bio-dbla-classifier 0.2.1 → 0.3.0

data/README.rdoc

@@ -1,57 +1,58 @@
 = bio-dbla-classifier
 
-DBL-alpha tags can be classified into six expression groups depending on the number of cysteines and presence of 
+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
+#create an instace of a new Bio::Sequence::AA class. This class simply extends the Bio::Sequence::AA class with methods
+#to classify and describe Dbla tags.
+
+#seq1 = 'DIGDIIRGRDLYSGNNKEKEQRKKLEKNGKTIVGKIYNEATNGQALQARYKGDDNNNYSKLREDRWTANRATIWEAITCDDDNKLSNASYVRPTSTDGQSGAQGKDKCRSANKTTGNTGDVNIVPTYFDYVPQYLR'
+#seq = Bio::Sequence::AA.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 = Bio::Sequence::AA.new(entry.seq)
+  #puts "#{entry.definition},#{tag.dsid},#{tag.cys_count},#{tag.cyspolv_group}"
+ #end
+
 = Copyright
 
 See LICENSE.txt for further details.

data/Rakefile

@@ -18,7 +18,7 @@ Jeweler::Tasks.new do |gem|
   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.description = %Q{A classification system for DBL-alpha sequence tags using the CysPolv approach described by Bull et al 2007}
   gem.email = "georgkam@gmail.com"
   gem.authors = ["George Githinji"]
   # dependencies defined in Gemfile

data/VERSION

@@ -1 +1 @@
-0.2.1
+0.3.0

data/bio-dbla-classifier.gemspec

@@ -5,12 +5,12 @@
 
 Gem::Specification.new do |s|
   s.name = "bio-dbla-classifier"
-  s.version = "0.2.1"
+  s.version = "0.3.0"
 
   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.date = "2011-10-10"
+  s.description = "A classification system for DBL-alpha sequence tags using the CysPolv approach described by Bull et al 2007"
   s.email = "georgkam@gmail.com"
   s.extra_rdoc_files = [
     "LICENSE.txt",
@@ -27,9 +27,9 @@ Gem::Specification.new do |s|
     "VERSION",
     "bio-dbla-classifier.gemspec",
     "lib/bio-dbla-classifier.rb",
-    "lib/bio/sequence/aa/dbla.rb",
+    "lib/bio/sequence/aa/aa.rb",
+    "spec/aa_spec.rb",
     "spec/bio-dbla-classifier_spec.rb",
-    "spec/dbla_spec.rb",
     "spec/spec_helper.rb"
   ]
   s.homepage = "http://github.com/georgeG/bioruby-dbla-classifier"

data/lib/bio-dbla-classifier.rb

@@ -1,2 +1,2 @@
- require 'bio'
- require File.join(File.expand_path(File.dirname(__FILE__)), 'bio','sequence/aa/dbla')
+require 'bio'
+require File.join(File.expand_path(File.dirname(__FILE__)), 'bio','sequence/aa/aa')

data/lib/bio/sequence/aa/{dbla.rb → aa.rb}

@@ -1,4 +1,16 @@
-class Dbla < Bio::Sequence::AA
+class Bio::Sequence::AA
+
+ def has_accepted_length?
+   true if accepted_length.include? self.length
+ end
+
+ def start_motif
+  self[0,5]
+ end
+
+ def end_motif
+  self[-5,self.length]
+ end
 
  def dsid
    "#{polv1}-#{polv2}-#{polv3}-#{cys_count.to_s}-#{polv4}-#{self.length}"
@@ -36,14 +48,14 @@ class Dbla < Bio::Sequence::AA
  #The third position of limited variability(polv3)
  def polv3
   if self =~ /WW/
-   polv3 = self[ww_pos + 10,4] 
+   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]
@@ -68,6 +80,13 @@ class Dbla < Bio::Sequence::AA
   end
   group
  end
+
+ private
+
+ def accepted_length
+   100..168
+ end
+
 end
 
 
@@ -75,7 +94,7 @@ end
 #to classify and describe Dbla properties
 
 #seq1 = 'DIGDIIRGRDLYSGNNKEKEQRKKLEKNGKTIVGKIYNEATNGQALQARYKGDDNNNYSKLREDRWTANRATIWEAITCDDDNKLSNASYVRPTSTDGQSGAQGKDKCRSANKTTGNTGDVNIVPTYFDYVPQYLR'
-#seq = Dbla.new(seq1)
+#seq = Bio::Sequence::AA.new(seq1)
 
 #get the positions of limited variability
 #puts seq.polv1
@@ -104,6 +123,8 @@ end
 
 #read the file
  #Bio::FlatFile.open(seq_file).each do |entry|
-  #tag = Dbla.new(entry.seq)
+  #tag = Bio::Sequence::AA.new(entry.seq)
+  #puts tag.start_motif
+  #puts tag.end_motif
   #puts "#{entry.definition},#{tag.dsid},#{tag.cys_count},#{tag.cyspolv_group}"
  #end

data/spec/{dbla_spec.rb → aa_spec.rb}

@@ -4,7 +4,7 @@ describe "Dbla" do
   context 'a group4 Dbla tag' do
    before(:each) do
     seq = 'YIGDIIRGRDLYLVNPQEKEQRDKLEENLKKIFKKIHDDVMKTSGRTNGAKARYGGDENFFKLREDWWTANRSTVWKAITCGTHDGASYFRATCSDGQSGAQAKNKCTCNNGDVPTYFDYVPQFLR'
-    @tag = Dbla.new(seq)
+    @tag = Bio::Sequence::AA.new(seq)
    end
 
   it "should return the number of cysteines" do
@@ -23,6 +23,10 @@ describe "Dbla" do
     @tag.length.should == 126
   end
 
+  it 'should return the start motif' do
+    @tag.start_motif == 'YIGDI'
+  end
+
  end
 end
 

data/spec/spec_helper.rb

@@ -8,5 +8,5 @@ require 'bio-dbla-classifier'
 Dir["#{File.dirname(__FILE__)}/support/**/*.rb"].each {|f| require f}
 
 RSpec.configure do |config|
-  
+
 end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: bio-dbla-classifier
 version: !ruby/object:Gem::Version
-  version: 0.2.1
+  version: 0.3.0
   prerelease: 
 platform: ruby
 authors:
@@ -9,11 +9,11 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2011-09-30 00:00:00.000000000Z
+date: 2011-10-10 00:00:00.000000000Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bio
-  requirement: &2166374180 !ruby/object:Gem::Requirement
+  requirement: &2155406420 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -21,10 +21,10 @@ dependencies:
         version: 1.4.2
   type: :runtime
   prerelease: false
-  version_requirements: *2166374180
+  version_requirements: *2155406420
 - !ruby/object:Gem::Dependency
   name: rspec
-  requirement: &2166373480 !ruby/object:Gem::Requirement
+  requirement: &2155405820 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -32,10 +32,10 @@ dependencies:
         version: 2.3.0
   type: :development
   prerelease: false
-  version_requirements: *2166373480
+  version_requirements: *2155405820
 - !ruby/object:Gem::Dependency
   name: bundler
-  requirement: &2166372700 !ruby/object:Gem::Requirement
+  requirement: &2155405200 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -43,10 +43,10 @@ dependencies:
         version: 1.0.0
   type: :development
   prerelease: false
-  version_requirements: *2166372700
+  version_requirements: *2155405200
 - !ruby/object:Gem::Dependency
   name: jeweler
-  requirement: &2166372220 !ruby/object:Gem::Requirement
+  requirement: &2155404460 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -54,10 +54,10 @@ dependencies:
         version: 1.6.4
   type: :development
   prerelease: false
-  version_requirements: *2166372220
+  version_requirements: *2155404460
 - !ruby/object:Gem::Dependency
   name: rcov
-  requirement: &2166371500 !ruby/object:Gem::Requirement
+  requirement: &2155403800 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -65,9 +65,9 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *2166371500
+  version_requirements: *2155403800
 description: A classification system for DBL-alpha sequence tags using the CysPolv
-  approach described by Bull et al 2005
+  approach described by Bull et al 2007
 email: georgkam@gmail.com
 executables: []
 extensions: []
@@ -85,9 +85,9 @@ files:
 - VERSION
 - bio-dbla-classifier.gemspec
 - lib/bio-dbla-classifier.rb
-- lib/bio/sequence/aa/dbla.rb
+- lib/bio/sequence/aa/aa.rb
+- spec/aa_spec.rb
 - spec/bio-dbla-classifier_spec.rb
-- spec/dbla_spec.rb
 - spec/spec_helper.rb
 homepage: http://github.com/georgeG/bioruby-dbla-classifier
 licenses:
@@ -104,7 +104,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
       version: '0'
       segments:
       - 0
-      hash: -1391751957910863879
+      hash: 1540756780338965641
 required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
   requirements: