bio-dbla-classifier 0.3.0 → 0.4.0

data/README.rdoc

@@ -1,11 +1,14 @@
 = 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
+DBL-alpha tags are small regions of the PfEMP1 protein that can be PCR amplified and are classified into six expression groups depending on the number of cysteines and presence of
+certain motifs within the tag region (Bull et al 2007). This plugin extends bioruby's amino acid class, Bio::Sequence::AA by adding methods to analyze DBL-alpha sequences tags.
+If you use this plugin please quote,
 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
+You need to have Ruby installed on your system. This plugin has been tested on Ruby 1.9.2-p290. See http://rubylang.info/ for
+information on Ruby and how to install it on your system. Once Ruby 1.9.2 is installed type the following command in the terminal to
+install the gem. This will install the bioruby gem if it is not already installed on your system.
 
  gem install bio-dbla-classifier
 
@@ -14,44 +17,62 @@ Bull et al “An approach to classifying sequence tags sampled from Plasmodium f
  gem uninstall bio-dbla-classifier
 
 = Usage
+ #create an instance of Bioruby's Bio::Sequence::AA class with methods to classify and describe DBL-alpha tags.
+
  require 'bio-dbla-classifier'
 
-#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.
+ seq ='DIGDIVRGRDMFKSNPEVEKGLKAVFRKINNGLTPQAKTHYADEDGSGNYVKLREDWWKANRDQVWKAITCKAPQSVHYFIKTSHGTRGFTSHGKCGRNETNVPTNLDYVPQYLR'
+ dbl_seq = Bio::Sequence::AA.new(seq)
+
+ #get the positions of limited variability
+ puts dbl_seq.polv1 #=> MFKS
+ puts dbl_seq.polv2 #=> LRED
+ puts dbl_seq.polv3 #=> KAIT
+ puts dbl_seq.polv4 #=> PTNL
+
+ #get the number of cysteines in the tag
+ puts dbl_seq.cys_count #=> 2
+
+ #get the distinct sequence identifier
+ puts dbl_seq.dsid #=>MFKS-LRED-KAIT-2-PTNL-115
+
+ #get the cyspolv group for this tag
+ puts dbl_seq.cyspolv_group #=> 1
+
+
+ #get the block sharing group for this tag
+ #puts dbl_seq.bs_group #to be implemented
+
+ #get the length of the tag
+ puts dbl_seq.size #=> 115
 
-#seq1 = 'DIGDIIRGRDLYSGNNKEKEQRKKLEKNGKTIVGKIYNEATNGQALQARYKGDDNNNYSKLREDRWTANRATIWEAITCDDDNKLSNASYVRPTSTDGQSGAQGKDKCRSANKTTGNTGDVNIVPTYFDYVPQYLR'
-#seq = Bio::Sequence::AA.new(seq1)
+= Finding the Position Specific Polymorphic Blocks(PSPB)
 
-#get the positions of limited variability
-#puts seq.polv1
-#puts seq.polv2
-#puts seq.polv3
-#puts seq.polv4
+The pspb methods take 2 arguments, an anchor position and a window length that defines the length of the pspb
 
-#get the number if cysteines in the tag
-#puts seq.cys_count
+ #get pspb1
+ puts seq.pspb1(0,14) #=> NPEVEKGLKAVFRK
 
-#get the distinct sequence identifier
-#puts seq.dsid
+ #get pspb2
+ puts seq.pspb2(0,14) #=> THYADEDGSGNYVK
 
-#get the cyspolv group for this tag
-#puts seq.cyspolv_group
+ #get pspb3
+ puts seq.pspb3(0,14) #=> CKAPQSVHYFIKTS
 
+ #get pspb4
+ puts seq.pspb4(0,14) #=> FTSHGKCGRNETNV
 
-#get the block sharing group for this tag
-#puts seq.bs_group #to be implemented
+= Processing fasta files
 
-#get the length of the tag
-#puts seq.size
+If the input is a fasta file,
 
-#if input file is a fasta file
- #seq_file = "#{ENV['HOME']}/sequences/878_kilifi_sequences.fasta"
+ seq_file = "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
+ #Process each entry in 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
 

data/Rakefile

@@ -17,8 +17,8 @@ Jeweler::Tasks.new do |gem|
   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 2007}
+  gem.summary = %Q{A tool to classify and manipulate PfEMP1 DBL-alpha sequence tags}
+  gem.description = %Q{Methods to classify and manipulate PfEMP1 DBL-alpha sequence tags}
   gem.email = "georgkam@gmail.com"
   gem.authors = ["George Githinji"]
   # dependencies defined in Gemfile

data/VERSION

@@ -1 +1 @@
-0.3.0
+0.4.0

data/bio-dbla-classifier.gemspec

@@ -5,12 +5,12 @@
 
 Gem::Specification.new do |s|
   s.name = "bio-dbla-classifier"
-  s.version = "0.3.0"
+  s.version = "0.4.0"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["George Githinji"]
-  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.date = "2011-10-13"
+  s.description = "Methods to classify and manipulate PfEMP1 DBL-alpha sequence tags"
   s.email = "georgkam@gmail.com"
   s.extra_rdoc_files = [
     "LICENSE.txt",
@@ -36,7 +36,7 @@ Gem::Specification.new do |s|
   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"
+  s.summary = "A tool to classify and manipulate PfEMP1 DBL-alpha sequence tags"
 
   if s.respond_to? :specification_version then
     s.specification_version = 3

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

@@ -41,19 +41,23 @@ class Bio::Sequence::AA
   elsif self =~ /VW/
    polv2 = self[vw_pos - 12,4]
   else
+   error = 'WW or VW motif missing'
   end
-  polv2
+  polv2 unless error
  end
 
  #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]
+    polv3 = self[vw_pos + 2,4]
   else
+    error = 'WW or VW motif missing'
   end
-  polv3
+
+  polv3 unless error
+
  end
 
  #The fourth position of limited variability(polv4)
@@ -81,19 +85,52 @@ class Bio::Sequence::AA
   group
  end
 
- private
+ #position specific polymorphic block 1
+ def pspb1(anchor_pos,win_len)
+  self[14 + anchor_pos,win_len]
+ end
+
+ #position specific polymorphic block 2
+ def pspb2(anchor_pos,win_len)
+  if self =~ /WW/
+   pspb2 = self[ww_pos - 4 - anchor_pos - win_len, win_len]
+  elsif self =~ /VW/
+   pspb2 = self[vw_pos - 12 - win_len - anchor_pos, win_len]
+  else
+    error = 'WW or VW motif missing'
+  end
+  pspb2
+ end
+
+ #position specific polymorphic block 3
+ def pspb3(anchor_pos,win_len)
+  if self =~ /WW/
+    pspb3 = self[ww_pos + 14 + anchor_pos, win_len]
+  elsif self =~ /VW/
+    pspb3 = self[vw_pos + 6 + anchor_pos, win_len]
+  else
+    error = 'WW or VW motif missing'
+  end
+  pspb3
+ end
 
+ #position specific polymorphic block 4
+ def pspb4(anchor_pos,win_len)
+  self[self.length - 12 - win_len - anchor_pos, win_len]
+ end
+
+
+ private
  def accepted_length
    100..168
  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'
+#seq1 ='DIGDIVRGRDMFKSNPEVEKGLKAVFRKINNGLTPQAKTHYADEDGSGNYVKLREDWWKANRDQVWKAITCKAPQSVHYFIKTSHGTRGFTSHGKCGRNETNVPTNLDYVPQYLR'
 #seq = Bio::Sequence::AA.new(seq1)
 
 #get the positions of limited variability
@@ -118,6 +155,19 @@ end
 #get the length of the tag
 #puts seq.size
 
+#get the pspb1
+#puts seq.pspb1(0,14)
+
+#get the pspb2
+#puts seq.pspb2(0,14)
+
+#get the pspb3
+#puts seq.pspb3(0,14)
+
+#get the pspb4
+#puts seq.pspb4(0,14)
+
+
 #if input file is a fasta file
  #seq_file = "#{ENV['HOME']}/sequences/878_kilifi_sequences.fasta"
 

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: bio-dbla-classifier
 version: !ruby/object:Gem::Version
-  version: 0.3.0
+  version: 0.4.0
   prerelease: 
 platform: ruby
 authors:
@@ -9,11 +9,11 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2011-10-10 00:00:00.000000000Z
+date: 2011-10-13 00:00:00.000000000Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bio
-  requirement: &2155406420 !ruby/object:Gem::Requirement
+  requirement: &2155795540 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -21,10 +21,10 @@ dependencies:
         version: 1.4.2
   type: :runtime
   prerelease: false
-  version_requirements: *2155406420
+  version_requirements: *2155795540
 - !ruby/object:Gem::Dependency
   name: rspec
-  requirement: &2155405820 !ruby/object:Gem::Requirement
+  requirement: &2155794860 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -32,10 +32,10 @@ dependencies:
         version: 2.3.0
   type: :development
   prerelease: false
-  version_requirements: *2155405820
+  version_requirements: *2155794860
 - !ruby/object:Gem::Dependency
   name: bundler
-  requirement: &2155405200 !ruby/object:Gem::Requirement
+  requirement: &2155787960 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -43,10 +43,10 @@ dependencies:
         version: 1.0.0
   type: :development
   prerelease: false
-  version_requirements: *2155405200
+  version_requirements: *2155787960
 - !ruby/object:Gem::Dependency
   name: jeweler
-  requirement: &2155404460 !ruby/object:Gem::Requirement
+  requirement: &2155786180 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -54,10 +54,10 @@ dependencies:
         version: 1.6.4
   type: :development
   prerelease: false
-  version_requirements: *2155404460
+  version_requirements: *2155786180
 - !ruby/object:Gem::Dependency
   name: rcov
-  requirement: &2155403800 !ruby/object:Gem::Requirement
+  requirement: &2155784980 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -65,9 +65,8 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *2155403800
-description: A classification system for DBL-alpha sequence tags using the CysPolv
-  approach described by Bull et al 2007
+  version_requirements: *2155784980
+description: Methods to classify and manipulate PfEMP1 DBL-alpha sequence tags
 email: georgkam@gmail.com
 executables: []
 extensions: []
@@ -104,7 +103,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
       version: '0'
       segments:
       - 0
-      hash: 1540756780338965641
+      hash: -1659999011793222104
 required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
   requirements:
@@ -116,5 +115,5 @@ rubyforge_project:
 rubygems_version: 1.8.10
 signing_key: 
 specification_version: 3
-summary: Classify PfEMP1 DBL-alpha tags using the cyspolv grouping approach
+summary: A tool to classify and manipulate PfEMP1 DBL-alpha sequence tags
 test_files: []