bio-dbla-classifier 0.2.1

data/.document

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

data/.rspec

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+--color

data/Gemfile

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+source "http://rubygems.org"
+
+ gem 'bio', '>= 1.4.2'
+
+# Needed to run rake, tests, features
+group :development do
+  gem "rspec", "~> 2.3.0"
+  gem "bundler", "~> 1.0.0"
+  gem "jeweler", "~> 1.6.4"
+  gem "rcov", ">= 0"
+end

data/Gemfile.lock

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+GEM
+  remote: http://rubygems.org/
+  specs:
+    bio (1.4.2)
+    diff-lcs (1.1.3)
+    git (1.2.5)
+    jeweler (1.6.4)
+      bundler (~> 1.0)
+      git (>= 1.2.5)
+      rake
+    rake (0.9.2)
+    rcov (0.9.10)
+    rspec (2.3.0)
+      rspec-core (~> 2.3.0)
+      rspec-expectations (~> 2.3.0)
+      rspec-mocks (~> 2.3.0)
+    rspec-core (2.3.1)
+    rspec-expectations (2.3.0)
+      diff-lcs (~> 1.1.2)
+    rspec-mocks (2.3.0)
+
+PLATFORMS
+  ruby
+
+DEPENDENCIES
+  bio (>= 1.4.2)
+  bundler (~> 1.0.0)
+  jeweler (~> 1.6.4)
+  rcov
+  rspec (~> 2.3.0)

data/LICENSE.txt

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+The Ruby License
+
+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.rdoc

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+= bio-dbla-classifier
+
+DBL-alpha tags can be classified into six expression groups depending on the number of cysteines and presence of 
+sequence certain motifs within the tag region (Bull et al 2007). DBLa adds methods for grouping DBL-alpha amino acid sequence tags.
+The DBLa class is a subclass of Bio::Sequence::AA. If you apply this method please quote this article
+Bull et al “An approach to classifying sequence tags sampled from Plasmodium falciparum var genes..” Molecular and Biochemical Parasitology 154 (1) (July): 98–102. doi:10.1016/j.molbiopara.2007.03.011.
+
+= Installation
+ 
+ gem install bio-dbla-classifier
+
+= Uninstall
+ 
+ gem uninstall bio-dbla-classifier
+
+= Usage
+ require 'bio'
+ require 'bio-dbla-classifier'
+
+ #create an instace of a new DBL-alpha tag. A dbla tag extends the Bio::Sequence::AA class with methods
+ #to classify and describe Dbla properties
+ seq = Dbla.new('DIGDIVRGRDMFKSNDDVEKGLKVVFKKIYKSLPSPAKSHYADHDKSGNYYKLREHWWIVNRKQLWEAITCIAPRDAHYFLKSSPDFKSFSDRKCGHYEGAPPTYLDYVPQYLR')
+
+ #get the positions of limited variability
+ puts seq.polv1
+ puts seq.polv2
+ puts seq.polv3
+ puts seq.polv4
+
+ #get the distinct sequence identifier
+ puts seq.dsid
+
+ #get the cyspolv group for this tag
+ puts seq.group
+
+ #get the number if cysteines in the tag
+ puts seq.cys_count
+
+ #get the block sharing group for this tag
+ #puts seq.bs_group
+ 
+ #get the length of the tag
+ #puts seq.size
+
+ #if input file is a fasta file
+ seq_file = "#{ENV['HOME']}/sequences/878_kilifi_sequences.fasta"
+
+ #read the file
+ Bio::FlatFile.open(seq_file).each do |entry|
+  puts  entry.definition
+  tag = Dbla.new(entry.seq)
+  puts tag.dsid
+  puts tag.get_group
+ end
+= Copyright
+
+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://docs.rubygems.org/read/chapter/20 for more options
+  gem.name = "bio-dbla-classifier"
+  gem.homepage = "http://github.com/georgeG/bioruby-dbla-classifier"
+  gem.license = "Ruby"
+  gem.summary = %Q{Classify PfEMP1 DBL-alpha tags using the cyspolv grouping approach}
+  gem.description = %Q{A classification system for DBL-alpha sequence tags using the CysPolv approach described by Bull et al 2005}
+  gem.email = "georgkam@gmail.com"
+  gem.authors = ["George Githinji"]
+  # dependencies defined in Gemfile
+end
+Jeweler::RubygemsDotOrgTasks.new
+
+require 'rspec/core'
+require 'rspec/core/rake_task'
+RSpec::Core::RakeTask.new(:spec) do |spec|
+  spec.pattern = FileList['spec/**/*_spec.rb']
+end
+
+RSpec::Core::RakeTask.new(:rcov) do |spec|
+  spec.pattern = 'spec/**/*_spec.rb'
+  spec.rcov = true
+end
+
+task :default => :spec
+
+require 'rake/rdoctask'
+Rake::RDocTask.new do |rdoc|
+  version = File.exist?('VERSION') ? File.read('VERSION') : ""
+
+  rdoc.rdoc_dir = 'rdoc'
+  rdoc.title = "bio-dbla-classifier #{version}"
+  rdoc.rdoc_files.include('README*')
+  rdoc.rdoc_files.include('lib/**/*.rb')
+end

data/VERSION

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+0.2.1

data/bio-dbla-classifier.gemspec

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+# Generated by jeweler
+# DO NOT EDIT THIS FILE DIRECTLY
+# Instead, edit Jeweler::Tasks in Rakefile, and run 'rake gemspec'
+# -*- encoding: utf-8 -*-
+
+Gem::Specification.new do |s|
+  s.name = "bio-dbla-classifier"
+  s.version = "0.2.1"
+
+  s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
+  s.authors = ["George Githinji"]
+  s.date = "2011-09-30"
+  s.description = "A classification system for DBL-alpha sequence tags using the CysPolv approach described by Bull et al 2005"
+  s.email = "georgkam@gmail.com"
+  s.extra_rdoc_files = [
+    "LICENSE.txt",
+    "README.rdoc"
+  ]
+  s.files = [
+    ".document",
+    ".rspec",
+    "Gemfile",
+    "Gemfile.lock",
+    "LICENSE.txt",
+    "README.rdoc",
+    "Rakefile",
+    "VERSION",
+    "bio-dbla-classifier.gemspec",
+    "lib/bio-dbla-classifier.rb",
+    "lib/bio/sequence/aa/dbla.rb",
+    "spec/bio-dbla-classifier_spec.rb",
+    "spec/dbla_spec.rb",
+    "spec/spec_helper.rb"
+  ]
+  s.homepage = "http://github.com/georgeG/bioruby-dbla-classifier"
+  s.licenses = ["Ruby"]
+  s.require_paths = ["lib"]
+  s.rubygems_version = "1.8.10"
+  s.summary = "Classify PfEMP1 DBL-alpha tags using the cyspolv grouping approach"
+
+  if s.respond_to? :specification_version then
+    s.specification_version = 3
+
+    if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
+      s.add_runtime_dependency(%q<bio>, [">= 1.4.2"])
+      s.add_development_dependency(%q<rspec>, ["~> 2.3.0"])
+      s.add_development_dependency(%q<bundler>, ["~> 1.0.0"])
+      s.add_development_dependency(%q<jeweler>, ["~> 1.6.4"])
+      s.add_development_dependency(%q<rcov>, [">= 0"])
+    else
+      s.add_dependency(%q<bio>, [">= 1.4.2"])
+      s.add_dependency(%q<rspec>, ["~> 2.3.0"])
+      s.add_dependency(%q<bundler>, ["~> 1.0.0"])
+      s.add_dependency(%q<jeweler>, ["~> 1.6.4"])
+      s.add_dependency(%q<rcov>, [">= 0"])
+    end
+  else
+    s.add_dependency(%q<bio>, [">= 1.4.2"])
+    s.add_dependency(%q<rspec>, ["~> 2.3.0"])
+    s.add_dependency(%q<bundler>, ["~> 1.0.0"])
+    s.add_dependency(%q<jeweler>, ["~> 1.6.4"])
+    s.add_dependency(%q<rcov>, [">= 0"])
+  end
+end
+

data/lib/bio-dbla-classifier.rb

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+ require 'bio'
+ require File.join(File.expand_path(File.dirname(__FILE__)), 'bio','sequence/aa/dbla')

data/lib/bio/sequence/aa/dbla.rb

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+class Dbla < Bio::Sequence::AA
+
+ def dsid
+   "#{polv1}-#{polv2}-#{polv3}-#{cys_count.to_s}-#{polv4}-#{self.length}"
+ end
+
+ def ww_pos
+  rindex("WW")
+ end
+
+ def vw_pos
+  rindex("VW")
+ end
+
+ #number of cysteines
+ def cys_count
+  scan(/C/).size
+ end
+
+ #The first position of limited variability(polv1)
+ def polv1
+  self[10,4]
+ end
+
+ #The second position of limited variability(polv2)
+ def polv2
+  if self =~ /WW/
+   polv2 = self[ww_pos - 4,4]
+  elsif self =~ /VW/
+   polv2 = self[vw_pos - 12,4]
+  else
+  end
+  polv2
+ end
+
+ #The third position of limited variability(polv3)
+ def polv3
+  if self =~ /WW/
+   polv3 = self[ww_pos + 10,4] 
+  elsif self =~ /VW/
+   polv3 = self[vw_pos + 2,4]
+  else
+  end
+  polv3
+ end
+ 
+ #The fourth position of limited variability(polv4)
+ def polv4
+  self[self.length - 12,4]
+ end
+
+ #Assigning dsid group based on cysteines coun and presence of
+ #REY motif in polv2, MFK in polv1,
+ def cyspolv_group
+  case
+   when cys_count > 4 || cys_count == 3 || cys_count < 2
+    group = 6
+   when cys_count == 4 && polv2 =~ /REY/i
+    group = 5
+   when cys_count == 4
+    group = 4
+   when cys_count == 2 && polv1 =~ /MFK/i
+    group = 1
+   when cys_count == 2 && polv2 =~ /REY/i
+    group =2
+   else
+    group = 3
+  end
+  group
+ end
+end
+
+
+#create an instace of a new DBL-alpha tag. A dbla tag extends the Bio::Sequence::AA class with methods
+#to classify and describe Dbla properties
+
+#seq1 = 'DIGDIIRGRDLYSGNNKEKEQRKKLEKNGKTIVGKIYNEATNGQALQARYKGDDNNNYSKLREDRWTANRATIWEAITCDDDNKLSNASYVRPTSTDGQSGAQGKDKCRSANKTTGNTGDVNIVPTYFDYVPQYLR'
+#seq = Dbla.new(seq1)
+
+#get the positions of limited variability
+#puts seq.polv1
+#puts seq.polv2
+#puts seq.polv3
+#puts seq.polv4
+
+#get the number if cysteines in the tag
+#puts seq.cys_count
+
+#get the distinct sequence identifier
+#puts seq.dsid
+
+#get the cyspolv group for this tag
+#puts seq.cyspolv_group
+
+
+#get the block sharing group for this tag
+#puts seq.bs_group #to be implemented
+
+#get the length of the tag
+#puts seq.size
+
+#if input file is a fasta file
+ #seq_file = "#{ENV['HOME']}/sequences/878_kilifi_sequences.fasta"
+
+#read the file
+ #Bio::FlatFile.open(seq_file).each do |entry|
+  #tag = Dbla.new(entry.seq)
+  #puts "#{entry.definition},#{tag.dsid},#{tag.cys_count},#{tag.cyspolv_group}"
+ #end

data/spec/bio-dbla-classifier_spec.rb

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+require File.expand_path(File.dirname(__FILE__) + '/spec_helper')
+
+describe "BioDblaClassifier" do
+end

data/spec/dbla_spec.rb

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+require File.expand_path(File.dirname(__FILE__) + '/spec_helper')
+
+describe "Dbla" do
+  context 'a group4 Dbla tag' do
+   before(:each) do
+    seq = 'YIGDIIRGRDLYLVNPQEKEQRDKLEENLKKIFKKIHDDVMKTSGRTNGAKARYGGDENFFKLREDWWTANRSTVWKAITCGTHDGASYFRATCSDGQSGAQAKNKCTCNNGDVPTYFDYVPQFLR'
+    @tag = Dbla.new(seq)
+   end
+
+  it "should return the number of cysteines" do
+   @tag.cys_count.should == 4
+  end
+
+  it 'should return a dsid' do
+    @tag.dsid.should == 'LYLV-LRED-KAIT-4-PTYF-126'
+  end
+
+  it 'should return the cyspolv group' do
+    @tag.cyspolv_group.should == 4
+  end
+
+  it 'should return the length' do
+    @tag.length.should == 126
+  end
+
+ end
+end
+

data/spec/spec_helper.rb

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+$LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
+$LOAD_PATH.unshift(File.dirname(__FILE__))
+require 'rspec'
+require 'bio-dbla-classifier'
+
+# Requires supporting files with custom matchers and macros, etc,
+# in ./support/ and its subdirectories.
+Dir["#{File.dirname(__FILE__)}/support/**/*.rb"].each {|f| require f}
+
+RSpec.configure do |config|
+  
+end

metadata

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+--- !ruby/object:Gem::Specification
+name: bio-dbla-classifier
+version: !ruby/object:Gem::Version
+  version: 0.2.1
+  prerelease: 
+platform: ruby
+authors:
+- George Githinji
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2011-09-30 00:00:00.000000000Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: bio
+  requirement: &2166374180 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 1.4.2
+  type: :runtime
+  prerelease: false
+  version_requirements: *2166374180
+- !ruby/object:Gem::Dependency
+  name: rspec
+  requirement: &2166373480 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 2.3.0
+  type: :development
+  prerelease: false
+  version_requirements: *2166373480
+- !ruby/object:Gem::Dependency
+  name: bundler
+  requirement: &2166372700 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.0.0
+  type: :development
+  prerelease: false
+  version_requirements: *2166372700
+- !ruby/object:Gem::Dependency
+  name: jeweler
+  requirement: &2166372220 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.6.4
+  type: :development
+  prerelease: false
+  version_requirements: *2166372220
+- !ruby/object:Gem::Dependency
+  name: rcov
+  requirement: &2166371500 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: *2166371500
+description: A classification system for DBL-alpha sequence tags using the CysPolv
+  approach described by Bull et al 2005
+email: georgkam@gmail.com
+executables: []
+extensions: []
+extra_rdoc_files:
+- LICENSE.txt
+- README.rdoc
+files:
+- .document
+- .rspec
+- Gemfile
+- Gemfile.lock
+- LICENSE.txt
+- README.rdoc
+- Rakefile
+- VERSION
+- bio-dbla-classifier.gemspec
+- lib/bio-dbla-classifier.rb
+- lib/bio/sequence/aa/dbla.rb
+- spec/bio-dbla-classifier_spec.rb
+- spec/dbla_spec.rb
+- spec/spec_helper.rb
+homepage: http://github.com/georgeG/bioruby-dbla-classifier
+licenses:
+- Ruby
+post_install_message: 
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  none: false
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+      segments:
+      - 0
+      hash: -1391751957910863879
+required_rubygems_version: !ruby/object:Gem::Requirement
+  none: false
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubyforge_project: 
+rubygems_version: 1.8.10
+signing_key: 
+specification_version: 3
+summary: Classify PfEMP1 DBL-alpha tags using the cyspolv grouping approach
+test_files: []