bioseqalign 0.0.3 → 0.0.4

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 0b96dd84832f04c18f665123a094d288a91c3030
-  data.tar.gz: 96d9c502f30a612eec662baeec5f0a275714e912
+  metadata.gz: eebe247527833046b360916889bc3e443b58ad88
+  data.tar.gz: 2627922393b2b810d35652fd1e4d8ecb73c83a89
 SHA512:
-  metadata.gz: 792e24c7020440b3377f9c4f9218b21bdf5c986d582d2ffcf76f0292547d938353544fafe20b02fc2e0a9fe65e622736782e13ca8903807e2a5977c25e407206
-  data.tar.gz: fb8c79b054f34495d921307902e0554841e2771742065243912c4a8ff0bf332ede46b8ccbbdcd1cab60884a3575b61b8aa4df3bdf22242dc8a8fc2c027caf678
+  metadata.gz: 38cedead4c547bbd32abe240de94f11ace65b67c9889ad1a7da33e70a5d83bab0a882844ab0031db401e7096b0644f887760b575f07b80a16428b74005a13687
+  data.tar.gz: b763ec760284ec0ae8ed9733ea77d1f67260e15e67f9288eb49df48ad66d9835b479db4e94f5bb0a58ee665058040ac8a1437a3cd7e0e49d433d5d2d6ef3310a

data/ext/bioseqalign/LocalAlign.cpp

@@ -13,10 +13,8 @@ Rice::Array LocalAlign::getAlignment() {
   assignSource(row(ali, 1), seq2);
   
   //localAlignment(ali, Score<int,Simple>(matchScore,mismatchScore,indelScore), SmithWaterman());
-  localAlignment(ali, Score<int>(matchScore,mismatchScore,indelScore), SmithWaterman());
-
-  //std::cout<<row(ali, 0)<<std::endl;
-  //std::cout<<row(ali, 1)<<std::endl;
+  //localAlignment(ali, Score<int>(matchScore,mismatchScore,indelScore), SmithWaterman());
+  localAlignment(ali, Score<int>(matchScore,mismatchScore,indelScore));
 
   typedef Iterator<TRow>::Type TRowIterator;
   TRowIterator it = begin(row(ali, 0));
@@ -34,10 +32,6 @@ Rice::Array LocalAlign::getAlignment() {
     else s_row2 += (*it2);
   }
 
-  // std::cout<<s_row1<<std::endl;
-  // std::cout<<s_row2<<std::endl;
-  // std::cout<<ali<<std::endl;
-  
   return getArrayFromAlignStr(s_row1+s_row2);
 }
 
@@ -48,6 +42,7 @@ void LocalAlign::run() {
   assignSource(row(ali, 0), seq1);
   assignSource(row(ali, 1), seq2);
   
-  score = localAlignment(ali, Score<int,Simple>(matchScore,mismatchScore,indelScore), SmithWaterman());
+  //score = localAlignment(ali, Score<int,Simple>(matchScore,mismatchScore,indelScore), SmithWaterman());
+  score = localAlignment(ali, Score<int,Simple>(matchScore,mismatchScore,indelScore));
 }
 

data/lib/bioseqalign/version.rb

@@ -1,6 +1,6 @@
 
 module BioSeqAlign
 
-  VERSION='0.0.3'
+  VERSION='0.0.4'
   
 end

metadata

@@ -1,29 +1,29 @@
 --- !ruby/object:Gem::Specification
 name: bioseqalign
 version: !ruby/object:Gem::Version
-  version: 0.0.3
+  version: 0.0.4
 platform: ruby
 authors:
 - Stefano R.B.
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-08-06 00:00:00.000000000 Z
+date: 2016-04-07 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rice
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - '>='
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: '0'
+        version: '2.1'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - '>='
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: '0'
+        version: '2.1'
 description: A simple gem to perform fast pairwise sequence alignment using seqan
 email: stefano.rb@gmail.com
 executables: []
@@ -32,32 +32,17 @@ extensions:
 extra_rdoc_files: []
 files:
 - ext/bioseqalign/FitAlign.cpp
-- ext/bioseqalign/FitAlign.cpp~
 - ext/bioseqalign/FitAlign.hpp
-- ext/bioseqalign/FitAlign.hpp~
 - ext/bioseqalign/GlobalAlign.cpp
-- ext/bioseqalign/GlobalAlign.cpp~
 - ext/bioseqalign/GlobalAlign.hpp
-- ext/bioseqalign/GlobalAlign.hpp~
 - ext/bioseqalign/LocalAlign.cpp
-- ext/bioseqalign/LocalAlign.cpp~
 - ext/bioseqalign/LocalAlign.hpp
-- ext/bioseqalign/LocalAlign.hpp~
-- ext/bioseqalign/Makefile
 - ext/bioseqalign/PairwiseAlign.cpp
-- ext/bioseqalign/PairwiseAlign.cpp~
 - ext/bioseqalign/PairwiseAlign.hpp
-- ext/bioseqalign/PairwiseAlign.hpp~
 - ext/bioseqalign/PrefixSuffixAlign.cpp
-- ext/bioseqalign/PrefixSuffixAlign.cpp~
 - ext/bioseqalign/PrefixSuffixAlign.hpp
-- ext/bioseqalign/PrefixSuffixAlign.hpp~
 - ext/bioseqalign/extconf.rb
-- ext/bioseqalign/extconf.rb~
 - ext/bioseqalign/fitalgntest.cpp
-- ext/bioseqalign/fitalgntest.cpp~
-- ext/bioseqalign/runTest.rb
-- ext/bioseqalign/runTest.rb~
 - lib/bioseqalign.rb
 - lib/bioseqalign/version.rb
 homepage: https://github.com/stefrb/bioseqalign
@@ -71,17 +56,17 @@ require_paths:
 - ext
 required_ruby_version: !ruby/object:Gem::Requirement
   requirements:
-  - - '>='
+  - - ">="
     - !ruby/object:Gem::Version
       version: '0'
 required_rubygems_version: !ruby/object:Gem::Requirement
   requirements:
-  - - '>='
+  - - ">="
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.4.3
+rubygems_version: 2.2.2
 signing_key: 
 specification_version: 4
 summary: Pairwise sequence alignment using seqan

data/ext/bioseqalign/FitAlign.cpp~

@@ -1,42 +0,0 @@
-#include "FitAlign.hpp"
-
-FitAlign::FitAlign() {}
-
-FitAlign::FitAlign(std::string s1, std::string s2) : PairwiseAlign(s1, s2) { }
-
-// unable to figure out how to properly overload constructor using RICE
-//FitAlign::FitAlign(std::string s1, std::string s2, int matchS, int mismatchS, int indelS) : PairwiseAlign(s1, s2, matchS, mismatchS, indelS) {}
-
-std::string FitAlign::getAlignment() {
-  TSequence tseq1 = seq1;
-  TSequence tseq2 = seq2;
-
-  TStringSet sequences;
-  appendValue(sequences,tseq1);
-  appendValue(sequences,tseq2);
-
-  TAlignGraph alignG(sequences);
-  
-  // don't penalize gaps on begin/end of seq2
-  globalAlignment(alignG, Score<int,Simple>(matchScore,mismatchScore,indelScore), AlignConfig<true, false, false, true>(), NeedlemanWunsch());
-
-  std::stringstream ss;
-  ss<<alignG;
-  return ss.str();
-}
-
-
-void FitAlign::run() {
-  TSequence tseq1 = seq1;
-  TSequence tseq2 = seq2;
-
-  TStringSet sequences;
-  appendValue(sequences,tseq1);
-  appendValue(sequences,tseq2);
-
-  TAlignGraph alignG(sequences);
-  
-  // don't penalize gaps on begin/end of seq2
-  score = globalAlignment(alignG, Score<int,Simple>(matchScore,mismatchScore,indelScore), AlignConfig<true, false, false, true>(), NeedlemanWunsch());
-  
-}

data/ext/bioseqalign/FitAlign.hpp~

@@ -1,20 +0,0 @@
-#include <iostream>
-#include <string>
-#include <seqan/align.h>
-
-#include "PairwiseAlign.hpp"
-
-using namespace seqan;
-
-class FitAlign : public PairwiseAlign {
-public:
-  FitAlign();
-  FitAlign(std::string s1, std::string s2);
-  //FitAlign(std::string s1, std::string s2, int matchS, int mismatchS, int indelS);
-  virtual ~FitAlign() {}
-  
-  virtual void run();
-  virtual std::string getAlignment();
-  
-};
-

data/ext/bioseqalign/GlobalAlign.cpp~

@@ -1,53 +0,0 @@
-// global alignment
-
-#include "GlobalAlign.hpp"
-
-GlobalAlign::GlobalAlign() {}
-
-GlobalAlign::GlobalAlign(std::string s1, std::string s2) : PairwiseAlign(s1, s2) { }
-
-Rice::Array GlobalAlign::getAlignment() {
-  TAlign ali;
-  resize(rows(ali), 2);
-  assignSource(row(ali, 0), seq1);
-  assignSource(row(ali, 1), seq2);
-  
-  //globalAlignment(ali, Score<int,Simple>(matchScore,mismatchScore,indelScore), SmithWaterman());
-  globalAlignment(ali, Score<int>(matchScore,mismatchScore,indelScore), SmithWaterman());
-
-  //std::cout<<row(ali, 0)<<std::endl;
-  //std::cout<<row(ali, 1)<<std::endl;
-
-  typedef Iterator<TRow>::Type TRowIterator;
-  TRowIterator it = begin(row(ali, 0));
-  TRowIterator itEnd = end(row(ali, 0));
-  std::string s_row1 = "";
-  for(; it != itEnd; ++it) {
-    if(isGap(it)) s_row1 += "-";
-    else s_row1 += (*it);
-  }
-  TRowIterator it2 = begin(row(ali, 1));
-  TRowIterator itEnd2 = end(row(ali, 1));
-  std::string s_row2 = "";
-  for(; it2 != itEnd2; ++it2) {
-    if(isGap(it2)) s_row2 += "-";
-    else s_row2 += (*it2);
-  }
-
-  // std::cout<<s_row1<<std::endl;
-  // std::cout<<s_row2<<std::endl;
-  // std::cout<<ali<<std::endl;
-  
-  return getArrayFromAlignStr(s_row1+s_row2);
-}
-
-
-void GlobalAlign::run() {
-  TAlign ali;
-  resize(rows(ali), 2);
-  assignSource(row(ali, 0), seq1);
-  assignSource(row(ali, 1), seq2);
-  
-  score = globalAlignment(ali, Score<int,Simple>(matchScore,mismatchScore,indelScore), SmithWaterman());
-}
-

data/ext/bioseqalign/GlobalAlign.hpp~

@@ -1,53 +0,0 @@
-// local alignment
-
-#include "LocalAlign.hpp"
-
-LocalAlign::LocalAlign() {}
-
-LocalAlign::LocalAlign(std::string s1, std::string s2) : PairwiseAlign(s1, s2) { }
-
-Rice::Array LocalAlign::getAlignment() {
-  TAlign ali;
-  resize(rows(ali), 2);
-  assignSource(row(ali, 0), seq1);
-  assignSource(row(ali, 1), seq2);
-  
-  //localAlignment(ali, Score<int,Simple>(matchScore,mismatchScore,indelScore), SmithWaterman());
-  localAlignment(ali, Score<int>(matchScore,mismatchScore,indelScore), SmithWaterman());
-
-  //std::cout<<row(ali, 0)<<std::endl;
-  //std::cout<<row(ali, 1)<<std::endl;
-
-  typedef Iterator<TRow>::Type TRowIterator;
-  TRowIterator it = begin(row(ali, 0));
-  TRowIterator itEnd = end(row(ali, 0));
-  std::string s_row1 = "";
-  for(; it != itEnd; ++it) {
-    if(isGap(it)) s_row1 += "-";
-    else s_row1 += (*it);
-  }
-  TRowIterator it2 = begin(row(ali, 1));
-  TRowIterator itEnd2 = end(row(ali, 1));
-  std::string s_row2 = "";
-  for(; it2 != itEnd2; ++it2) {
-    if(isGap(it2)) s_row2 += "-";
-    else s_row2 += (*it2);
-  }
-
-  // std::cout<<s_row1<<std::endl;
-  // std::cout<<s_row2<<std::endl;
-  // std::cout<<ali<<std::endl;
-  
-  return getArrayFromAlignStr(s_row1+s_row2);
-}
-
-
-void LocalAlign::run() {
-  TAlign ali;
-  resize(rows(ali), 2);
-  assignSource(row(ali, 0), seq1);
-  assignSource(row(ali, 1), seq2);
-  
-  score = localAlignment(ali, Score<int,Simple>(matchScore,mismatchScore,indelScore), SmithWaterman());
-}
-

data/ext/bioseqalign/LocalAlign.cpp~

@@ -1 +0,0 @@
-// local alignment

data/ext/bioseqalign/LocalAlign.hpp~

@@ -1 +0,0 @@
-// local alignment

data/ext/bioseqalign/Makefile

@@ -1,314 +0,0 @@
-
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-
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-.m.o:
-	$(ECHO) compiling $(<)
-	$(Q) $(CC) $(INCFLAGS) $(CPPFLAGS) $(CFLAGS) $(COUTFLAG)$@ -c $<
-
-.m.S:
-	$(ECHO) translating $(<)
-	$(Q) $(CC) $(INCFLAGS) $(CPPFLAGS) $(CFLAGS) $(COUTFLAG)$@ -S $<
-
-$(DLLIB): $(OBJS) Makefile
-	$(ECHO) linking shared-object $(DLLIB)
-	-$(Q)$(RM) $(@)
-	$(Q) $(LDSHAREDXX) -o $@ $(OBJS) $(LIBPATH) $(DLDFLAGS) $(LOCAL_LIBS) $(LIBS)
-
-
-
-$(OBJS): $(HDRS) $(ruby_headers)

data/ext/bioseqalign/PairwiseAlign.cpp~

@@ -1,23 +0,0 @@
-#include "PairwiseAlign.hpp"
-
-PairwiseAlign::PairwiseAlign() {}
-
-PairwiseAlign::PairwiseAlign(std::string s1, std::string s2) {
-  seq1 = s1;
-  seq2 = s2;  
-  score = -10000;
-  matchScore = 1;
-  mismatchScore = -1;
-  indelScore = -1;
-}
-
-// unable to properly figure out how to overload constructor when using RICE
-// PairwiseAlign::PairwiseAlign(std::string s1, std::string s2, int matchS, int mismatchS, int indelS) {
-//   seq1 = s1;
-//   seq2 = s2;  
-//   score = -10000;
-//   matchScore = matchS;
-//   mismatchScore = mismatchS;
-//   indelScore = indelS;
-// }
-

data/ext/bioseqalign/PairwiseAlign.hpp~

@@ -1,54 +0,0 @@
-#ifndef PAIRWISE_ALIGN_HPP
-#define PAIRWISE_ALIGN_HPP
-
-#include <iostream>
-#include <string>
-#include <seqan/align.h>
-
-#include "rice/String.hpp"
-#include "rice/Array.hpp"
-
-using namespace seqan;
-
-typedef String<char> TSequence;                 // sequence type
-typedef StringSet<TSequence> TStringSet;       // container for strings
-typedef StringSet<TSequence, Dependent<> > TDepStringSet;   // dependent string set
-typedef Graph<Alignment<TDepStringSet> > TAlignGraph;   // alignment graph
-
-typedef Align<TSequence,ArrayGaps> TAlign;
-typedef Row<TAlign>::Type TRow;
-
-class PairwiseAlign {
-protected:
-  std::string seq1;
-  std::string seq2;
-  int score;
-  TAlignGraph alignG;
-  int matchScore;
-  int mismatchScore;
-  int indelScore;
-  // return a ruby array of the alignment matrix string
-  Rice::Array getArrayFromAlignStr(std::string alignMat);
-  
-public:
-  PairwiseAlign();
-  PairwiseAlign(std::string s1, std::string s2);
-  //PairwiseAlign(std::string s1, std::string s2, int matchS, int mismatchS, int indelS);
-  virtual ~PairwiseAlign() {}
-  
-  virtual void run() {}
-  int getAlignScore() { return score; }
-  //virtual std::string getAlignment() { return ""; }
-  virtual Rice::Array getAlignment() { Rice::Array tmp; return tmp; }
-  
-  void setMatchScore(int mS) { matchScore = mS; }
-  void setMismatchScore(int mS) { mismatchScore = mS; }
-  void setIndelScore(int idS) { indelScore = idS; }
-
-  std::string getSeq1() { return seq1; }
-  std::string getSeq2() { return seq2; }
-  
-};
-
-
-#endif

data/ext/bioseqalign/PrefixSuffixAlign.cpp~

@@ -1,42 +0,0 @@
-#include "PrefixSuffixAlign.hpp"
-
-PrefixSuffixAlign::PrefixSuffixAlign() {}
-
-PrefixSuffixAlign::PrefixSuffixAlign(std::string s1, std::string s2) : PairwiseAlign(s1, s2) { }
-
-// unable to figure out how to properly overload constructor using RICE
-//PrefixSuffixAlign::PrefixSuffixAlign(std::string s1, std::string s2, int matchS, int mismatchS, int indelS) : PairwiseAlign(s1, s2, matchS, mismatchS, indelS) {}
-
-std::string PrefixSuffixAlign::getAlignment() {
-  TSequence tseq1 = seq1;
-  TSequence tseq2 = seq2;
-
-  TStringSet sequences;
-  appendValue(sequences,tseq1);
-  appendValue(sequences,tseq2);
-
-  TAlignGraph alignG(sequences);
-  
-  // don't penalize gaps on begin/end of seq2
-  globalAlignment(alignG, Score<int,Simple>(matchScore,mismatchScore,indelScore), AlignConfig<true, false, false, true>(), NeedlemanWunsch());
-
-  std::stringstream ss;
-  ss<<alignG;
-  return ss.str();
-}
-
-
-void PrefixSuffixAlign::run() {
-  TSequence tseq1 = seq1;
-  TSequence tseq2 = seq2;
-
-  TStringSet sequences;
-  appendValue(sequences,tseq1);
-  appendValue(sequences,tseq2);
-
-  TAlignGraph alignG(sequences);
-  
-  // don't penalize gaps on begin/end of seq2
-  score = globalAlignment(alignG, Score<int,Simple>(matchScore,mismatchScore,indelScore), AlignConfig<true, false, false, true>(), NeedlemanWunsch());
-  
-}

data/ext/bioseqalign/PrefixSuffixAlign.hpp~

@@ -1,20 +0,0 @@
-#include <iostream>
-#include <string>
-#include <seqan/align.h>
-
-#include "PairwiseAlign.hpp"
-
-using namespace seqan;
-
-class PrefixSuffixAlign : public PairwiseAlign {
-public:
-  FitAlign();
-  FitAlign(std::string s1, std::string s2);
-  //FitAlign(std::string s1, std::string s2, int matchS, int mismatchS, int indelS);
-  virtual ~FitAlign() {}
-  
-  virtual void run();
-  virtual std::string getAlignment();
-  
-};
-

data/ext/bioseqalign/extconf.rb~

@@ -1,2 +0,0 @@
-require 'mkmf-rice'
-create_makefile('FitAlign')

data/ext/bioseqalign/fitalgntest.cpp~

@@ -1,37 +0,0 @@
-#include "rice/Data_Type.hpp"
-#include "rice/Constructor.hpp"
-//#include "PairwiseAlign.hpp"
-#include "FitAlign.hpp"
-#include "PrefixSuffixAlign.hpp"
-using namespace Rice;
-
-extern "C"
-
-//void Init_FitAlign()
-void Init_SeqAlign()
-{
-  Data_Type<PairwiseAlign> rb_cPairwiseAlign = define_class<PairwiseAlign>("PairwiseAlign")
-    .define_constructor(Constructor<PairwiseAlign>())
-    .define_constructor(Constructor<PairwiseAlign,std::string,std::string>())
-    //.define_constructor(Constructor<PairwiseAlign,std::string,std::string,int,int,int>())
-    .define_method("getAlignScore", &PairwiseAlign::getAlignScore)
-    .define_method("getSeq1", &PairwiseAlign::getSeq1)
-    .define_method("getSeq2", &PairwiseAlign::getSeq2)
-    .define_method("run", &PairwiseAlign::run)
-    .define_method("getAlignment", &PairwiseAlign::getAlignment)
-    .define_method("setMatchScore", &PairwiseAlign::setMatchScore)
-    .define_method("setMismatchScore", &PairwiseAlign::setMismatchScore)
-    .define_method("setIndelScore", &PairwiseAlign::setIndelScore);
-  Data_Type<FitAlign> rb_cFitAlign = define_class<FitAlign,PairwiseAlign>("FitAlign")
-    .define_constructor(Constructor<FitAlign>())
-    .define_constructor(Constructor<FitAlign,std::string,std::string>())
-    //.define_constructor(Constructor<FitAlign,std::string,std::string,int,int,int>())
-    .define_method("run", &FitAlign::run)
-    .define_method("getAlignment", &FitAlign::getAlignment);
-  Data_Type<PrefixSuffixAlign> rb_cPrefixSuffixAlign = define_class<PrefixSuffixAlign,PairwiseAlign>("PrefixSuffixAlign")
-    .define_constructor(Constructor<PrefixSuffixAlign>())
-    .define_constructor(Constructor<PrefixSuffixAlign,std::string,std::string>())
-    .define_method("run", &PrefixSuffixAlign::run)
-    .define_method("getAlignment", &PrefixSuffixAlign::getAlignment);
-    //.define_method("getAlignmentArray", &PrefixSuffixAlign::getAlignmentArray);
-}

data/ext/bioseqalign/runTest.rb

@@ -1,35 +0,0 @@
-require './SeqAlign'
-
-
-module BSA
-  
-  include SeqAlign
-
-end
-
-fa = BSA::FitAlign.new("AAAACCCAAA", "CCC")
-fa.run
-puts fa.getAlignScore
-
-#fa = SeqAlign::FitAlign.new("AAAACCCAAA", "CCC")
-#puts fa
-#fa = BSA::FitAlign.new("AAAACCCAAA", "CCC")
-
-
-Process.exit(0)
-
-require './SeqAlign'
-
-sa = PairwiseAlign.new("TCGA", "TCGA")
-puts sa.getSeq1
-
-#__END__
-fa = FitAlign.new("AAAAAAAATCGAGGG", "TCGA")
-fa.setMatchScore(2)
-fa.setMismatchScore(-1)
-fa.setIndelScore(-1)
-puts fa.getSeq1
-fa.run
-puts fa.getAlignScore
-puts fa.getAlignment
-

data/ext/bioseqalign/runTest.rb~

@@ -1,8 +0,0 @@
-require './FitAlign'
-
-fa = FitAlign.new("TCGA", "TCGA")
-puts fa.getSeq1
-fa.run
-puts fa.getAlignScore
-puts fa.getAlignment
-