bio-dbla-classifier 0.5.1 → 0.7.1

data/.travis.yml

@@ -0,0 +1,8 @@
+language: ruby
+rvm:
+  - 1.9.2
+  - 1.9.3
+  #- jruby-19mode # JRuby in 1.9 mode
+  - rbx-19mode
+ #uncomment this line if your project needs to run something other than `rake`:
+script: bundle exec rspec spec

data/Gemfile

@@ -1,12 +1,11 @@
 source "http://rubygems.org"
 
- gem 'bio', '>= 1.4.2'
+ gem 'bio', '>= 1.4.3'
 
 # Needed to run rake, tests, features
 group :development do
-  gem "rspec", "~> 2.3.0"
-  gem "bundler", "~> 1.1.rc.7"
-  gem "jeweler", "~> 1.6.4"
-  gem "rcov", ">= 0"
-  gem "rake", "~> 0.9.2.2"
+  gem "rspec",   ">= 2.8.0"
+  gem "bundler", ">= 1.0.22" #"~> 1.1.rc.7"
+  gem "jeweler", ">= 1.6.4"
+  gem "rake", ">= 0.9.2.2"
 end

data/Gemfile.lock

@@ -1,31 +1,33 @@
 GEM
   remote: http://rubygems.org/
   specs:
-    bio (1.4.2)
+    bio (1.4.3)
     diff-lcs (1.1.3)
     git (1.2.5)
-    jeweler (1.6.4)
+    jeweler (1.8.4)
       bundler (~> 1.0)
       git (>= 1.2.5)
       rake
-    rake (0.9.2.2)
-    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)
+      rdoc
+    json (1.7.7)
+    rake (10.0.3)
+    rdoc (3.12.1)
+      json (~> 1.4)
+    rspec (2.12.0)
+      rspec-core (~> 2.12.0)
+      rspec-expectations (~> 2.12.0)
+      rspec-mocks (~> 2.12.0)
+    rspec-core (2.12.2)
+    rspec-expectations (2.12.1)
+      diff-lcs (~> 1.1.3)
+    rspec-mocks (2.12.2)
 
 PLATFORMS
   ruby
 
 DEPENDENCIES
-  bio (>= 1.4.2)
-  bundler (~> 1.1.rc.7)
-  jeweler (~> 1.6.4)
-  rake (~> 0.9.2.2)
-  rcov
-  rspec (~> 2.3.0)
+  bio (>= 1.4.3)
+  bundler (>= 1.0.22)
+  jeweler (>= 1.6.4)
+  rake (>= 0.9.2.2)
+  rspec (>= 2.8.0)

data/README.rdoc

@@ -1,3 +1,4 @@
+{<img src="https://secure.travis-ci.org/georgeG/bioruby-dbla-classifier.png?branch=master" alt="Build Status" />}[http://travis-ci.org/georgeG/bioruby-dbla-classifier]
 = bio-dbla-classifier
 
 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
@@ -38,7 +39,6 @@ install the gem. This will install the bioruby gem if it is not already installe
  #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 #=> 1
 
@@ -69,6 +69,19 @@ window length is 14
  #get pspb4
  puts seq.pspb4 #=> FTSHGKCGRNETNV
 
+ #get a pspb as an amino acid
+ puts seq.pspb4_as_dna
+
+= Finding polv2 to polv3 regions
+  Only the Amino acid regions are supported for now 
+  
+  #get polv1 to polv2 region
+  puts seq.polv1_to_polv2
+
+  #get polv3 to polv4 region
+  puts seq.polv3_to_polv4
+
+
 = Processing a flatfile for example fasta, genbank or embl
 
  seq_file = "sequences.fasta"

data/Rakefile

@@ -31,10 +31,10 @@ 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
+#RSpec::Core::RakeTask.new(:rcov) do |spec|
+  #spec.pattern = 'spec/**/*_spec.rb'
+  #spec.rcov = true
+#end
 
 task :default => :spec
 

data/VERSION

@@ -1 +1 @@
-0.5.1
+0.7.1

data/bio-dbla-classifier.gemspec

@@ -5,11 +5,11 @@
 
 Gem::Specification.new do |s|
   s.name = "bio-dbla-classifier"
-  s.version = "0.5.1"
+  s.version = "0.7.1"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["George Githinji"]
-  s.date = "2012-02-20"
+  s.date = "2013-02-22"
   s.description = "Methods to classify and manipulate PfEMP1 DBL-alpha sequence tags"
   s.email = "georgkam@gmail.com"
   s.extra_rdoc_files = [
@@ -19,6 +19,7 @@ Gem::Specification.new do |s|
   s.files = [
     ".document",
     ".rspec",
+    ".travis.yml",
     "Gemfile",
     "Gemfile.lock",
     "LICENSE.txt",
@@ -28,41 +29,40 @@ Gem::Specification.new do |s|
     "bio-dbla-classifier.gemspec",
     "lib/bio-dbla-classifier.rb",
     "lib/bio/sequence/aa/aa.rb",
+    "lib/bio/sequence/na/na.rb",
     "spec/aa_spec.rb",
     "spec/bio-dbla-classifier_spec.rb",
+    "spec/na_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 = "1.8.12"
+  s.rubygems_version = "1.8.25"
   s.summary = "A tool to classify and manipulate PfEMP1 DBL-alpha sequence tags"
 
   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>, ["~> 1.1.rc.7"])
-      s.add_development_dependency(%q<jeweler>, ["~> 1.6.4"])
-      s.add_development_dependency(%q<rcov>, [">= 0"])
-      s.add_development_dependency(%q<rake>, ["~> 0.9.2.2"])
+      s.add_runtime_dependency(%q<bio>, [">= 1.4.3"])
+      s.add_development_dependency(%q<rspec>, [">= 2.8.0"])
+      s.add_development_dependency(%q<bundler>, [">= 1.0.22"])
+      s.add_development_dependency(%q<jeweler>, [">= 1.6.4"])
+      s.add_development_dependency(%q<rake>, [">= 0.9.2.2"])
     else
-      s.add_dependency(%q<bio>, [">= 1.4.2"])
-      s.add_dependency(%q<rspec>, ["~> 2.3.0"])
-      s.add_dependency(%q<bundler>, ["~> 1.1.rc.7"])
-      s.add_dependency(%q<jeweler>, ["~> 1.6.4"])
-      s.add_dependency(%q<rcov>, [">= 0"])
-      s.add_dependency(%q<rake>, ["~> 0.9.2.2"])
+      s.add_dependency(%q<bio>, [">= 1.4.3"])
+      s.add_dependency(%q<rspec>, [">= 2.8.0"])
+      s.add_dependency(%q<bundler>, [">= 1.0.22"])
+      s.add_dependency(%q<jeweler>, [">= 1.6.4"])
+      s.add_dependency(%q<rake>, [">= 0.9.2.2"])
     end
   else
-    s.add_dependency(%q<bio>, [">= 1.4.2"])
-    s.add_dependency(%q<rspec>, ["~> 2.3.0"])
-    s.add_dependency(%q<bundler>, ["~> 1.1.rc.7"])
-    s.add_dependency(%q<jeweler>, ["~> 1.6.4"])
-    s.add_dependency(%q<rcov>, [">= 0"])
-    s.add_dependency(%q<rake>, ["~> 0.9.2.2"])
+    s.add_dependency(%q<bio>, [">= 1.4.3"])
+    s.add_dependency(%q<rspec>, [">= 2.8.0"])
+    s.add_dependency(%q<bundler>, [">= 1.0.22"])
+    s.add_dependency(%q<jeweler>, [">= 1.6.4"])
+    s.add_dependency(%q<rake>, [">= 0.9.2.2"])
   end
 end
 

data/lib/bio-dbla-classifier.rb

@@ -1,2 +1,5 @@
 require 'bio'
 require File.join(File.expand_path(File.dirname(__FILE__)), 'bio','sequence/aa/aa')
+require File.join(File.expand_path(File.dirname(__FILE__)), 'bio','sequence/na/na')
+
+

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

@@ -5,12 +5,12 @@ class Bio::Sequence::AA
   end
 
   def start_motif
-    warn "[DEPRECATION] 'start_motif' is deprecated.  Please use `n_terminal_motif` instead."
+    #warn "[DEPRECATION] 'start_motif' is deprecated.  Please use `n_terminal_motif` instead."
     n_terminal_motif
   end
 
   def end_motif
-    warn "[DEPRECATION] 'end_motif' is deprecated.  Please use `c_terminal_motif` instead."    
+    #warn "[DEPRECATION] 'end_motif' is deprecated.  Please use `c_terminal_motif` instead."    
     c_terminal_motif
   end
 
@@ -35,6 +35,16 @@ class Bio::Sequence::AA
     scan(/C/).size
   end
 
+  #get the 5' end of the sequence from the 'middle'
+  def polv1_to_polv2
+    slice(rindex(polv1),rindex(polv2) - 6)
+  end
+
+  #get the 3'end of the sequence from the "middle"
+  def polv3_to_polv4
+    slice(rindex(polv3),(rindex(polv4) - rindex(polv3) + 4))
+  end
+
   #The first position of limited variability(polv1)
   def polv1
     self[10,4]
@@ -86,19 +96,36 @@ class Bio::Sequence::AA
     group
   end
 
+  def polv1_pos
+    index(polv1)
+  end
+
+  def polv2_pos
+    index(polv2)
+  end
+
+  def polv3_pos
+    index(polv3)
+  end
+
+  def polv4_pos
+    index(polv4)
+  end
+
+
   #return the block sharing group
   def bs_group
     case
     when self =~ /(?:R(?:HYADHDKSGNYYK|NENNNLGKLSNEQ|I(?:RHYDDGSGNY(?:SK|YK)|THYN(?:GVSGNCVK|DGSGNYVK))|E(?:RYKDLKDVEIDD|HYKEVKNGNY(?:YK|IK)|KYKDLKD(?:VEIDD|LPIDD))|VKETYKDDPNYYK|KNNSSLRKLTNEQ)|G(?:G(?:RGRK(?:KLEDNL(?:IE|KE)|QLEENLQK)|GGRKKLEDNLKE)|I(?:N(?:D(?:Y(?:ND(?:GSGNYFK|ISGNYYK)|D(?:RDGPE(?:HYK|YYK)|GDGPEYYK))|CDRDGPEYYK)|AYNDGSENYYK)|IDYDHDGPHYYK)|P(?:SQEK(?:IKLEENLK|KKLEENLK)|KQEKKELEENLK)|K(?:NYPDDGSGN(?:YYK|FYK)|K(?:YYND(?:G(?:SGNYYK|TGNYVK)|ETGNYYK)|KEKEKIYGNIE)|QYYNDENGNYYK)|QTYPDDGSGNYYK)|MESNANLKKHTLER|S(?:STNTQCRCATNDV|HY(?:TDTHGSIDYDK|ED(?:GDKSGNYYK|KDKSGNYIK)|ADHDKSGNY(?:YK|LK))|NKEKEKIENSLQN|DYKDDD(?:GSGNYYK|IDGNYY(?:K|Q))|E(?:GKCGHKETERDL|KVEYGLRKLFKK)|VQERYGNDPNFFQ|KI(?:NDYDGDPNYYK|TDYDNDPNYYK)|QGQCGRNENNGYP|F(?:S(?:SEYCGH(?:RQGS(?:V|A)|GDNEV|EQGNV)|N(?:GQCGHRDENV|SKCGHGEHEV|DYCGH(?:RQGSV|NENKV)|PKCGH(?:G(?:DNEV|EHEV)|NENKV|EQGNV)|EYCGHRQGSV)|D(?:RKCGHYEGAP|HKCGH(?:GDKDV|YEGAP|DENAP)))|TN(?:GQCGHNEENV|PKCG(?:RGDNEV|H(?:G(?:DNEV|EHEV)|DENKV)))|ADAYCGRGDENV)|LILPYSKCGRDTD)|H(?:HYKDDDISGNYSK|SKEKEKLQTNLKN|N(?:H(?:IKKPLLENLEQ|KKKPLL(?:DNLEK|ENLEQ))|NKKKALLDNLEK|QKKINLEKSLHR)|EQG(?:YNKLEAI(?:SKT|LKT)|NNKLEA(?:RLKT|ILKT))|QQRK(?:RKLEENLRN|GKLEENLRN))|C(?:RAP(?:N(?:GANYFRKGL|EANYFKNVA)|KNAHYFIKSS|QKANYFKNVA)|G(?:TGENDTYFKNSS|A(?:G(?:EKDTYF(?:TYS(?:N|K)|VQLD)|A(?:RDEYFIKPS|KDTYFTYSK))|TMNDIFSKNIG|LPKSAY(?:VLQSE|F(?:MQLE|LQSE))))|S(?:VPYEAYYFTYKS|A(?:G(?:PKDTYFIKSG|QKDTYFIKPN)|D(?:GSE(?:DYFIKSS|EYF(?:IQSE|KKQS))|DSEDYFI(?:RSE|QSE))|P(?:RDA(?:DYFIKNS|QYFIKSS)|GD(?:VNYFRK(?:GL|IS|ES|FS)|AKYVK(?:YFP|NFP))|HNAQYVKYVP|Y(?:GANYYRKYS|HPGYFRQSK|YADYF(?:RKGS|K(?:SVA|KK(?:S|P)))|NAHYFIKSS|CADYFKKKS|DANYVRRKS|EA(?:YYFTYKS|QYFIKSS)|KSQYFIKSS)|D(?:YAKYFRQTC|NAKY(?:VKYFP|FKPPK)))|QNNEVYFINSE))|Y(?:IPY(?:YVNYFK(?:NIS|DIS|K(?:T(?:S|P)|KS))|CVNYFKNIS)|APNNANYFIGSG)|NAP(?:GD(?:VHYFRKDP|AHYFRKDP)|Y(?:DANY(?:YR(?:KYS|QTC)|VRRKS|FRKTS)|EAQY(?:YIKSS|FIK(?:SS|PS))|K(?:SRYF(?:M(?:HSE|QSE)|IQSE)|A(?:QYYIKSS|WYFMHSE)))|NISGYFMQS(?:G|E)|D(?:NVNYFRKYS|KAEYFVYKS))|TAP(?:YGANYYRKYS|D(?:NVNYFRKYS|KANYFIYKS))|IAPRDAHYFLKSS|D(?:TEESDTYFKQSS|A(?:SYKSGYFMQSE|P(?:RDA(?:HYFLKSS|NFFIKNS|DYF(?:RKGS|KNVA))|YKSRYF(?:MQSE|IQSE)|KDANYFIGSG|QKVDYFRK(?:GS|IS))))|EA(?:SKNANFFIK(?:NS|DS)|P(?:GDAHYFRKGP|ENAYIIKRRI|KDANYFIGSG|QKVDYFRKG(?:S|L)))|VA(?:GEGNTYFIQLD|PENAYFRKTEA)|KA(?:S(?:RNA(?:HYFLKSS|NYFRK(?:IS|AL))|KNANFFIKNS)|P(?:GDVN(?:YFRKIS|FFIKNS)|NGANYFRKKS|TGA(?:HYFLKSS|DYF(?:VYKP|KKKS))|PKVDYSRNIS|EDADYFRKGS|K(?:GANYFRKES|DA(?:HYFLKSS|N(?:YFIGSG|FFIKIS)|DYFRKGS))|Q(?:GANYFRNIS|SVHYFIKTS|DANYF(?:R(?:N(?:IS|VS)|K(?:GL|IS))|TKES)|K(?:VDYFRKGS|ANYFRKGS)))|KEGDIYSKTTD)|FA(?:HNTEEYFIKSE|DGSEEYFI(?:KSS|QS(?:S|E)))|AAR(?:GNDLYSKNIG|YHPGYFKKSD))|Y(?:NERDR(?:DKKRKLQE|EKKRKLQD|AQKKKLQD)|DEKEKNRRKQLEN|KAP(?:RKA(?:NYFIYKS|DYFRNIS)|KDAHYFLKSS|QDANYFRNVS))|N(?:RKEKGKLQTNLKN|GDYK(?:EKVSNNL(?:RA|KT)|KKVSNNLKT)|HYKDD(?:NGS(?:GNYYK|ENYYK)|D(?:GSGNYYK|ISGNY(?:SK|YK)))|SDDKVE(?:NGLKKVF|KGLREVF)|Y(?:Y(?:NNTGNN(?:V(?:NYAK|DYVK)|ANYAK)|ADGDKSGNYYK)|NYDEDGSGNY(?:YK|VK))|N(?:HDNVE(?:NGL(?:REVF|KAVF)|KGLK(?:KVF|AVF))|D(?:ND(?:RVKKEKLQN|K(?:IKK(?:GKLRG|EKL(?:RG|QE))|VKKEKL(?:RG|QN)))|DDKIKKGKLRG|V(?:EKGL(?:DVVFKK|KVVFKK)|VKGLDVVFKK))|E(?:SE(?:IKRKEKLRG|KKKREELQG)|TDKEQKVKLEK|KDM(?:REKQKLQS|TEKQKLQS))|VDAVQEGLKVVF|KE(?:NEKLQENLKR|KEKIEKSLQN))|TVDK(?:IHEGLKVVF|VHEGLKVVF)|D(?:NVE(?:NGLREVFKK|KGLK(?:KVFDK|AVFRK))|DVEKGLKIVFEK|EDDVEKGLKIVF|K(?:D(?:YVENGLKKVF|A(?:V(?:RHGLKVVF|QKGLRAVF)|AQKVLRTVF))|EKDQRKKLDE(?:N|I)|VE(?:NGL(?:REVFKK|KKVFDK)|KGL(?:REVF(?:RK|KK)|QVVFGK)))|QD(?:DVEKGLKIVF|EVWNGLRSVF)|ADKV(?:EKGLQVVF|QKGLQVVF))|P(?:E(?:DKVHEGLKVVF|VE(?:NGLREVFNK|KGLKAVFRK))|QDKVQ(?:EGLK(?:NVF|VVF)|KGLREVF))|E(?:MVEIGLKKVFKK|HYKEVKNGNYVK|NVEKGL(?:K(?:IVFEK|KVFDK)|QVVFGK)|D(?:DKVQKGLQVVF|VEKGLKVVF(?:KK|QK))|EDAVQKGL(?:RAVF|K(?:VVF|KVF))|K(?:DAVQNGLKKVF|VE(?:YGLRKLFKK|IGLKKVF(?:DK|EK|KK)))|QDEVWKGLRDVF)|VH(?:YK(?:DDGS(?:GNYYK|ENYYK)|EVKNGNYVK)|DKVE(?:RGLREVF|TGLREVF|KGL(?:REVF|QVV(?:F|L))))|K(?:HDNIEKGLREVF|N(?:NVPL(?:HNLSLDK|DKLSLDK)|K(?:SPLDKLSLEQ|PPLDKLSVDK)|VEIGLK(?:NVFKN|KVFDK))|DDK(?:IEKSLRAIF|V(?:EKGLRAIF|QKGL(?:RAVF|KAVF|QVVF)))|Q(?:RKKILQEKLEN|EKEKREKLDEN))|FSNPKCGH(?:DEGIV|KQGNV)|QEDKVQEGLKVVF|LILTHPKCGHDTD)|I(?:SYYNADEKGNFYK|HNYDDNGSGNYYK|E(?:TRY(?:GSDTTNYYQ|ENDGPNYYQ)|ARYKKDDDNYYQ)|VSFDQCGHND(?:MDV|VDV)|KNDKTLNNLSNGQ|FSNEHCGHKQGSV)|T(?:SEGQCGHNDKMRP|HYADEDGS(?:GNYVK|ENYYK)|D(?:N(?:D(?:EVW(?:TGLRSVF|KGL(?:RSVF|GSVF))|AVQKGLRAVF)|VE(?:NGLREVFKK|KGLRAVFGK))|K(?:D(?:YVENGLK(?:KVF|AVF)|DVENGLREVF|EV(?:KEGLKVVF|WKGLRAVF)|AVQKGLRAVF)|VENGLK(?:EVFDK|KVFD(?:N|K))))|E(?:GYCGRNENNGYP|TLYKDEEGNYLK|KDDVEKGLKIVF)|V(?:S(?:SNKCGHNDMDV|NAKRREGDENP|FDQCGHNDM(?:HV|DV))|K(?:GTYKDDPYYYK|ETYKDDPNYYK))|F(?:S(?:GYWCGHYEGAP|NDYCGHGEHEV)|TYTKCGHDENKV))|D(?:SRTDKLEENLRKI|NNSDKLRDLSVDK|DDVEKGLKIVFEK|K(?:GEKKKLEKNLKD|NRGKLGALSLDD))|P(?:SY(?:IKCGHNNKDDP|LKCGHNNKDDP)|HYTNDRGLADYVK)|E(?:HY(?:EDVDGSGNYLK|KDVDGSGNYYK)|YY(?:NDTNNKINYVK|EDKDPDKNYYQ)|KNY(?:YNDGTGNYYK|PDDGSGNYSK)|FT(?:GGYCGRDETDV|SGYCGRNETNV))|V(?:NGNDKLESNLKKI|KAHY(?:KKDAPYYYK|QKDAPNYYK)|FSNRQCGHYED(?:VP|AP))|K(?:RYYNDDTD(?:NN(?:FYQ|LYQ)|DNFYQ)|GINDYDGDPNYYK|SYY(?:NAD(?:GEGNFYK|EKGNYYK)|DADEKGNYYK)|HY(?:TDTHGSIDYDK|A(?:H(?:GDGSGNY(?:SK|YK|LK)|DDGS(?:GNYYK|VNYYK))|DEDGSGNYYK))|YYNDTNNKINYVK|N(?:Y(?:YNPD(?:G(?:SGNYYK|AGNYYK)|EAGNYYK)|NYD(?:EDGPEYYK|KDGPEYYK))|NDRTLNNLSIGQ|DYNPDGSGNY(?:YK|FK)|E(?:SE(?:IKRKEKLQR|K(?:RTKEKLQG|NTKKKLQG))|NTDLNKLTTEK)|KNTKLSTLTLEK|AYPDDG(?:SGNY(?:YK|FK)|FGNYYK))|T(?:SN(?:SN(?:MDTLSLEQ|LKELSLDK)|TNMNTLSLDK)|IYADLKDVEIDD)|I(?:NDYDGDGPEYYK|THYDDISGNYYK|KDYDGDGPEYYK)|D(?:HY(?:KDEKDGNFFQ|QDDGTGNYYK)|YYNADEKGNYYK)|PHYKDDGFGNYYK|E(?:YYQDDGTGNYYK|ISDYDNDPNYYK|EYGDLKDVPIDD|KYGDLKDVPIDD)|V(?:HYKENKDGNY(?:YK|VK)|KY(?:PDL(?:ND(?:IEIDD|VEIDD)|KDLQIDD)|QDLKDVEIDD))|K(?:HY(?:ENDTDKNYYQ|KKDEDPNYYK)|VYPEDVTGNY(?:YK|FK)|KKKGLSELSTEK)|FS(?:SDRCGHNEGDP|ERKCGH(?:NEGSP|DENAP))|Q(?:HYK(?:DDGSVNYYK|EDKDENYYK)|NNKKLKDLTDKH)|A(?:RYKDRKDPNYYK|K(?:YEDLKTLPIDD|ERYKDIKNYYQ)))|F(?:S(?:S(?:SGPCGRDEAPV|HGKCGHNEGAP|DRCGHNNNDGP|E(?:GKCGHKEGTV|YCGHYKNGDP)|QGQCGHTEGTV)|N(?:RGPCGRNETDV|S(?:G(?:TRGRKELTV|PCGRKELTV|KCGGKEAPV)|KCGHHNNDGP)|N(?:GPCGRNETDV|KCGHSNGGDP)|PKCGHSNGGDP|E(?:HCGH(?:HNNDDP|YKNGDP)|YCGH(?:YKNGDP|KKNEDP)))|DNG(?:HCGRNETNV|PCGRKELIV))|T(?:RQGYCGHSETNV|GGGQC(?:RRNDNSV|GRNETDV)|S(?:HGKCG(?:RNETNV|HSEGAP)|IGKCGHNKGSV|EG(?:RCGHSETNV|KCG(?:RNETNV|HNDNRV)|Q(?:RGHSETNV|C(?:RRNDNSV|GH(?:SETNV|NDKSV|DENKV))))|VGYCGHNKG(?:SV|IR)|QG(?:YCG(?:RKE(?:LTV|APV)|HSETNV)|QCG(?:RNERNV|H(?:SETNV|TEGTV|KEGTV)))|AGKCR(?:RNDNSV|HNDNSV))|NDGKCG(?:RYEGAP|H(?:YE(?:GAP|NNI|D(?:NV|AP))|TEGTV))|TEGYCGR(?:NEGAP|DEGAP)|D(?:GHCGRTQEGHV|IGKCG(?:GKEAPV|H(?:GDKDV|N(?:EGAP|KGSV)|KQGNV))|DGKCGHYEGAP))|ENAGKC(?:RRNDNKV|GHNDNRV)|WDRKCGHSN(?:GGDP|EGA(?:P|L))|LYPKCGHNNKNDL)|Q(?:GIIDYDNDPNYYK|NYY(?:KDDPKKNYYK|ADDGSGNY(?:SK|VK))|ISDY(?:TGDHPNYYK|DGDGPEYYK)|K(?:SDSSLQRLSIEK|HYEDDGSGNYYK|NNSALKKLTDKQ|IY(?:EDINNLPIDD|KDLNNLPIDD))|QNNNTLENLTDKQ)|L(?:K(?:TRYKKDDDNYYQ|KHYQKDAPNYYK)|F(?:S(?:N(?:RQCGH(?:GEHEV|NEGAP|DENKV|EQGNV)|SKCGH(?:RQGNV|DE(?:SKV|NKV)|EQGNV)|YKCGHYEDAP|DYCGHKQGNV|PKCGH(?:EQG(?:NV|TV)|KQGKV)|AYCGHYEGSP)|D(?:GHCGNKDGTV|HKCGHEESRV|YKCGHYE(?:GSP|DAP)))|DYNCGHHKDNNV|WDRKCGHDERNV)|Q(?:TRYTNDGDNYFK|ERYNDPKGDFFQ|ARYKKDGDDFFK)|WNDKCGHHVDKDV|LFSNYKCGHYEGS)|A(?:RYKKDEEDGNYY(?:K|Q)|VSSNKCGHNDMNV|KNDYTGDHPNYYK|LKHYKDDTKNYYQ))/
       block_sharing = 1  
-    when self =~ /(?:RE(?:PGKQHLEERLER|KGKSRLEARLKT)|G(?:G(?:HYKNCHCIGGDV|TYKNCRCASGNV)|P(?:NQEKKLLENKLK|DQEKKKLEENLR)|ANAIKAGDNVSIV)|S(?:FTNGQCGRDGENV|WYPKCGHHVKQDV|AKEHYQDTENYYK)|H(?:NRRKEKLETRLEE|E(?:PG(?:IQ(?:HLEKRLES|YLEKRLES)|KQHL(?:GERLEQ|EERLE(?:R|Q)))|QG(?:YNRLEARLKT|NNRLEARLKT|INRLEARLKT))|QQRKHLLEKRLET)|C(?:RAEEK(?:GTYFKNRE|D(?:TYFKNRE|IYSKTTD)|EIYSKTTD)|G(?:TEDKDTYFIKSG|VEENAKYFRESS|A(?:GMKDIYSKTMN|SEDAKYKVIGP|T(?:MNDIFSKNIR|VDDI(?:SSKNIR|FSKNIR))|P(?:SDAQYFRNTC|KEAKYFRKTA)))|HAPPDAQYTKKGP|NA(?:P(?:TGADYFVYKP|KDANYFEYNS)|WGNTYFRKTCS)|DAG(?:QKDTYFKQSS|AADEYFKKSG)|EA(?:GTSDKYFRKTA|KSDDKYNVIGP)|KA(?:NDDAEYFRKKD|P(?:DKANYF(?:EPPK|KPPK)|EEDHYFKPAQ)|EVDDIYSKTAN|K(?:EGDIYSKT(?:MN|AN)|KG(?:GIYSKTMN|DIYSKTMN))))|Y(?:SQKYKDEKSKLEE|NE(?:TDKVQKAILQQ|KDQEEKRKLQE))|N(?:YYEDNDTDKNYYQ|NNAAKLSELSTAQ|THESAQRKKLEEN|DEEKKKRDELEKN|KN(?:NPPLYKLSLEK|KSPLDKLSLDK))|T(?:RYKKDDEDGNFFQ|PTQGKCHCIDGT(?:N|V)|L(?:FDYKCGHDENAP|WNEKCGHGDYNL))|I(?:EHYKDDPEENFYE|KS(?:NYNDSEGNYFK|QYDDNEGNYFK)|LFDYKCAHDNDKV)|D(?:RKEKVKLEENLKN|KGEKKKLEENLKN|Q(?:ERK(?:HLLEKRLET|QHLEKRLET)|QEK(?:LYLENNLKK|AKLENNLKR))|AKKHYGDDENYYK)|P(?:NKCRCEDANADQV|CSVQKCTCINGDP)|E(?:SN(?:M(?:GQCRCFSGDP|VQCRCFSGDP)|KGQCRCFSGDP)|THGYCRCVNRVDV|F(?:SGGKCGHKDNNV|T(?:GGQCGRDGENV|DGHCGH(?:RQGNV|NEENV))))|VKDRYQNDGPDFFK|K(?:S(?:SYNDDGTGNYFK|YYKNDNDRNYFK)|N(?:HYNDTSKNYYK|NNN(?:ELNNLSLDK|KLSNLSTKE))|D(?:HYKGDEANNYFQ|NNTKLNDLSIQE)|K(?:TNPALKSFTNEE|KLEENLRNIFKN)|FSNPKCGHNEGSP)|F(?:SNDQCGHNN(?:RGDP|GGAP)|WYPKC(?:GHHV(?:RQDV|KQ(?:DV|EV))|SHHVKQDV))|Q(?:RNNIKLQ(?:NIPLHE|TLTLHQ)|N(?:NNTKLQNIPLHE|KNENLKSLSLDK)|KENGDINTLKPEE)|L(?:FYYKCGHYVYKDV|WN(?:Y(?:NCGHHVN(?:RDV|QDV)|KCGHHVNQDV)|DKCGHHVKQDV))|ARDHYNDTSGNYYQ)/
-     block_sharing = 2 
+      when self =~ /(?:RE(?:PGKQHLEERLER|KGKSRLEARLKT)|G(?:G(?:HYKNCHCIGGDV|TYKNCRCASGNV)|P(?:NQEKKLLENKLK|DQEKKKLEENLR)|ANAIKAGDNVSIV)|S(?:FTNGQCGRDGENV|WYPKCGHHVKQDV|AKEHYQDTENYYK)|H(?:NRRKEKLETRLEE|E(?:PG(?:IQ(?:HLEKRLES|YLEKRLES)|KQHL(?:GERLEQ|EERLE(?:R|Q)))|QG(?:YNRLEARLKT|NNRLEARLKT|INRLEARLKT))|QQRKHLLEKRLET)|C(?:RAEEK(?:GTYFKNRE|D(?:TYFKNRE|IYSKTTD)|EIYSKTTD)|G(?:TEDKDTYFIKSG|VEENAKYFRESS|A(?:GMKDIYSKTMN|SEDAKYKVIGP|T(?:MNDIFSKNIR|VDDI(?:SSKNIR|FSKNIR))|P(?:SDAQYFRNTC|KEAKYFRKTA)))|HAPPDAQYTKKGP|NA(?:P(?:TGADYFVYKP|KDANYFEYNS)|WGNTYFRKTCS)|DAG(?:QKDTYFKQSS|AADEYFKKSG)|EA(?:GTSDKYFRKTA|KSDDKYNVIGP)|KA(?:NDDAEYFRKKD|P(?:DKANYF(?:EPPK|KPPK)|EEDHYFKPAQ)|EVDDIYSKTAN|K(?:EGDIYSKT(?:MN|AN)|KG(?:GIYSKTMN|DIYSKTMN))))|Y(?:SQKYKDEKSKLEE|NE(?:TDKVQKAILQQ|KDQEEKRKLQE))|N(?:YYEDNDTDKNYYQ|NNAAKLSELSTAQ|THESAQRKKLEEN|DEEKKKRDELEKN|KN(?:NPPLYKLSLEK|KSPLDKLSLDK))|T(?:RYKKDDEDGNFFQ|PTQGKCHCIDGT(?:N|V)|L(?:FDYKCGHDENAP|WNEKCGHGDYNL))|I(?:EHYKDDPEENFYE|KS(?:NYNDSEGNYFK|QYDDNEGNYFK)|LFDYKCAHDNDKV)|D(?:RKEKVKLEENLKN|KGEKKKLEENLKN|Q(?:ERK(?:HLLEKRLET|QHLEKRLET)|QEK(?:LYLENNLKK|AKLENNLKR))|AKKHYGDDENYYK)|P(?:NKCRCEDANADQV|CSVQKCTCINGDP)|E(?:SN(?:M(?:GQCRCFSGDP|VQCRCFSGDP)|KGQCRCFSGDP)|THGYCRCVNRVDV|F(?:SGGKCGHKDNNV|T(?:GGQCGRDGENV|DGHCGH(?:RQGNV|NEENV))))|VKDRYQNDGPDFFK|K(?:S(?:SYNDDGTGNYFK|YYKNDNDRNYFK)|N(?:HYNDTSKNYYK|NNN(?:ELNNLSLDK|KLSNLSTKE))|D(?:HYKGDEANNYFQ|NNTKLNDLSIQE)|K(?:TNPALKSFTNEE|KLEENLRNIFKN)|FSNPKCGHNEGSP)|F(?:SNDQCGHNN(?:RGDP|GGAP)|WYPKC(?:GHHV(?:RQDV|KQ(?:DV|EV))|SHHVKQDV))|Q(?:RNNIKLQ(?:NIPLHE|TLTLHQ)|N(?:NNTKLQNIPLHE|KNENLKSLSLDK)|KENGDINTLKPEE)|L(?:FYYKCGHYVYKDV|WN(?:Y(?:NCGHHVN(?:RDV|QDV)|KCGHHVNQDV)|DKCGHHVKQDV))|ARDHYNDTSGNYYQ)/
+      block_sharing = 2 
     else
       block_sharing = 0
     end
     block_sharing
   end
-  
+
   def is_var1_cp1?
     return true if cyspolv_group == 1 && self =~ /NVHDKVEKGLREVF|NVHDKVETGLREVF/i
   end
@@ -111,11 +138,30 @@ class Bio::Sequence::AA
     return true if is_var1_cp1? || is_var1_cp2? 
   end
 
+  def var1_status
+    if is_var1?
+      status = 'var1'
+    else
+      status = 'other'
+    end
+    status
+  end
+
   # return var group A like tags. Group A like sequences are associated with disease severity.
   def is_groupA_like?
     return true if cys_count == 2 && bs_group == 1
   end
 
+  def groupA_status
+    if is_groupA_like?
+      status = 'groupA_like'
+    else
+      status = 'other'
+    end
+    status
+  end
+
+
   #distict sequence identifier(DSID)
   def dsid
     "#{polv1}-#{polv2}-#{polv3}-#{cys_count.to_s}-#{polv4}-#{self.length}"
@@ -153,7 +199,6 @@ class Bio::Sequence::AA
     self[self.length - 12 - win_len - anchor_pos, win_len]
   end
 
-  private
   def accepted_length
     100..168
   end
@@ -169,4 +214,17 @@ class Bio::Sequence::AA
   def vw_ww_missing?
     true if ww_missing? && vw_missing?
   end
+
+  def sig2_like?
+    return true if self =~ /AKLSELSTAQ|CRAEEKDTYF|KCGHHVNQDV|HEPGKQHLEE|EPGKQHLEER|PGKQHLEERL|GKQHLEERLE|KQHLEERLEQ|QHLEERLEQM|HLEERLEQMF|LEERLEQMFE|EERLEQMFEN|ERLEQMFENI|RLEQMFENIK|LEQMFENIKN|EQMFENIKNN|QMFENIKNNN|MFENIKNNNA|FENIKNNNAA|ENIKNNNAAK|NIKNNNAAKL|IKNNNAAKLS|KNNNAAKLSE|NNNAAKLSEL|NNAAKLSELS|NAAKLSELST|AAKLSELSTA|RAEEKDTYFK|AEEKDTYFKN|EEKDTYFKNR|EKDTYFKNRE|KDTYFKNREN|DTYFKNRENG|TYFKNRENGK|YFKNRENGKL|FKNRENGKLL|KNRENGKLLL|NRENGKLLLW|RENGKLLLWN|ENGKLLLWNY|NGKLLLWNYK|GKLLLWNYKC|KLLLWNYKCG|LLLWNYKCGH|LLWNYKCGHH|LWNYKCGHHV|WNYKCGHHVN|NYKCGHHVNQ|YKCGHHVNQD|AKLSELSTAQ|CKAKEGDIYS|NCGHHVNQDV|HEPGKQHLEE|EPGKQHLEER|PGKQHLEERL|GKQHLEERLE|KQHLEERLEQ|QHLEERLEQM|HLEERLEQMF|LEERLEQMFE|EERLEQMFEN|ERLEQMFENI|RLEQMFENIK|LEQMFENIKN|EQMFENIKNN|QMFENIKNNN|MFENIKNNNA|FENIKNNNAA|ENIKNNNAAK|NIKNNNAAKL|IKNNNAAKLS|KNNNAAKLSE|NNNAAKLSEL|NNAAKLSELS|NAAKLSELST|AAKLSELSTA|KAKEGDIYSK|AKEGDIYSKT|KEGDIYSKTA|EGDIYSKTAN|GDIYSKTANG|DIYSKTANGN|IYSKTANGNT|YSKTANGNTT|SKTANGNTTL|KTANGNTTLW|TANGNTTLWN|ANGNTTLWNY|NGNTTLWNYN|GNTTLWNYNC|NTTLWNYNCG|TTLWNYNCGH|TLWNYNCGHH|LWNYNCGHHV|WNYNCGHHVN|NYNCGHHVNQ|YNCGHHVNQD|GDINTLKPEE|CRAEEKDIYS|NCGHHVNQDV|HEPGKQHLEE|EPGKQHLEER|PGKQHLEERL|GKQHLEERLE|KQHLEERLER|QHLEERLERI|HLEERLERIF|LEERLERIFA|EERLERIFAN|ERLERIFANI|RLERIFANIQ|LERIFANIQK|ERIFANIQKE|RIFANIQKEN|IFANIQKENG|FANIQKENGD|ANIQKENGDI|NIQKENGDIN|IQKENGDINT|QKENGDINTL|KENGDINTLK|ENGDINTLKP|NGDINTLKPE|RAEEKDIYSK|AEEKDIYSKT|EEKDIYSKTT|EKDIYSKTTD|KDIYSKTTDN|DIYSKTTDNG|IYSKTTDNGK|YSKTTDNGKL|SKTTDNGKLI|KTTDNGKLIL|TTDNGKLILW|TDNGKLILWN|DNGKLILWNY|NGKLILWNYN|GKLILWNYNC|KLILWNYNCG|LILWNYNCGH|ILWNYNCGHH|LWNYNCGHHV|WNYNCGHHVN|NYNCGHHVNQ|YNCGHHVNQD/
+  end
+
+  def sig2_status
+    if sig2_like? 
+      sig2 = 'sig2_like'
+    else
+      sig2 = 'other'
+    end
+    sig2
+  end
 end

data/lib/bio/sequence/na/na.rb

@@ -0,0 +1,85 @@
+class Bio::Sequence::NA
+  attr_accessor :mut_pos
+
+  #position specific polymorphic block 1
+  def pspb1_dna(anchor_pos=0,win_len=42)
+    self[42 + anchor_pos,win_len]
+  end
+
+  #position specific polymorphic block 2
+  def pspb2_dna(anchor_pos=0,win_len=42)
+    if !ww_missing?
+      return self[(ww_pos * 3) - 12 - anchor_pos - win_len, win_len]
+    elsif !vw_missing?
+      return self[(vw_pos * 3) - 36 - win_len - anchor_pos, win_len]
+    else
+      return '....'
+    end
+  end
+
+  #position specific polymorphic block 3
+  def pspb3_dna(anchor_pos=0,win_len=42)
+    if !ww_missing?
+      return self[(ww_pos * 3) + 42 + anchor_pos, win_len]
+    elsif !vw_missing?
+      return self[(vw_pos * 3) + 8 + anchor_pos, win_len]
+    else
+      return '....'
+    end
+  end
+
+  #position specific polymorphic block 4
+  def pspb4_dna(anchor_pos=0,win_len=42)
+    self[self.length - 36 - win_len - anchor_pos, win_len]
+  end
+
+  def polv1_dna_pos
+    mut_pos.map{|mut| mut - (aa_seq.polv1_pos * 3)}
+  end
+
+  def polv2_dna_pos
+    mut_pos.map{|mut| mut - (aa_seq.polv2_pos * 3)}
+  end
+
+  def polv3_dna_pos
+    mut_pos.map{|mut| mut - (aa_seq.polv3_pos * 3)}
+  end
+
+  def polv4_dna_pos
+    mut_pos.map{|mut| mut - (aa_seq.polv4_pos * 3)}
+  end
+
+  #return an array of distances from each polv
+  def dist_from_polvs
+    [polv1_dna_pos, polv2_dna_pos, polv3_dna_pos, polv4_dna_pos]
+  end
+
+  private
+  def accepted_length
+    aa_seq.accepted_length #300..500
+  end
+
+  def aa_seq
+    self.translate
+  end
+
+  def ww_pos
+    aa_seq.ww_pos #rindex("WW")
+  end
+
+  def vw_pos
+    aa_seq.vw_pos #rindex("VW")
+  end
+
+  def ww_missing?
+    aa_seq.ww_missing? #true unless aa_seq =~ /WW/i
+  end
+
+  def vw_missing?
+    aa_seq.vw_missing? #true unless aa_seq =~ /VW/i
+  end
+
+  def vw_ww_missing?
+    aa_seq.vw_ww_missing? #true if ww_missing? && vw_missing?
+  end
+end

data/spec/aa_spec.rb

@@ -3,8 +3,10 @@ require File.expand_path(File.dirname(__FILE__) + '/spec_helper')
 describe "Dbla" do
   context 'Group4 Dbla tag' do
     before(:each) do
-      seq = 'YIGDIIRGRDLYLVNPQEKEQRDKLEENLKKIFKKIHDDVMKTSGRTNGAKARYGGDENFFKLREDWWTANRSTVWKAITCGTHDGASYFRATCSDGQSGAQAKNKCTCNNGDVPTYFDYVPQFLR'
-      @tag = Bio::Sequence::AA.new(seq)
+      seq1 = 'YIGDIIRGRDLYLVNPQEKEQRDKLEENLKKIFKKIHDDVMKTSGRTNGAKARYGGDENFFKLREDWWTANRSTVWKAITCGTHDGASYFRATCSDGQSGAQAKNKCTCNNGDVPTYFDYVPQFLR'
+      seq2 = 'DIGDIVRGRDLYLGYDQKEKEQREKLEKNLKDIFGDIYEELTKNGKTLQERHGSDTTNYYKLREDWRTANRHTVWEALTCEAPESAHYFKPSENNTQYFSNKYCGRDEKKVPTNLDYVPQFLR'
+      @tag = Bio::Sequence::AA.new(seq1)
+      @tag2 = Bio::Sequence::AA.new(seq2)
     end
 
     it "should return the number of cysteines" do
@@ -31,6 +33,13 @@ describe "Dbla" do
       @tag.is_var1?.should be_false
     end
 
+    it 'should return the polv1 to polv2 part of the sequence' do
+      @tag.polv1_to_polv2.should == 'LYLVNPQEKEQRDKLEENLKKIFKKIHDDVMKTSGRTNGAKARYGGDENFFKLRED'
+    end
+
+    it 'should return the polv3 to polv4 part of the sequence' do
+      @tag.polv3_to_polv4.should == 'KAITCGTHDGASYFRATCSDGQSGAQAKNKCTCNNGDVPTYF'
+    end
   end
 
   context 'Group2 Dbla tag' do
@@ -50,5 +59,19 @@ describe "Dbla" do
     it 'should return false for cp2 var1' do
       @tag2.is_var1_cp2?.should be_false
     end
+
+    it 'should return other unless var1' do
+      @tag2.var1_status.should == 'other'
+    end
+  end
+
+  context 'mutations in tag' do
+    before(:each) do
+      seq = 'DIGDIVRGTDLFLGGPSQEKKKLEENLKKILENIKNKNTKLSTLTLEKVREYWWALNRNDVWKALTCSAPYEAQYFIKSSDKEHSFSSEYCGHHNNDDPLTNLDYVPQFLR'
+      @tag3 = Bio::Sequence::AA.new(seq)
+    end
+    it 'should return the position of polv1' do
+      @tag3.polv1_pos.should == 10
+    end
   end
 end

data/spec/na_spec.rb

@@ -0,0 +1,41 @@
+require 'csv'
+
+require File.expand_path(File.dirname(__FILE__) + '/spec_helper')
+
+describe 'dbla' do
+  context 'nucleic' do
+    before(:each) do
+      dna = 'gatataggtgatattgtaagaggaagagatctatttcatggtaatccacaagaaaaagaaaaaagagaagacttagaaaagaaattgaaagaaattttccaacaaatacatagtggattgtcgaagaacggcgcacaaacttactacaatgataatgatactgacaaaaactattacaaattacgagaagattggtggacggcgaatcgcgccacaatctgggaagctatcacatgtgaagcaaaaactgatgataaatattttagaaatacatgtaatggaggaagtccaactaaaggtgactgccgatgtgctgccggagatgttcctacatattttgactacgttccgcagtatcttcgc'
+      aa  = 'DIGDIVRGRDLFHGNPQEKEKREDLEKKLKEIFQQIHSGLSKNGAQTYYNDNDTDKNYYKLREDWWTANRATIWEAITCEAKTDDKYFRNTCNGGSPTKGDCRCAAGDVPTYFDYVPQYLR'
+      @tag_as_dna = Bio::Sequence::NA.new(dna)
+      @tag_as_aa  = Bio::Sequence::AA.new(aa)
+    end
+
+    it 'should return the pspb1 in dna format' do
+      Bio::Sequence::NA.new(@tag_as_dna.pspb1_dna).translate.should == @tag_as_aa.pspb1
+    end
+
+    it 'should return the pspb2 in dna format' do
+      Bio::Sequence::NA.new(@tag_as_dna.pspb2_dna).translate.should == @tag_as_aa.pspb2
+    end
+
+    it 'should return the pspb3 in dna format' do
+      Bio::Sequence::NA.new(@tag_as_dna.pspb3_dna).translate.should == @tag_as_aa.pspb3
+    end
+
+    it 'should return the pspb4 in dna format' do
+      Bio::Sequence::NA.new(@tag_as_dna.pspb4_dna).translate.should == @tag_as_aa.pspb4
+    end
+
+    it 'should return distance from anchor point given a position' do
+      #@tag_as_dna.mut_pos = [380,369,67,62,56]
+      #@tag_as_dna.polv1_dna_pos.should == -27
+      #@tag_as_dna.coordinates.each do |row|
+       #puts row.to_csv
+     #end
+    end
+
+    it 'should return an array of coordinates ' do
+    end
+  end
+end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: bio-dbla-classifier
 version: !ruby/object:Gem::Version
-  version: 0.5.1
+  version: 0.7.1
   prerelease: 
 platform: ruby
 authors:
@@ -9,74 +9,88 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2012-02-20 00:00:00.000000000 Z
+date: 2013-02-22 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bio
-  requirement: &2152826100 !ruby/object:Gem::Requirement
+  requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
       - !ruby/object:Gem::Version
-        version: 1.4.2
+        version: 1.4.3
   type: :runtime
   prerelease: false
-  version_requirements: *2152826100
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 1.4.3
 - !ruby/object:Gem::Dependency
   name: rspec
-  requirement: &2152823580 !ruby/object:Gem::Requirement
+  requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
-    - - ~>
+    - - ! '>='
       - !ruby/object:Gem::Version
-        version: 2.3.0
+        version: 2.8.0
   type: :development
   prerelease: false
-  version_requirements: *2152823580
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 2.8.0
 - !ruby/object:Gem::Dependency
   name: bundler
-  requirement: &2152837840 !ruby/object:Gem::Requirement
+  requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
-    - - ~>
+    - - ! '>='
       - !ruby/object:Gem::Version
-        version: 1.1.rc.7
+        version: 1.0.22
   type: :development
   prerelease: false
-  version_requirements: *2152837840
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 1.0.22
 - !ruby/object:Gem::Dependency
   name: jeweler
-  requirement: &2152835560 !ruby/object:Gem::Requirement
+  requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
-    - - ~>
+    - - ! '>='
       - !ruby/object:Gem::Version
         version: 1.6.4
   type: :development
   prerelease: false
-  version_requirements: *2152835560
-- !ruby/object:Gem::Dependency
-  name: rcov
-  requirement: &2152831480 !ruby/object:Gem::Requirement
+  version_requirements: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
       - !ruby/object:Gem::Version
-        version: '0'
-  type: :development
-  prerelease: false
-  version_requirements: *2152831480
+        version: 1.6.4
 - !ruby/object:Gem::Dependency
   name: rake
-  requirement: &2153076260 !ruby/object:Gem::Requirement
+  requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
-    - - ~>
+    - - ! '>='
       - !ruby/object:Gem::Version
         version: 0.9.2.2
   type: :development
   prerelease: false
-  version_requirements: *2153076260
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 0.9.2.2
 description: Methods to classify and manipulate PfEMP1 DBL-alpha sequence tags
 email: georgkam@gmail.com
 executables: []
@@ -87,6 +101,7 @@ extra_rdoc_files:
 files:
 - .document
 - .rspec
+- .travis.yml
 - Gemfile
 - Gemfile.lock
 - LICENSE.txt
@@ -96,8 +111,10 @@ files:
 - bio-dbla-classifier.gemspec
 - lib/bio-dbla-classifier.rb
 - lib/bio/sequence/aa/aa.rb
+- lib/bio/sequence/na/na.rb
 - spec/aa_spec.rb
 - spec/bio-dbla-classifier_spec.rb
+- spec/na_spec.rb
 - spec/spec_helper.rb
 homepage: http://github.com/georgeG/bioruby-dbla-classifier
 licenses:
@@ -114,7 +131,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
       version: '0'
       segments:
       - 0
-      hash: 762142858629813033
+      hash: 1678830180674382549
 required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
   requirements:
@@ -123,7 +140,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 1.8.12
+rubygems_version: 1.8.25
 signing_key: 
 specification_version: 3
 summary: A tool to classify and manipulate PfEMP1 DBL-alpha sequence tags