bio-dbla-classifier 0.4.0 → 0.5.0

data/Gemfile

@@ -5,7 +5,7 @@ source "http://rubygems.org"
 # Needed to run rake, tests, features
 group :development do
   gem "rspec", "~> 2.3.0"
-  gem "bundler", "~> 1.0.0"
+  gem "bundler", "~> 1.1.rc.7"
   gem "jeweler", "~> 1.6.4"
   gem "rcov", ">= 0"
 end

data/Gemfile.lock

@@ -24,7 +24,7 @@ PLATFORMS
 
 DEPENDENCIES
   bio (>= 1.4.2)
-  bundler (~> 1.0.0)
+  bundler (~> 1.1.rc.7)
   jeweler (~> 1.6.4)
   rcov
   rspec (~> 2.3.0)

data/README.rdoc

@@ -6,9 +6,8 @@ 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.
+Ruby must be installed on your system. 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. The plugin has been tested on Ruby 1.9.2-p290.
 
  gem install bio-dbla-classifier
 
@@ -41,34 +40,36 @@ install the gem. This will install the bioruby gem if it is not already installe
 
 
  #get the block sharing group for this tag
- #puts dbl_seq.bs_group #to be implemented
+ puts dbl_seq.bs_group #=> 1
 
  #get the length of the tag
  puts dbl_seq.size #=> 115
 
+ dbl_seq.is_var1? #=> false
+
 = Finding the Position Specific Polymorphic Blocks(PSPB)
 
-The pspb methods take 2 arguments, an anchor position and a window length that defines the length of the pspb
+The pspb methods take 2 arguments, an anchor position and a window length that
+defines the length of the pspb.The default anchor position is 0 and the default
+window length is 14
 
  #get pspb1
- puts seq.pspb1(0,14) #=> NPEVEKGLKAVFRK
+ puts seq.pspb1 #=> NPEVEKGLKAVFRK
 
  #get pspb2
- puts seq.pspb2(0,14) #=> THYADEDGSGNYVK
+ puts seq.pspb2 #=> THYADEDGSGNYVK
 
  #get pspb3
- puts seq.pspb3(0,14) #=> CKAPQSVHYFIKTS
+ puts seq.pspb3 #=> CKAPQSVHYFIKTS
 
  #get pspb4
- puts seq.pspb4(0,14) #=> FTSHGKCGRNETNV
-
-= Processing fasta files
+ puts seq.pspb4 #=> FTSHGKCGRNETNV
 
-If the input is a fasta file,
+= Processing a flatfile for example fasta, genbank or embl
 
  seq_file = "sequences.fasta"
 
- #Process each entry in the file
+ #for 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}"
@@ -76,5 +77,4 @@ If the input is a fasta file,
 
 = Copyright
 
-See LICENSE.txt for further details.
-
+See LICENSE.txt for further details

data/VERSION

@@ -1 +1 @@
-0.4.0
+0.5.0

data/bio-dbla-classifier.gemspec

@@ -5,11 +5,11 @@
 
 Gem::Specification.new do |s|
   s.name = "bio-dbla-classifier"
-  s.version = "0.4.0"
+  s.version = "0.5.0"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["George Githinji"]
-  s.date = "2011-10-13"
+  s.date = "2012-02-20"
   s.description = "Methods to classify and manipulate PfEMP1 DBL-alpha sequence tags"
   s.email = "georgkam@gmail.com"
   s.extra_rdoc_files = [
@@ -35,7 +35,7 @@ Gem::Specification.new do |s|
   s.homepage = "http://github.com/georgeG/bioruby-dbla-classifier"
   s.licenses = ["Ruby"]
   s.require_paths = ["lib"]
-  s.rubygems_version = "1.8.10"
+  s.rubygems_version = "1.8.12"
   s.summary = "A tool to classify and manipulate PfEMP1 DBL-alpha sequence tags"
 
   if s.respond_to? :specification_version then
@@ -44,20 +44,20 @@ Gem::Specification.new do |s|
     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<bundler>, ["~> 1.1.rc.7"])
       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<bundler>, ["~> 1.1.rc.7"])
       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<bundler>, ["~> 1.1.rc.7"])
     s.add_dependency(%q<jeweler>, ["~> 1.6.4"])
     s.add_dependency(%q<rcov>, [">= 0"])
   end

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

@@ -1,180 +1,156 @@
 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}"
- 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
-   error = 'WW or VW motif missing'
-  end
-  polv2 unless error
- 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
-    error = 'WW or VW motif missing'
-  end
-
-  polv3 unless error
-
- 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
-
- #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
+  def has_accepted_length?
+    true if accepted_length.include? self.length
+  end
 
-end
+  def start_motif
+    self[0,5]
+  end
+
+  def end_motif
+    self[-5,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 !ww_missing?
+      return self[ww_pos - 4,4]
+    elsif !vw_missing?
+      return self[vw_pos - 12,4]
+    else
+      return '....'
+    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
+  #The third position of limited variability(polv3)
+  def polv3
+    if !ww_missing?
+      return self[ww_pos + 10,4]
+    elsif !vw_missing?
+      return self[vw_pos + 2,4]
+    else
+      return '....'
+    end
+  end
 
-#seq1 ='DIGDIVRGRDMFKSNPEVEKGLKAVFRKINNGLTPQAKTHYADEDGSGNYVKLREDWWKANRDQVWKAITCKAPQSVHYFIKTSHGTRGFTSHGKCGRNETNVPTNLDYVPQYLR'
-#seq = Bio::Sequence::AA.new(seq1)
+  #The fourth position of limited variability(polv4)
+  def polv4
+    self[self.length - 12,4]
+  end
 
-#get the positions of limited variability
-#puts seq.polv1
-#puts seq.polv2
-#puts seq.polv3
-#puts seq.polv4
+  #Assigning dsid group based on number of cysteines, presence of REY motif in polv2 and 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
 
-#get the number if cysteines in the tag
-#puts seq.cys_count
+  def is_var1_cp1?
+    return true if cyspolv_group == 1 && self =~ /NVHDKVEKGLREVF|NVHDKVETGLREVF/i
+  end
 
-#get the distinct sequence identifier
-#puts seq.dsid
+  def is_var1_cp2?
+    return true if cyspolv_group == 2 && self =~ /APNKEKIKLEENLKK/i
+  end
 
-#get the cyspolv group for this tag
-#puts seq.cyspolv_group
+  def is_var1?
+    return true if is_var1_cp1? || is_var1_cp2? 
+  end
 
+  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 
+    else
+      block_sharing = 0
+    end
+    block_sharing
+  end
 
-#get the block sharing group for this tag
-#puts seq.bs_group #to be implemented
+  #distict sequence identifier(DSID)
+  def dsid
+    "#{polv1}-#{polv2}-#{polv3}-#{cys_count.to_s}-#{polv4}-#{self.length}"
+  end
 
-#get the length of the tag
-#puts seq.size
+  #position specific polymorphic block 1
+  def pspb1(anchor_pos=0,win_len=14)
+    self[14 + anchor_pos,win_len]
+  end
 
-#get the pspb1
-#puts seq.pspb1(0,14)
+  #position specific polymorphic block 2
+  def pspb2(anchor_pos=0,win_len=14)
+    if !ww_missing?
+      return self[ww_pos - 4 - anchor_pos - win_len, win_len]
+    elsif !vw_missing?
+      return self[vw_pos - 12 - win_len - anchor_pos, win_len]
+    else
+      return '....'
+    end
+  end
 
-#get the pspb2
-#puts seq.pspb2(0,14)
+  #position specific polymorphic block 3
+  def pspb3(anchor_pos=0,win_len=14)
+    if !ww_missing?
+      return self[ww_pos + 14 + anchor_pos, win_len]
+    elsif !vw_missing?
+      return self[vw_pos + 6 + anchor_pos, win_len]
+    else
+      return '....'
+    end
+  end
 
-#get the pspb3
-#puts seq.pspb3(0,14)
+  #position specific polymorphic block 4
+  def pspb4(anchor_pos=0,win_len=14)
+    self[self.length - 12 - win_len - anchor_pos, win_len]
+  end
 
-#get the pspb4
-#puts seq.pspb4(0,14)
+  private
+  def accepted_length
+    100..168
+  end
 
+  def ww_missing?
+    true unless self =~ /WW/i
+  end
 
-#if input file is a fasta file
- #seq_file = "#{ENV['HOME']}/sequences/878_kilifi_sequences.fasta"
+  def vw_missing?
+    true unless self =~ /VW/i
+  end
 
-#read the file
- #Bio::FlatFile.open(seq_file).each do |entry|
-  #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
+  def vw_ww_missing?
+    true if ww_missing? && vw_missing?
+  end
+end

data/spec/aa_spec.rb

@@ -1,32 +1,54 @@
 require File.expand_path(File.dirname(__FILE__) + '/spec_helper')
 
 describe "Dbla" do
-  context 'a group4 Dbla tag' do
-   before(:each) do
-    seq = 'YIGDIIRGRDLYLVNPQEKEQRDKLEENLKKIFKKIHDDVMKTSGRTNGAKARYGGDENFFKLREDWWTANRSTVWKAITCGTHDGASYFRATCSDGQSGAQAKNKCTCNNGDVPTYFDYVPQFLR'
-    @tag = Bio::Sequence::AA.new(seq)
-   end
-
-  it "should return the number of cysteines" do
-   @tag.cys_count.should == 4
-  end
+  context 'Group4 Dbla tag' do
+    before(:each) do
+      seq = 'YIGDIIRGRDLYLVNPQEKEQRDKLEENLKKIFKKIHDDVMKTSGRTNGAKARYGGDENFFKLREDWWTANRSTVWKAITCGTHDGASYFRATCSDGQSGAQAKNKCTCNNGDVPTYFDYVPQFLR'
+      @tag = Bio::Sequence::AA.new(seq)
+    end
 
-  it 'should return a dsid' do
-    @tag.dsid.should == 'LYLV-LRED-KAIT-4-PTYF-126'
-  end
+    it "should return the number of cysteines" do
+      @tag.cys_count.should == 4
+    end
 
-  it 'should return the cyspolv group' do
-    @tag.cyspolv_group.should == 4
-  end
+    it 'should return a dsid' do
+      @tag.dsid.should == 'LYLV-LRED-KAIT-4-PTYF-126'
+    end
 
-  it 'should return the length' do
-    @tag.length.should == 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
+
+    it 'should return the start motif' do
+      @tag.start_motif.should == 'YIGDI'
+    end
+
+    it 'should return false for var1' do
+      @tag.is_var1?.should be_false
+    end
 
-  it 'should return the start motif' do
-    @tag.start_motif == 'YIGDI'
   end
 
- end
-end
+  context 'Group2 Dbla tag' do
+    before(:each) do
+      seq = 'DIGDIVRGTDLFLGGPSQEKKKLEENLKKILENIKNKNTKLSTLTLEKVREYWWALNRNDVWKALTCSAPYEAQYFIKSSDKEHSFSSEYCGHHNNDDPLTNLDYVPQFLR'
+      @tag2 = Bio::Sequence::AA.new(seq)
+    end
+
+    it 'should return the number of cysteines' do 
+      @tag2.cys_count.should == 2
+    end
 
+    it 'should return the block sharing group 1' do
+      @tag2.bs_group.should == 1
+    end
+
+    it 'should return false for cp2 var1' do
+      @tag2.is_var1_cp2?.should be_false
+    end
+  end
+end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: bio-dbla-classifier
 version: !ruby/object:Gem::Version
-  version: 0.4.0
+  version: 0.5.0
   prerelease: 
 platform: ruby
 authors:
@@ -9,11 +9,11 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2011-10-13 00:00:00.000000000Z
+date: 2012-02-20 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bio
-  requirement: &2155795540 !ruby/object:Gem::Requirement
+  requirement: &2152850760 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -21,10 +21,10 @@ dependencies:
         version: 1.4.2
   type: :runtime
   prerelease: false
-  version_requirements: *2155795540
+  version_requirements: *2152850760
 - !ruby/object:Gem::Dependency
   name: rspec
-  requirement: &2155794860 !ruby/object:Gem::Requirement
+  requirement: &2152849320 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -32,21 +32,21 @@ dependencies:
         version: 2.3.0
   type: :development
   prerelease: false
-  version_requirements: *2155794860
+  version_requirements: *2152849320
 - !ruby/object:Gem::Dependency
   name: bundler
-  requirement: &2155787960 !ruby/object:Gem::Requirement
+  requirement: &2152848240 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
-        version: 1.0.0
+        version: 1.1.rc.7
   type: :development
   prerelease: false
-  version_requirements: *2155787960
+  version_requirements: *2152848240
 - !ruby/object:Gem::Dependency
   name: jeweler
-  requirement: &2155786180 !ruby/object:Gem::Requirement
+  requirement: &2152846960 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -54,10 +54,10 @@ dependencies:
         version: 1.6.4
   type: :development
   prerelease: false
-  version_requirements: *2155786180
+  version_requirements: *2152846960
 - !ruby/object:Gem::Dependency
   name: rcov
-  requirement: &2155784980 !ruby/object:Gem::Requirement
+  requirement: &2152855080 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -65,7 +65,7 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *2155784980
+  version_requirements: *2152855080
 description: Methods to classify and manipulate PfEMP1 DBL-alpha sequence tags
 email: georgkam@gmail.com
 executables: []
@@ -103,7 +103,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
       version: '0'
       segments:
       - 0
-      hash: -1659999011793222104
+      hash: 3330781070760048632
 required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
   requirements:
@@ -112,7 +112,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 1.8.10
+rubygems_version: 1.8.12
 signing_key: 
 specification_version: 3
 summary: A tool to classify and manipulate PfEMP1 DBL-alpha sequence tags