bio-location-rdfize 0.0.0

checksums.yaml

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+SHA1:
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+  data.tar.gz: 5c55e227f676456077aa813aa2ee7cfa8033f2c3
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data/.document

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+lib/**/*.rb
+bin/*
+- 
+features/**/*.feature
+LICENSE.txt

data/.travis.yml

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+language: ruby
+rvm:
+  - 1.9.2
+  - 1.9.3
+  - jruby-19mode # JRuby in 1.9 mode
+
+# - rbx-19mode
+#  - 1.8.7
+#  - jruby-18mode # JRuby in 1.8 mode
+#  - rbx-18mode
+
+# uncomment this line if your project needs to run something other than `rake`:
+# script: bundle exec rspec spec

data/Gemfile

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+source "http://rubygems.org"
+# Add dependencies required to use your gem here.
+# Example:
+#   gem "activesupport", ">= 2.3.5"
+
+gem "bio", ">= 1.4.2"
+
+# Add dependencies to develop your gem here.
+# Include everything needed to run rake, tests, features, etc.
+group :development do
+  gem "rake"
+  gem "rdoc"
+  gem "jeweler"
+  gem "bundler", ">= 1.0.21"
+end

data/LICENSE.txt

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+Copyright (c) 2014 Naohisa Goto
+
+Permission is hereby granted, free of charge, to any person obtaining
+a copy of this software and associated documentation files (the
+"Software"), to deal in the Software without restriction, including
+without limitation the rights to use, copy, modify, merge, publish,
+distribute, sublicense, and/or sell copies of the Software, and to
+permit persons to whom the Software is furnished to do so, subject to
+the following conditions:
+
+The above copyright notice and this permission notice shall be
+included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
+LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
+WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

data/README.md

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+# bio-location-rdfize
+
+[![Build Status](https://secure.travis-ci.org/ngoto/bioruby-location-rdfize.png)](http://travis-ci.org/ngoto/bioruby-location-rdfize)
+
+Full description goes here
+
+Note: this software is under active development!
+
+## Installation
+
+```sh
+gem install bio-location-rdfize
+```
+
+## Usage
+
+```ruby
+require 'bio-location-rdfize'
+```
+
+The API doc is online. For more code examples see the test files in
+the source tree.
+        
+## Project home page
+
+Information on the source tree, documentation, examples, issues and
+how to contribute, see
+
+  http://github.com/ngoto/bioruby-location-rdfize
+
+The BioRuby community is on IRC server: irc.freenode.org, channel: #bioruby.
+
+## Cite
+
+If you use this software, please cite one of
+  
+* [BioRuby: bioinformatics software for the Ruby programming language](http://dx.doi.org/10.1093/bioinformatics/btq475)
+* [Biogem: an effective tool-based approach for scaling up open source software development in bioinformatics](http://dx.doi.org/10.1093/bioinformatics/bts080)
+
+## Biogems.info
+
+This Biogem is published at (http://biogems.info/index.html#bio-location-rdfize)
+
+## Copyright
+
+Copyright (c) 2014 Naohisa Goto. See LICENSE.txt for further details.
+

data/README.rdoc

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+= bio-location-rdfize
+
+{<img
+src="https://secure.travis-ci.org/ngoto/bioruby-location-rdfize.png"
+/>}[http://travis-ci.org/#!/ngoto/bioruby-location-rdfize]
+
+Full description goes here
+
+Note: this software is under active development!
+
+== Installation
+
+        gem install bio-location-rdfize
+
+== Usage
+
+== Developers
+
+To use the library 
+
+        require 'bio-location-rdfize'
+
+The API doc is online. For more code examples see also the test files in
+the source tree.
+        
+== Project home page
+
+Information on the source tree, documentation, issues and how to contribute, see
+
+  http://github.com/ngoto/bioruby-location-rdfize
+
+The BioRuby community is on IRC server: irc.freenode.org, channel: #bioruby.
+
+== Cite
+
+  If you use this software, please cite one of
+ 
+* [BioRuby: bioinformatics software for the Ruby programming language](http://dx.doi.org/10.1093/bioinformatics/btq475)
+* [Biogem: an effective tool-based approach for scaling up open source software development in bioinformatics](http://dx.doi.org/10.1093/bioinformatics/bts080)
+
+== Biogems.info
+
+This Biogem is published at http://biogems.info/index.html#bio-location-rdfize
+
+== Copyright
+
+Copyright (c) 2014 Naohisa Goto. See LICENSE.txt for further details.
+

data/Rakefile

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+# encoding: utf-8
+
+require 'rubygems'
+require 'bundler'
+begin
+  Bundler.setup(:default, :development)
+rescue Bundler::BundlerError => e
+  $stderr.puts e.message
+  $stderr.puts "Run `bundle install` to install missing gems"
+  exit e.status_code
+end
+require 'rake'
+
+require 'jeweler'
+Jeweler::Tasks.new do |gem|
+  # gem is a Gem::Specification... see http://guides.rubygems.org/specification-reference/ for more options
+  gem.name = "bio-location-rdfize"
+  gem.homepage = "http://github.com/ngoto/bioruby-location-rdfize"
+  gem.license = "MIT"
+  gem.summary = %Q{FALDO location output method for Bio::Location in BioRuby}
+  gem.description = %Q{This is a BioRuby plugin providing FALDO location RDF output method for Bio::Location objects. A method Bio::Location#rdfize is added.}
+  gem.email = "ng@bioruby.org"
+  gem.authors = [ "Joachim Baran", "Naohisa Goto" ]
+  # dependencies defined in Gemfile
+end
+Jeweler::RubygemsDotOrgTasks.new
+
+require 'rake/testtask'
+Rake::TestTask.new(:test) do |test|
+  test.libs << 'lib' << 'test'
+  test.pattern = 'test/**/test_*.rb'
+  test.verbose = true
+end
+
+desc "Code coverage detail"
+task :simplecov do
+  ENV['COVERAGE'] = "true"
+  Rake::Task['test'].execute
+end
+
+task :default => :test
+
+require 'rdoc/task'
+Rake::RDocTask.new do |rdoc|
+  version = File.exist?('VERSION') ? File.read('VERSION') : ""
+
+  rdoc.rdoc_dir = 'rdoc'
+  rdoc.title = "bio-location-rdfize #{version}"
+  rdoc.rdoc_files.include('README*')
+  rdoc.rdoc_files.include('lib/**/*.rb')
+end

data/VERSION

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+0.0.0

data/lib/bio-location-rdfize.rb

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+# Please require your code below, respecting the naming conventions in the
+# bioruby directory tree.
+#
+# For example, say you have a plugin named bio-plugin, the only uncommented
+# line in this file would be 
+#
+#   require 'bio/bio-plugin/plugin'
+#
+# In this file only require other files. Avoid other source code.
+
+require 'bio'
+require 'bio-location-rdfize/location-rdfize.rb'
+

data/lib/bio-location-rdfize/location-rdfize.rb

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+#
+# Copyright::	Copyright (C) 2014 Joachim Baran <joachim.baran@gmail.com>
+# License::	The Ruby License
+
+module Bio
+
+# Bio::Location is a class in BioRuby.
+# For adding methods, the module Bio::Location::RDFize is included.
+class Location
+
+# Bio::Location::RDFize is a module for providing
+# Bio::Location#rdfize method. 
+# For the usage of the method, see the documentation of
+# Bio::Location::RDFize#rdfize.
+#
+module RDFize
+
+  # Base URI of FALDO for use with rdfize and rdfize_positions:
+  FALDO = 'http://biohackathon.org/resource/faldo#'.freeze
+
+  # Returns a FALDO based representation of the location
+  # in RDF Turtle format.
+  # *Arguments*:
+  # * (required) _prefix_: URI prefix of the location's URIs
+  # *Returns*::
+  # * a string containing the location formatted using FALDO
+  #   in RDF Turtle format; the URI prefix will be prepended
+  #   before either xref ID or a composite string that captures
+  #   the location uniquely
+  def rdfize(prefix)
+    # Less-than/greater-than (@lt, @gt) are currently not holding
+    # enough information to determine whether a single seq. position
+    # is affected, or whether start/end positions are targeted by
+    # the relation.
+    # For example, "<500..>1000" and ">500..<1000" are both encoded
+    # as:
+    #   @lt = @gt = true
+    #   @from = 500
+    #   @to = 1000
+    # It is an ambiguous representation and the original meaning
+    # can no longer be determined.
+    if @lt or @gt
+      raise "Error: cannot RDFize locations with < or > in them. Sorry."
+    end
+
+    if @strand == 1
+      faldo_begin, faldo_end = @from, @to
+    else
+      # Reverse begin/end, if on the reverse strand (5'-3' FALDO requirement)
+      faldo_end, faldo_begin = faldo_begin, faldo_end
+    end
+    
+    id = @xref_id
+    unless id
+      id = "Location#{faldo_begin}-#{faldo_end}:#{@strand}"
+    end
+
+    if @caret
+      return """<#{prefix}#{id}> a <#{FALDO}InBetweenPosition> ;
+    <#{FALDO}after> <#{prefix}#{id}:begin> ;
+    <#{FALDO}before> <#{prefix}#{id}:end> .
+
+#{rdfize_positions("#{prefix}#{id}", faldo_begin, faldo_end)}
+"""
+    end
+
+    if @from == @to
+      begin_uri_suffix = 'position'
+      end_uri_suffix = 'position'
+    else
+      begin_uri_suffix = 'begin'
+      end_uri_suffix = 'end'
+    end
+
+    return """<#{prefix}#{id}> a <#{FALDO}Region> ;
+    <#{FALDO}begin> <#{prefix}#{id}:#{begin_uri_suffix}> ;
+    <#{FALDO}end> <#{prefix}#{id}:#{end_uri_suffix}> .
+
+#{rdfize_positions("#{prefix}#{id}", faldo_begin, faldo_end, begin_uri_suffix, end_uri_suffix)}
+"""
+  end
+
+private
+
+  # Returns FALDO ExactPosition RDF Turtle for @from and @to. Will only
+  # serialize a single position if begin/end URI suffixes coincide.
+  #
+  # *Arguments*:
+  # * (required) _location_prefix_: URI prefix of the location object
+  #                                 whose positions are being described here
+  # * (required) _faldo_begin_: start coordinate of the location
+  # * (required) _faldo_end_: end coordinate of the location
+  # * (optional) _begin_suffix_ : URI suffix that should be used for faldo_begin coodinate
+  # * (optional) _end_suffix_ : URI suffix that should be used for faldo_end coodinate
+  # *Returns*::
+  # * a string containing FALDO ExactPosition instances that represent
+  #   the location's start/end coordinates.
+  def rdfize_positions(location_prefix, faldo_begin, faldo_end, begin_suffix = 'begin', end_suffix = 'end')
+    if @strand == 1
+      strandtype = "<#{FALDO}ForwardStrandedPosition>"
+    else
+      strandtype = "<#{FALDO}ReverseStrandedPosition>"
+    end
+
+    begin_uri = """<#{location_prefix}:#{begin_suffix}> a <#{FALDO}ExactPosition>, #{strandtype} ;
+    <#{FALDO}position> #{faldo_begin} .
+"""
+
+    if begin_suffix == end_suffix
+      end_uri = ''
+    else
+      end_uri = """<#{location_prefix}:#{end_suffix}> a <#{FALDO}ExactPosition>, #{strandtype} ;
+    <#{FALDO}position> #{faldo_end} .
+"""
+    end
+
+    return begin_uri + end_uri
+  end
+
+end #module RDFize
+
+# adding the above methods to Bio::Locations
+include RDFize
+
+end # Locations
+
+end # Bio

data/test/helper.rb

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+#
+#require 'simplecov'
+#
+#module SimpleCov::Configuration
+#  def clean_filters
+#    @filters = []
+#  end
+#end
+#
+#SimpleCov.configure do
+#  clean_filters
+#  load_adapter 'test_frameworks'
+#end
+#
+#ENV["COVERAGE"] && SimpleCov.start do
+#  add_filter "/.rvm/"
+#end
+#
+require 'rubygems'
+#require 'bundler'
+#begin
+#  Bundler.setup(:default, :development)
+#rescue Bundler::BundlerError => e
+#  $stderr.puts e.message
+#  $stderr.puts "Run `bundle install` to install missing gems"
+#  exit e.status_code
+#end
+require 'test/unit'
+#require 'shoulda'
+
+$LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
+$LOAD_PATH.unshift(File.dirname(__FILE__))
+require 'bio-location-rdfize'
+
+class Test::Unit::TestCase
+end

data/test/test_bio-location-rdfize.rb

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+
+# To run this test,
+#  % bundle exec rake test
+# or
+#  % rake test
+#
+
+require 'helper'
+require 'bio'
+
+class TestBioLocationRdfize < Test::Unit::TestCase
+
+  PREFIX = "http://localhost/test#".freeze
+
+  def test_forward
+    loc = Bio::Locations.new("123..456")[0]
+
+    expected = <<EXPECTED
+<http://localhost/test#Location123-456:1> a <http://biohackathon.org/resource/faldo#Region> ;
+    <http://biohackathon.org/resource/faldo#begin> <http://localhost/test#Location123-456:1:begin> ;
+    <http://biohackathon.org/resource/faldo#end> <http://localhost/test#Location123-456:1:end> .
+
+<http://localhost/test#Location123-456:1:begin> a <http://biohackathon.org/resource/faldo#ExactPosition>, <http://biohackathon.org/resource/faldo#ForwardStrandedPosition> ;
+    <http://biohackathon.org/resource/faldo#position> 123 .
+<http://localhost/test#Location123-456:1:end> a <http://biohackathon.org/resource/faldo#ExactPosition>, <http://biohackathon.org/resource/faldo#ForwardStrandedPosition> ;
+    <http://biohackathon.org/resource/faldo#position> 456 .
+
+EXPECTED
+
+    assert_equal(expected, loc.rdfize(PREFIX))
+  end
+
+  def test_reverse
+    loc = Bio::Locations.new("complement(123..456)")[0]
+
+    expected = <<EXPECTED
+<http://localhost/test#Location-:-1> a <http://biohackathon.org/resource/faldo#Region> ;
+    <http://biohackathon.org/resource/faldo#begin> <http://localhost/test#Location-:-1:begin> ;
+    <http://biohackathon.org/resource/faldo#end> <http://localhost/test#Location-:-1:end> .
+
+<http://localhost/test#Location-:-1:begin> a <http://biohackathon.org/resource/faldo#ExactPosition>, <http://biohackathon.org/resource/faldo#ReverseStrandedPosition> ;
+    <http://biohackathon.org/resource/faldo#position>  .
+<http://localhost/test#Location-:-1:end> a <http://biohackathon.org/resource/faldo#ExactPosition>, <http://biohackathon.org/resource/faldo#ReverseStrandedPosition> ;
+    <http://biohackathon.org/resource/faldo#position>  .
+
+EXPECTED
+
+    assert_equal(expected, loc.rdfize(PREFIX))
+  end
+
+end

metadata

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+--- !ruby/object:Gem::Specification
+name: bio-location-rdfize
+version: !ruby/object:Gem::Version
+  version: 0.0.0
+platform: ruby
+authors:
+- Joachim Baran
+- Naohisa Goto
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2014-11-10 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: bio
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 1.4.2
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 1.4.2
+- !ruby/object:Gem::Dependency
+  name: rake
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: rdoc
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: jeweler
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: bundler
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 1.0.21
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 1.0.21
+description: This is a BioRuby plugin providing FALDO location RDF output method for
+  Bio::Location objects. A method Bio::Location#rdfize is added.
+email: ng@bioruby.org
+executables: []
+extensions: []
+extra_rdoc_files:
+- LICENSE.txt
+- README.md
+- README.rdoc
+files:
+- ".document"
+- ".travis.yml"
+- Gemfile
+- LICENSE.txt
+- README.md
+- README.rdoc
+- Rakefile
+- VERSION
+- lib/bio-location-rdfize.rb
+- lib/bio-location-rdfize/location-rdfize.rb
+- test/helper.rb
+- test/test_bio-location-rdfize.rb
+homepage: http://github.com/ngoto/bioruby-location-rdfize
+licenses:
+- MIT
+metadata: {}
+post_install_message: 
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+required_rubygems_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubyforge_project: 
+rubygems_version: 2.2.2
+signing_key: 
+specification_version: 4
+summary: FALDO location output method for Bio::Location in BioRuby
+test_files: []