message:
|
60
|
+
rdoc_options:
|
61
|
+
- --charset=UTF-8
|
62
|
+
require_paths:
|
63
|
+
- lib
|
64
|
+
required_ruby_version: !ruby/object:Gem::Requirement
|
65
|
+
none: false
|
66
|
+
requirements:
|
67
|
+
- - ">="
|
68
|
+
- !ruby/object:Gem::Version
|
69
|
+
hash: 3
|
70
|
+
segments:
|
71
|
+
- 0
|
72
|
+
version: "0"
|
73
|
+
required_rubygems_version: !ruby/object:Gem::Requirement
|
74
|
+
none: false
|
75
|
+
requirements:
|
76
|
+
- - ">="
|
77
|
+
- !ruby/object:Gem::Version
|
78
|
+
hash: 3
|
79
|
+
segments:
|
80
|
+
- 0
|
81
|
+
version: "0"
|
82
|
+
requirements: []
|
83
|
+
|
84
|
+
rubyforge_project:
|
85
|
+
rubygems_version: 1.3.7
|
86
|
+
signing_key:
|
87
|
+
specification_version: 3
|
88
|
+
summary: Classes to help parsing EuPathDB data files
|
89
|
+
test_files:
|
90
|
+
- test/helper.rb
|
91
|
+
- test/test_eupathdb_gene_information_table.rb
|