bio-liftover 1.0.0

data/.document

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+lib/**/*.rb
+bin/*
+- 
+features/**/*.feature
+LICENSE.txt

data/.travis.yml

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+language: ruby
+rvm:
+  - 1.9.2
+  - 1.9.3
+  - jruby-19mode # JRuby in 1.9 mode
+
+# - rbx-19mode
+#  - 1.8.7
+#  - jruby-18mode # JRuby in 1.8 mode
+#  - rbx-18mode
+
+# uncomment this line if your project needs to run something other than `rake`:
+# script: bundle exec rspec spec

data/Gemfile

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+source "http://rubygems.org"
+# Add dependencies required to use your gem here.
+# Example:
+#   gem "activesupport", ">= 2.3.5"
+gem "interval-tree", ">= 0.1.3"
+# Add dependencies to develop your gem here.
+# Include everything needed to run rake, tests, features, etc.
+group :development do
+  gem "shoulda", ">= 0"
+  gem "rdoc", "~> 3.12"
+  gem "simplecov", ">= 0"
+  gem "jeweler", "~> 2.0.1", :git => "https://github.com/technicalpickles/jeweler.git"
+  gem "bundler", ">= 1.0.21"
+  gem "bio", ">= 1.4.2"
+  gem "rdoc", "~> 3.12"
+end

data/LICENSE.txt

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+Copyright (c) 2014 Andrei Rozanski
+
+Permission is hereby granted, free of charge, to any person obtaining
+a copy of this software and associated documentation files (the
+"Software"), to deal in the Software without restriction, including
+without limitation the rights to use, copy, modify, merge, publish,
+distribute, sublicense, and/or sell copies of the Software, and to
+permit persons to whom the Software is furnished to do so, subject to
+the following conditions:
+
+The above copyright notice and this permission notice shall be
+included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
+LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
+WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

data/README.md

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+# bio-liftover
+
+[![Build Status](https://secure.travis-ci.org/andreirozanski/bioruby-liftover.png)](http://travis-ci.org/andreirozanski/bioruby-liftover)
+
+Full description goes here
+
+Note: this software is under active development!
+
+## Installation
+
+```sh
+gem install bio-liftover
+```
+
+## Usage
+
+Inside script:
+
+```ruby
+require 'bio-liftover'
+
+```
+
+As bin file:
+
+bio-liftover -h --help
+
+bio-liftover
+
+Usage:
+  bio-liftover.rb ([-v] -b <genome1> <genome2> <file>|[-v] -c <genome1> <genome2> <chromosome> <start> <end>)
+  bio-liftover.rb -h | --help
+  bio-liftover.rb -v | --verbose
+
+Options:
+  -h --help     Show this screen.
+  -v --verbose  Increase information during run.
+  -b --bed      Bed file as input.
+  -c --coord    Coordinate as input i.e. hg19,hg18,chr2,55000.
+
+
+The API doc is online. For more code examples see the test files in
+the source tree.
+        
+## Project home page
+
+Information on the source tree, documentation, examples, issues and
+how to contribute, see
+
+  http://github.com/andreirozanski/bioruby-liftover
+
+The BioRuby community is on IRC server: irc.freenode.org, channel: #bioruby.
+
+## Cite
+
+If you use this software, please cite one of
+  
+* [BioRuby: bioinformatics software for the Ruby programming language](http://dx.doi.org/10.1093/bioinformatics/btq475)
+* [Biogem: an effective tool-based approach for scaling up open source software development in bioinformatics](http://dx.doi.org/10.1093/bioinformatics/bts080)
+
+## Biogems.info
+
+This Biogem is published at (http://biogems.info/index.html#bio-liftover)
+
+## Copyright
+
+Copyright (c) 2014 Andrei Rozanski. See LICENSE.txt for further details.
+

data/README.rdoc

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+= bio-liftover
+
+{<img
+src="https://secure.travis-ci.org/andreirozanski/bioruby-liftover.png"
+/>}[http://travis-ci.org/#!/andreirozanski/bioruby-liftover]
+
+Full description goes here
+
+Note: this software is under active development!
+
+== Installation
+
+        gem install bio-liftover
+
+== Usage
+
+== Developers
+
+To use the library 
+
+        require 'bio-liftover'
+
+The API doc is online. For more code examples see also the test files in
+the source tree.
+        
+== Project home page
+
+Information on the source tree, documentation, issues and how to contribute, see
+
+  http://github.com/andreirozanski/bioruby-liftover
+
+The BioRuby community is on IRC server: irc.freenode.org, channel: #bioruby.
+
+== Cite
+
+  If you use this software, please cite one of
+ 
+* [BioRuby: bioinformatics software for the Ruby programming language](http://dx.doi.org/10.1093/bioinformatics/btq475)
+* [Biogem: an effective tool-based approach for scaling up open source software development in bioinformatics](http://dx.doi.org/10.1093/bioinformatics/bts080)
+
+== Biogems.info
+
+This Biogem is published at http://biogems.info/index.html#bio-liftover
+
+== Copyright
+
+Copyright (c) 2014 Andrei Rozanski. See LICENSE.txt for further details.
+

data/Rakefile

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+# encoding: utf-8
+
+require 'rubygems'
+require 'bundler'
+begin
+  Bundler.setup(:default, :development)
+rescue Bundler::BundlerError => e
+  $stderr.puts e.message
+  $stderr.puts "Run `bundle install` to install missing gems"
+  exit e.status_code
+end
+require 'rake'
+
+require 'jeweler'
+Jeweler::Tasks.new do |gem|
+  # gem is a Gem::Specification... see http://docs.rubygems.org/read/chapter/20 for more options
+  gem.name = "bio-liftover"
+  gem.homepage = "http://github.com/andreirozanski/bioruby-liftover"
+  gem.license = "MIT"
+  gem.summary = %Q{Ruby solution for UCSC LiftOver tool- (UCSC http://genome.ucsc.edu/cgi-bin/hgLiftOver)}
+  gem.description = %Q{Simple, under development Ruby solution for UCSC LiftOver tool}
+  gem.email = "andrei@ruivo.org"
+  gem.authors = ["Andrei Rozanski"]
+  # dependencies defined in Gemfile
+end
+Jeweler::RubygemsDotOrgTasks.new
+
+require 'rake/testtask'
+Rake::TestTask.new(:test) do |test|
+  test.libs << 'lib' << 'test'
+  test.pattern = 'test/**/test_*.rb'
+  test.verbose = true
+end
+
+task :default => :test
+
+require 'rdoc/task'
+Rake::RDocTask.new do |rdoc|
+  version = File.exist?('VERSION') ? File.read('VERSION') : ""
+
+  rdoc.rdoc_dir = 'rdoc'
+  rdoc.title = "bio-liftover #{version}"
+  rdoc.rdoc_files.include('README*')
+  rdoc.rdoc_files.include('lib/**/*.rb')
+end

data/VERSION

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+1.0.0

data/bin/bio-liftover

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+#!/usr/bin/ruby  
+
+# Copyright::   Copyright (C) 2009
+#               Andrei Rozanski <rozanski.andrei@gmail.com>
+# License::     The Ruby License
+# == Description
+# This file containts a liftover for Ruby
+
+require 'zlib'
+require 'open-uri'
+require 'interval-tree'
+require 'docopt'
+
+doc = <<DOCOPT
+bio-liftover
+
+Usage:
+  #{__FILE__} ([-v] -c <genome1> <genome2> <chromosome> <start> <end>)
+  #{__FILE__} ([-v] -f <chain_file> -c <genome1> <genome2> <chromosome> <start> <end>)
+  #{__FILE__} -h | --help
+  #{__FILE__} -v | --verbose
+
+Options:
+  -h --help  Show this screen.
+  -v --verbose  Increase information during run.
+  -c --coord  Coordinate as input i.e. hg19,hg18,chr2,55000.
+  -f --file  Load local chain file.
+
+DOCOPT
+
+@@doc=nil
+begin
+  @@doc=Docopt::docopt(doc)
+#{"-v"=>false, "-c"=>true, "<genome1>"=>"hg19", "<genome2>"=>"Hg18", "<chromosome>"=>"chr2", "<start>"=>"10", "<end>"=>"100", "-f"=>false, "<chain_file>"=>nil, "-h"=>false, "--help"=>false, "--verbose"=>false}
+rescue Docopt::Exit => e
+  puts e.message
+end
+
+module LiftOver
+  class Query
+    def initilize;end
+
+    #Given a pair of genomes, fetch chain file and parse it into a array.
+    def self.parse_chain_file
+      @chains=[]
+      @chains_complete=[]
+      @@gen1=@@doc["<genome1>"] #parse DOCOPT value for reference genome
+      @@gen2=@@doc["<genome2>"] #parse DOCOPT value for query genome 
+      @@chr_input=@@doc["<chromosome>"] #parse DOCOPT value for reference chromosome
+      @@coord_start=@@doc["<start>"].to_i #parse DOCOPT value for reference start coordinate
+      @@coord_end=@@doc["<end>"].to_i #parse DOCOPT value for reference end coordinate
+      if @@doc["<chain_file>"].nil? #switch between local/remote parse file
+        LiftOver::Query.parse_remote_chain
+      else
+        LiftOver::Query.parse_local_chain
+      end
+    end #parse_chain_file
+
+    #Retrieve and parse remote chain file from http://hgdownload.cse.ucsc.edu/goldenPath/
+    def self.parse_remote_chain
+      begin
+        puts "Downloading chain file...\n" if @@doc["--verbose"]
+        open("http://hgdownload.cse.ucsc.edu/goldenPath/#{@@gen1}/liftOver/#{@@gen1}To#{@@gen2}.over.chain.gz") do |rmt_file|
+          puts "Download finished\n" if @@doc["--verbose"]
+          puts "Unpacking remote file...\n" if @@doc["--verbose"]
+          gz=Zlib::GzipReader.new(rmt_file).read
+          puts "Unpack finished\n" if @@doc["--verbose"]
+          flag=0
+          header=""
+          coords=[]
+          result=[]
+          gz.split("\n").each do |line|
+            if line.start_with?("chain")
+              qry=LiftOver::Query.search_for_chain_by_interval(line)
+              if qry == true
+                flag=1
+                header=line
+              else
+                flag=0
+                if header!=""
+                  a={"#{header.chomp}"=>coords}
+                  result.push(a)
+                end
+                a=""
+                header=""
+                coords=[]
+              end
+            else
+              if flag==1
+                coords.push(line.chomp.split("\t").map(&:to_i))
+              end
+            end
+          end
+        scores=[]
+        if not result.empty?
+          result.each do |hits|
+            hits.keys.each do |ev|
+              scores.push(ev.split(" ")[1].to_i)
+            end      
+          end
+        else
+          puts "Candidate chain not found"
+        end
+        start_val=""
+        end_val=""
+        res=[]
+        result.each do |hits|
+          start_val=LiftOver::Query.lift(hits,@@coord_start)
+          end_val=LiftOver::Query.lift(hits,@@coord_end)
+	  puts "\"Lifting event\"...\n" if @@doc["--verbose"] 
+          if hits.keys[0].split(" ")[9] != "-"
+            res.push("#{hits.keys[0].split(" ")[7]}:#{start_val}-#{end_val}")
+          else
+            res.push("#{hits.keys[0].split(" ")[7]}:#{end_val}-#{end_val}")
+          end
+          start_val=""
+          end_val=""
+        end
+	puts "Done\n" if @@doc["--verbose"] 
+        puts res
+        end
+      rescue SocketError => e
+        puts "There's a connection problem with your request.\n Error message: #{e.message}."
+      rescue SystemCallError => e
+        puts "There's a problem with your request.\n Error message: #{e.message}."
+      rescue OpenURI::HTTPError => e 
+        puts "Couldn't retrieve chain file. Genome names are case sensitive. Please check http://hgdownload.cse.ucsc.edu/goldenPath\n Error message: #{e.message}."
+      exit
+      end
+    end #parse_remote_chain
+
+    #Parse local chain file
+    def self.parse_local_chain
+      puts "Unpacking local file...\n" if @@doc["--verbose"]
+      gz_file=open(@@doc["<chain_file>"])
+      gz=Zlib::GzipReader.new(gz_file)
+      puts "Unpack finished\n" if @@doc["--verbose"]
+      flag=0
+      header=""
+      coords=[]
+      result=[]
+      gz.each_line do |line|
+        if line.chomp.start_with?("chain")
+          qry=LiftOver::Query.search_for_chain_by_interval(line)
+          if qry == true
+            flag=1
+            header=line
+          else
+            flag=0
+            if header!=""
+              a={"#{header.chomp}"=>coords}
+              result.push(a)
+            end
+            a=""
+            header=""
+            coords=[]
+          end
+        else
+          if flag==1
+            coords.push(line.chomp.split("\t").map(&:to_i))
+          end
+        end          
+      end
+      scores=[]
+      if not result.empty?
+        result.each do |hits|
+          hits.keys.each do |ev|
+            scores.push(ev.split(" ")[1].to_i)
+          end
+        end
+      else
+        puts "Candidate chain not found"
+      end
+      start_val=""
+      end_val=""
+      res=[]
+      result.each do |hits|
+        start_val=LiftOver::Query.lift(hits,@@coord_start)
+        end_val=LiftOver::Query.lift(hits,@@coord_end)
+        if hits.keys[0].split(" ")[9] != "-"
+          res.push("#{hits.keys[0].split(" ")[7]}:#{start_val}-#{end_val}")
+        else
+          res.push("#{hits.keys[0].split(" ")[7]}:#{end_val}-#{end_val}")
+        end
+        start_val=""
+        end_val=""
+      end
+    puts res
+    end #parse_local_chain
+
+    #Search for chains that fits on coordinates given to be "lifted"
+    def self.search_for_chain_by_interval(string)
+      hits=[]
+      field=string.split(" ")
+      if @@chr_input==field[2]
+        itval=IntervalTree::InclusiveTree.new(field[5].to_i...field[6].to_i)
+        res=itval.search(@@coord_start...@@coord_end)  
+        if not res.nil?
+          if not res.empty?
+            return true
+          else
+            return false
+          end
+        else
+          return false
+        end
+      end
+    end #search_for_chain_by_interval
+
+    #Lift coordinates
+    def self.lift(array,coordinate)  
+      res_chr=""
+      res_start=""
+      flag_st=0
+      result=[]
+      array.each do |k,v|
+        start_ref=k.split(" ")[5].to_i
+        start_query=k.split(" ")[10].to_i
+        incr=nil
+        end_incr=0
+        gap=0
+        fl_st=0
+        strand=k.split(" ")[9]
+        q_size=k.split(" ")[8].to_i
+        res_chr=k.split(" ")[7]
+        v.each do |val|
+          break if flag_st==1
+          if incr.nil?
+            end_incr=val[2]
+            gap=val[1]
+            incr=val[0]+gap
+            itval0=IntervalTree::InclusiveTree.new(start_ref...start_ref+val[0].to_i)
+            res1=itval0.search(coordinate)
+            fl_st=start_ref+val[0]+gap
+            if not res1.empty?
+              if strand=="-"
+                res_start = "#{q_size-start_query-(coordinate-start_ref)}"
+                flag_st=1
+              else
+                res_start = "#{start_query+(coordinate-start_ref)}"
+                flag_st=1
+              end
+            end
+          else
+            if gap != 0
+              itval1=IntervalTree::InclusiveTree.new(fl_st...fl_st+gap.to_i)
+              res2=itval1.search(coordinate)
+              if not res2.empty?
+                if strand=="-"
+                  res_start = "#{q_size-start_query-(coordinate-start_ref)}"
+                  flag_st=1
+                else
+                  res_start = "#{start_query+(coordinate-start_ref)+end_incr}"
+                  flag_st=1
+                end
+              end
+              fl_st=fl_st+gap
+            else
+              incr=val[0].to_i
+              if val[0].to_i !=0
+                itval2=IntervalTree::InclusiveTree.new(fl_st...fl_st+val[0].to_i)
+                res3=itval2.search(coordinate)
+                if not res3.empty?
+                  if strand=="-"
+                    res_start = "#{q_size-start_query-(coordinate-start_ref)}"
+                    flag_st=1
+                  else
+                    res_start = "#{start_query+(coordinate-start_ref)+end_incr}"
+                    flag_st=1
+                  end
+                end
+
+                fl_st=fl_st+val[0].to_i+gap
+                end_incr=end_incr+val[2].to_i
+                gap=val[1].to_i 
+              else
+                fl_st=fl_st+val[0].to_i+gap
+                end_incr=end_incr+val[2].to_i
+                gap=val[1].to_i
+              end
+            end
+          end
+          gap=val[1].to_i
+        end
+      end
+      a= "#{res_start.to_i}"
+     return a
+    end #lift
+        end #Query 
+end #LiftOver 
+
+if not @@doc.nil?
+  LiftOver::Query.parse_chain_file
+end

data/lib/bio-liftover.rb

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+#!/usr/bin/ruby  
+
+# Copyright::   Copyright (C) 2009
+#               Andrei Rozanski <rozanski.andrei@gmail.com>
+# License::     The Ruby License
+# == Description
+# This file containts a liftover for Ruby
+
+require 'zlib'
+require 'open-uri'
+require 'interval-tree'
+
+module LiftOver
+  class Query
+    def initilize;end
+
+    #Given a pair of genomes, fetch chain file and parse it into a array.
+    def self.parse_chain_file(gen1,gen2,chr_input,coord_start,coord_end,chain_file)
+      @chains=[]
+      @chains_complete=[]
+      @@gen1=gen1
+      @@gen2=gen2
+      @@chr_input=chr_input
+      @@coord_start=coord_start.to_i
+      @@coord_end=coord_end.to_i
+      if chain_file.nil? #switch between local/remote parse file
+        LiftOver::Query.parse_remote_chain
+      else
+        LiftOver::Query.parse_local_chain
+      end
+    end #parse_chain_file
+
+    #Retrieve and parse remote chain file from http://hgdownload.cse.ucsc.edu/goldenPath/
+    def self.parse_remote_chain
+      begin
+        open("http://hgdownload.cse.ucsc.edu/goldenPath/#{@@gen1}/liftOver/#{@@gen1}To#{@@gen2}.over.chain.gz") do |rmt_file|
+          gz=Zlib::GzipReader.new(rmt_file).read
+          flag=0
+          header=""
+          coords=[]
+          result=[]
+          gz.split("\n").each do |line|
+            if line.start_with?("chain")
+              qry=LiftOver::Query.search_for_chain_by_interval(line)
+              if qry == true
+                flag=1
+                header=line
+              else
+                flag=0
+                if header!=""
+                  a={"#{header.chomp}"=>coords}
+                  result.push(a)
+                end
+                a=""
+                header=""
+                coords=[]
+              end
+            else
+              if flag==1
+                coords.push(line.chomp.split("\t").map(&:to_i))
+              end
+            end
+          end
+        scores=[]
+        if not result.empty?
+          result.each do |hits|
+            hits.keys.each do |ev|
+              scores.push(ev.split(" ")[1].to_i)
+            end      
+          end
+        else
+          puts "Candidate chain not found"
+        end
+        start_val=""
+        end_val=""
+        res=[]
+        result.each do |hits|
+          start_val=LiftOver::Query.lift(hits,@@coord_start)
+          end_val=LiftOver::Query.lift(hits,@@coord_end)
+          if hits.keys[0].split(" ")[9] != "-"
+            res.push("#{hits.keys[0].split(" ")[7]}:#{start_val}-#{end_val}")
+          else
+            res.push("#{hits.keys[0].split(" ")[7]}:#{end_val}-#{end_val}")
+          end
+          start_val=""
+          end_val=""
+        end
+        puts res
+        end
+      rescue SocketError => e
+        puts "There's a connection problem with your request.\n Error message: #{e.message}."
+      rescue SystemCallError => e
+        puts "There's a problem with your request.\n Error message: #{e.message}."
+      rescue OpenURI::HTTPError => e 
+        puts "Couldn't retrieve chain file. Genome names are case sensitive. Please check http://hgdownload.cse.ucsc.edu/goldenPath\n Error message: #{e.message}."
+      exit
+      end
+    end #parse_remote_chain
+
+    #Parse local chain file
+    def self.parse_local_chain
+      gz_file=open(doc["<chain_file>"])
+      gz=Zlib::GzipReader.new(gz_file)
+      flag=0
+      header=""
+      coords=[]
+      result=[]
+      gz.each_line do |line|
+        if line.chomp.start_with?("chain")
+          qry=LiftOver::Query.search_for_chain_by_interval(line)
+          if qry == true
+            flag=1
+            header=line
+          else
+            flag=0
+            if header!=""
+              a={"#{header.chomp}"=>coords}
+              result.push(a)
+            end
+            a=""
+            header=""
+            coords=[]
+          end
+        else
+          if flag==1
+            coords.push(line.chomp.split("\t").map(&:to_i))
+          end
+        end          
+      end
+      scores=[]
+      if not result.empty?
+        result.each do |hits|
+          hits.keys.each do |ev|
+            scores.push(ev.split(" ")[1].to_i)
+          end
+        end
+      else
+        puts "Candidate chain not found"
+      end
+      start_val=""
+      end_val=""
+      res=[]
+      result.each do |hits|
+        start_val=LiftOver::Query.lift(hits,@@coord_start)
+        end_val=LiftOver::Query.lift(hits,@@coord_end)
+        if hits.keys[0].split(" ")[9] != "-"
+          res.push("#{hits.keys[0].split(" ")[7]}:#{start_val}-#{end_val}")
+        else
+          res.push("#{hits.keys[0].split(" ")[7]}:#{end_val}-#{end_val}")
+        end
+        start_val=""
+        end_val=""
+      end
+    puts res
+    end #parse_local_chain
+
+    #Search for chains that fits on coordinates given to be "lifted"
+    def self.search_for_chain_by_interval(string)
+      hits=[]
+      field=string.split(" ")
+      if @@chr_input==field[2]
+        itval=IntervalTree::InclusiveTree.new(field[5].to_i...field[6].to_i)
+        res=itval.search(@@coord_start...@@coord_end)  
+        if not res.nil?
+          if not res.empty?
+            return true
+          else
+            return false
+          end
+        else
+          return false
+        end
+      end
+    end #search_for_chain_by_interval
+
+    #Lift coordinates
+    def self.lift(array,coordinate)  
+      res_chr=""
+      res_start=""
+      flag_st=0
+      result=[]
+      array.each do |k,v|
+        start_ref=k.split(" ")[5].to_i
+        start_query=k.split(" ")[10].to_i
+        incr=nil
+        end_incr=0
+        gap=0
+        fl_st=0
+        strand=k.split(" ")[9]
+        q_size=k.split(" ")[8].to_i
+        res_chr=k.split(" ")[7]
+        v.each do |val|
+          break if flag_st==1
+          if incr.nil?
+            end_incr=val[2]
+            gap=val[1]
+            incr=val[0]+gap
+            itval0=IntervalTree::InclusiveTree.new(start_ref...start_ref+val[0].to_i)
+            res1=itval0.search(coordinate)
+            fl_st=start_ref+val[0]+gap
+            if not res1.empty?
+              if strand=="-"
+                res_start = "#{q_size-start_query-(coordinate-start_ref)}"
+                flag_st=1
+              else
+                res_start = "#{start_query+(coordinate-start_ref)}"
+                flag_st=1
+              end
+            end
+          else
+            if gap != 0
+              itval1=IntervalTree::InclusiveTree.new(fl_st...fl_st+gap.to_i)
+              res2=itval1.search(coordinate)
+              if not res2.empty?
+                if strand=="-"
+                  res_start = "#{q_size-start_query-(coordinate-start_ref)}"
+                  flag_st=1
+                else
+                  res_start = "#{start_query+(coordinate-start_ref)+end_incr}"
+                  flag_st=1
+                end
+              end
+              fl_st=fl_st+gap
+            else
+              incr=val[0].to_i
+              if val[0].to_i !=0
+                itval2=IntervalTree::InclusiveTree.new(fl_st...fl_st+val[0].to_i)
+                res3=itval2.search(coordinate)
+                if not res3.empty?
+                  if strand=="-"
+                    res_start = "#{q_size-start_query-(coordinate-start_ref)}"
+                    flag_st=1
+                  else
+                    res_start = "#{start_query+(coordinate-start_ref)+end_incr}"
+                    flag_st=1
+                  end
+                end
+
+                fl_st=fl_st+val[0].to_i+gap
+                end_incr=end_incr+val[2].to_i
+                gap=val[1].to_i 
+              else
+                fl_st=fl_st+val[0].to_i+gap
+                end_incr=end_incr+val[2].to_i
+                gap=val[1].to_i
+              end
+            end
+          end
+          gap=val[1].to_i
+        end
+      end
+      a= "#{res_start.to_i}"
+     return a
+    end #lift
+        end #Query 
+end #LiftOver 
+

data/test/test_bio-liftover.rb

@@ -0,0 +1,11 @@
+#!/usr/bin/ruby
+
+require_relative 'bio-liftover'
+
+gen1="hg19"
+gen2="Hg18"
+chr_input="chr2"
+coord_start="55000"
+coord_end="55100"
+
+LiftOver::Query.parse_chain_file(gen1,gen2,chr_input,coord_start,coord_end,nil)

metadata

@@ -0,0 +1,191 @@
+--- !ruby/object:Gem::Specification
+name: bio-liftover
+version: !ruby/object:Gem::Version
+  version: 1.0.0
+  prerelease: 
+platform: ruby
+authors:
+- Andrei Rozanski
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2014-03-11 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: interval-tree
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 0.1.3
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 0.1.3
+- !ruby/object:Gem::Dependency
+  name: shoulda
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: rdoc
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '3.12'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '3.12'
+- !ruby/object:Gem::Dependency
+  name: simplecov
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: jeweler
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 2.0.1
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 2.0.1
+- !ruby/object:Gem::Dependency
+  name: bundler
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 1.0.21
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 1.0.21
+- !ruby/object:Gem::Dependency
+  name: bio
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 1.4.2
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 1.4.2
+- !ruby/object:Gem::Dependency
+  name: rdoc
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '3.12'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '3.12'
+description: Simple, under development Ruby solution for UCSC LiftOver tool
+email: andrei@ruivo.org
+executables:
+- bio-liftover
+extensions: []
+extra_rdoc_files:
+- LICENSE.txt
+- README.md
+- README.rdoc
+files:
+- .document
+- .travis.yml
+- Gemfile
+- LICENSE.txt
+- README.md
+- README.rdoc
+- Rakefile
+- VERSION
+- bin/bio-liftover
+- lib/bio-liftover.rb
+- test/test_bio-liftover.rb
+homepage: http://github.com/andreirozanski/bioruby-liftover
+licenses:
+- MIT
+post_install_message: 
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  none: false
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+      segments:
+      - 0
+      hash: -1033425692335380436
+required_rubygems_version: !ruby/object:Gem::Requirement
+  none: false
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubyforge_project: 
+rubygems_version: 1.8.23
+signing_key: 
+specification_version: 3
+summary: Ruby solution for UCSC LiftOver tool- (UCSC http://genome.ucsc.edu/cgi-bin/hgLiftOver)
+test_files: []