qu-pcr 1.0.0

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data/.gitignore

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+*.gem
+*.rbc
+.bundle
+.config
+.yardoc
+Gemfile.lock
+InstalledFiles
+_yardoc
+coverage
+doc/
+lib/bundler/man
+pkg
+rdoc
+spec/reports
+test/tmp
+test/version_tmp
+tmp

data/Gemfile

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+source 'https://rubygems.org'
+
+# Specify your gem's dependencies in qu-pcr.gemspec
+gemspec
+gem 'qu/utils'
+gem 'qu/cmdwrapper'

data/LICENSE.txt

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+Copyright (c) 2013 Wubin Qu
+
+MIT License
+
+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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+# Qu::Pcr
+
+A package for PCR, including primers, products, primer3 parser, virtual electrophoresis, etc.
+
+## Installation
+
+Add this line to your application's Gemfile:
+
+    gem 'qu-pcr'
+
+And then execute:
+
+    $ bundle
+
+Or install it yourself as:
+
+    $ gem install qu-pcr
+
+## Usage
+
+mobility = Qu::Pcr::VirtualGel.cal_mobility(size)
+
+## Contributing
+
+1. Fork it
+2. Create your feature branch (`git checkout -b my-new-feature`)
+3. Commit your changes (`git commit -am 'Add some feature'`)
+4. Push to the branch (`git push origin my-new-feature`)
+5. Create new Pull Request

data/Rakefile

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+require "bundler/gem_tasks"

data/lib/qu/pcr.rb

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+require 'qu/utils'
+require 'qu/cmdwrapper'
+
+require_relative "pcr/version"
+require_relative "pcr/primer3"
+require_relative "pcr/primer3_parameters"
+
+module Qu
+  module Pcr
+    class Primer 
+      attr_reader :type, :tm, :penalty, :pos, :seq, :gc
+      def initialize(seq = nil, 
+                     type = nil,
+                     gc = nil,
+                     tm = nil,
+                     penalty = nil,
+                     pos = nil)
+
+
+        # type should be "forward" or "reverse"
+        @type = type
+
+        @gc = gc.to_f
+        @tm = tm.to_f
+        @penalty = penalty.to_f
+        # position of primer's 5' end
+        @pos = pos.to_i
+        @seq = Bio::Sequence::NA.new(seq)
+      end
+    end
+
+    class Product
+      attr_reader :tm, :opt_a, :seq, :size, :id, :penalty
+      def initialize(seq = nil, 
+                     tm = nil,
+                     opt_a = nil,
+                     size = nil,
+                     id = nil,
+                     penalty = nil)
+        @tm = tm.to_f
+        @size = size.to_i
+        @opt_a = opt_a.to_f
+        @seq = Bio::Sequence::NA.new(seq)
+        @id = id.to_s
+        @penalty = penalty.to_f
+      end
+  
+    end
+
+    class VirtualGel
+      PARA = {
+        0.5 => {
+        'a' => 2.7094,
+        'b' => 0.2691,
+        'k' => 464.4412
+      },
+        1.0 => {
+        'a' => 2.3977,
+        'b' => 0.2700,
+        'k' => 73.9788
+      },
+        1.5 => {
+        'a' => 2.3221,
+        'b' => 0.2634,
+        'k' => 48.0873
+      },
+        2.0 => {
+        'a' => 2.1333,
+        'b' => 0.2561,
+        'k' => 18.5417
+      }}
+
+      def self.get_para(gel_conc)
+        a = PARA[gel_conc]['a']
+        b = PARA[gel_conc]['b']
+        k = PARA[gel_conc]['k']
+        return a, b, k
+      end
+
+      def self.cal_mobility(size, gel_conc=1.0, ref_mobility=50)
+        a, b, k = get_para(gel_conc)
+        return ((a - b * Math.log(size + k)) * ref_mobility.to_f).round(2)
+      end
+
+      def self.cal_size(mobility, gel_conc=1.0, ref_mobility=50)
+        a, b, k = get_para(gel_conc)
+        return (Math.exp((a - mobility / ref_mobility.to_f) / b) - k).round
+      end
+
+      def self.cal_size_range(size, offset=2, gel_conc=1.0, ref_mobility=50)
+        y = cal_mobility(size, gel_conc, ref_mobility)
+        x_min = cal_size(y + offset, gel_conc, ref_mobility)
+        x_max = cal_size(y - offset, gel_conc, ref_mobility)
+        return x_min, x_max
+      end
+    end # VirtualGel
+  end
+end

data/lib/qu/pcr/primer3.rb

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+#!/usr/bin/env ruby
+
+require 'csv'
+
+module Qu
+  module Pcr  
+    class Primer3
+      attr_accessor :para
+
+      def initialize(custom_para=nil)
+        @para = {}
+
+        # set default values
+        PRIMER3_OPTIONS.each_pair do |opt, value|
+          @para[opt] = value
+        end
+
+        # set custom value
+        unless custom_para.nil?
+          custom_para.each_pair do |opt, value|
+            @para[opt] = value
+          end
+        end
+
+      end
+      
+      def out
+        p3_string = create_p3_input()
+        p3_input_file = Tempfile.new('p3_input')
+        p3_input_file.write(p3_string)
+        p3_input_file.close
+
+        p3_out = Cmdwrapper::primer3_core(p3_input_file)
+
+        p3_input_file.unlink
+
+        return Primer3Parser.new(p3_out).records
+      end
+
+      private
+      def create_p3_input()
+        lines = []
+        @para.each_pair do |key, value|
+          next if value.to_s.empty?
+          lines << "#{key}=#{value}"
+        end
+        lines << "="
+        return lines.join("\n")
+      end
+    end # End Primer3 class
+
+    class Amplicon
+      attr_reader :fp, :rp, :product
+      def initialize(record, i, type='primer3')
+        if type == 'primer3'
+          (fp_5_pos, fp_size) = record["PRIMER_LEFT_%s" %[i]].split(',')
+          (rp_5_pos, rp_size) = record["PRIMER_RIGHT_%s" %[i]].split(',')
+          fp_seq = record["PRIMER_LEFT_%s_SEQUENCE" % [i]]
+          rp_seq = record["PRIMER_RIGHT_%s_SEQUENCE" % [i]]
+          fp_gc = record["PRIMER_LEFT_%s_GC_PERCENT" % [i]].to_f
+          rp_gc = record["PRIMER_RIGHT_%s_GC_PERCENT" % [i]].to_f
+          fp_tm = record["PRIMER_LEFT_%s_TM" % [i]].to_f
+          rp_tm = record["PRIMER_RIGHT_%s_TM" % [i]].to_f
+          product_opt_a = record["PRIMER_PAIR_%s_T_OPT_A" % [i]].to_f
+          product_size = record["PRIMER_PAIR_%s_PRODUCT_SIZE" % [i]].to_i
+          product_tm = record["PRIMER_PAIR_%s_PRODUCT_TM" % [i]].to_f
+          penalty = record["PRIMER_PAIR_%s_PENALTY" % [i]].to_f
+          fp_penalty = record["PRIMER_LEFT_%s_PENALTY" % [i]].to_f
+          rp_penalty = record["PRIMER_RIGHT_%s_PENALTY" % [i]].to_f   
+          id = record["SEQUENCE_ID"].to_s
+          product_seq = record["SEQUENCE_TEMPLATE"].to_s[fp_5_pos.to_i..rp_5_pos.to_i]
+
+          @fp = Primer.new(seq = fp_seq,
+                           type = 'forward',
+                           gc = fp_gc,
+                           tm = fp_tm,
+                           penalty = fp_penalty,
+                           pos = fp_5_pos,
+                          )
+
+          @rp = Primer.new(seq = rp_seq,
+                           type = 'reverse',
+                           gc = rp_gc,
+                           tm = rp_tm,
+                           penalty = rp_penalty,
+                           pos = rp_5_pos,
+                          )
+
+          @product = Product.new(seq = product_seq,
+                                 tm = product_tm,
+                                 opt_a = product_opt_a,
+                                 size = product_size,
+                                 id = id,
+                                 penalty = penalty,
+                                )
+        end
+      end
+    end # Amplicon
+
+    class Primer3Parser
+      def initialize(p3_out)
+        if p3_out.class != String
+          $stderr.puts "Need primer3 output file content (not file name) for parsing."
+        end
+        @p3_out = p3_out
+      end
+
+      private
+      def parse
+        result = []
+        if @p3_out.empty?
+          return result
+        end
+        @p3_out.split(/\n=\n/).each do |record|
+          record_result = {}
+          record.each_line do |line|
+            line.strip!
+            items = line.split('=')
+            record_result[items[0]] = items[1]
+          end
+          result << record_result
+        end
+
+        return result
+      end
+
+      public
+      def records
+        p3_hash = {}
+        p3_record = parse
+        p3_record.each do |record|
+          seq_id = record['SEQUENCE_ID']
+          if record.has_key?('PRIMER_ERROR')
+            $stderr.puts "#{record['PRIMER_ERROR']}"
+            return p3_hash
+          end
+          pp_num = record['PRIMER_PAIR_NUM_RETURNED'].to_i
+          if pp_num < 1
+            $stderr.puts "Failed design for %s" % [seq_id]
+            $stderr.puts "Left: #{record['PRIMER_LEFT_EXPLAIN']}"
+            $stderr.puts "Right: #{record['PRIMER_RIGHT_EXPLAIN']}"
+            $stderr.puts "Pair: #{record['PRIMER_PAIR_EXPLAIN']}"
+            #exit
+          end
+          p3_hash[seq_id] = []
+          (0...pp_num).each do |i|
+            p3_hash[seq_id] << Amplicon.new(record, i, type='primer3')
+          end
+        end
+
+        return p3_hash
+      end
+    end # Primer3Parser
+
+  end # end Pcr module
+
+end # end Qu module

data/lib/qu/pcr/primer3_parameters.rb

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+# Primer3 Parameters
+
+module Qu
+  module Pcr
+    PRIMER3_OPTIONS = {
+      SEQUENCE_ID: "",
+      SEQUENCE_TARGET: "",
+      SEQUENCE_EXCLUDED_REGION: "",
+      SEQUENCE_FORCE_LEFT_START: -1000000,
+      SEQUENCE_FORCE_LEFT_END: -1000000,
+      SEQUENCE_FORCE_RIGHT_START: -1000000,
+      SEQUENCE_FORCE_RIGHT_END: -1000000,
+      SEQUENCE_PRIMER: '',
+      SEQUENCE_PRIMER_REVCOMP: '',
+      PRIMER_PRODUCT_SIZE_RANGE: '100-200 200-300 300-400 400-500',
+      PRIMER_MIN_SIZE: 18,
+      PRIMER_OPT_SIZE: 22,
+      PRIMER_MAX_SIZE: 28,
+      PRIMER_MIN_TM: 55,
+      PRIMER_OPT_TM: 60,
+      PRIMER_MAX_TM: 65,
+      PRIMER_MIN_GC: 40,
+      PRIMER_OPT_GC: 50,
+      PRIMER_MAX_GC: 60,
+      PRIMER_MAX_POLY_X: 4,
+      PRIMER_MAX_HAIRPIN_TH: 47,
+      PRIMER_MAX_SELF_ANY_TH: 47,
+      PRIMER_MAX_SELF_END_TH: 47,
+      SEQUENCE_TEMPLATE: "",
+      PRIMER_THERMODYNAMIC_PARAMETERS_PATH: Cmdwrapper::THERMO_PATH,
+      PRIMER_PICK_LEFT_PRIMER: 1,
+      PRIMER_PICK_INTERNAL_OLIGO: 0,
+      PRIMER_PICK_RIGHT_PRIMER: 1,
+      PRIMER_NUM_RETURN: 10,
+      PRIMER_MAX_NS_ACCEPTED: 0,
+      PRIMER_THERMODYNAMIC_ALIGNMENT: 1,
+      PRIMER_TM_FORMULA: 1,
+      PRIMER_SALT_CORRECTIONS: 1,
+      PRIMER_SALT_MONOVALENT: 50.0,
+      PRIMER_SALT_DIVALENT: 1.5,
+      PRIMER_DNTP_CONC: 0.25,
+      PRIMER_DNA_CONC: 50.0,
+      P3_FILE_FLAG: 0,
+      PRIMER_EXPLAIN_FLAG: 1,
+      PRIMER_PRODUCT_MAX_TM: 100000,
+      PRIMER_PICK_ANYWAY: 0,
+      PRIMER_TASK: "generic",
+      SEQUENCE_PRIMER_PAIR_OK_REGION_LIST: "",
+      PRIMER_MIN_LEFT_THREE_PRIME_DISTANCE: 2,
+      PRIMER_LOWERCASE_MASKING: 1,
+    }
+
+    # Parameters not shown to users for editing
+    USER_SPECIFIC_OPTIONS = [
+			:SEQUENCE_ID,
+			:SEQUENCE_TARGET,
+			:SEQUENCE_EXCLUDED_REGION,
+			:SEQUENCE_FORCE_LEFT_START,
+			:SEQUENCE_FORCE_LEFT_END,
+			:SEQUENCE_FORCE_RIGHT_START,
+			:SEQUENCE_FORCE_RIGHT_END,
+			:SEQUENCE_PRIMER,
+			:SEQUENCE_PRIMER_REVCOMP,
+			:PRIMER_PRODUCT_SIZE_RANGE,
+			:PRIMER_MIN_SIZE,
+			:PRIMER_OPT_SIZE,
+			:PRIMER_MAX_SIZE,
+			:PRIMER_MIN_TM,
+			:PRIMER_OPT_TM,
+			:PRIMER_MAX_TM,
+			:PRIMER_MIN_GC,
+			:PRIMER_OPT_GC,
+			:PRIMER_MAX_GC,
+			:PRIMER_MAX_POLY_X,
+			:PRIMER_MAX_HAIRPIN_TH,
+			:PRIMER_MAX_SELF_ANY_TH,
+			:PRIMER_MAX_SELF_END_TH,
+    ]
+  end
+end

data/lib/qu/pcr/version.rb

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+module Qu
+  module Pcr
+    VERSION = "1.0.0"
+  end
+end

data/qu-pcr.gemspec

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+# coding: utf-8
+lib = File.expand_path('../lib', __FILE__)
+$LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
+require 'qu/pcr/version'
+
+Gem::Specification.new do |spec|
+  spec.name          = "qu-pcr"
+  spec.version       = Qu::Pcr::VERSION
+  spec.authors       = ["Wubin Qu"]
+  spec.email         = ["quwubin@gmail.com"]
+  spec.description   = %q{A package for PCR, including primers, products, primer3 parser, virtual electrophoresis, etc.}
+  spec.summary       = %q{A ruby library for PCR}
+  spec.homepage      = "https://github.com/quwubin/qu-pcr"
+  spec.license       = "MIT"
+
+  spec.files         = `git ls-files`.split($/)
+  spec.executables   = spec.files.grep(%r{^bin/}) { |f| File.basename(f) }
+  spec.test_files    = spec.files.grep(%r{^(test|spec|features)/})
+  spec.require_paths = ["lib"]
+
+  spec.add_runtime_dependency 'qu-utils', '~> 1.0'
+  spec.add_runtime_dependency 'qu-cmdwrapper', '~> 1.0'
+
+  spec.add_development_dependency "bundler", "~> 1.3"
+  spec.add_development_dependency "rake"
+end

metadata

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+--- !ruby/object:Gem::Specification
+name: qu-pcr
+version: !ruby/object:Gem::Version
+  version: 1.0.0
+platform: ruby
+authors:
+- Wubin Qu
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2014-04-28 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: qu-utils
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.0'
+- !ruby/object:Gem::Dependency
+  name: qu-cmdwrapper
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.0'
+- !ruby/object:Gem::Dependency
+  name: bundler
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.3'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.3'
+- !ruby/object:Gem::Dependency
+  name: rake
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+description: A package for PCR, including primers, products, primer3 parser, virtual
+  electrophoresis, etc.
+email:
+- quwubin@gmail.com
+executables: []
+extensions: []
+extra_rdoc_files: []
+files:
+- ".gitignore"
+- Gemfile
+- LICENSE.txt
+- README.md
+- Rakefile
+- lib/qu/pcr.rb
+- lib/qu/pcr/primer3.rb
+- lib/qu/pcr/primer3_parameters.rb
+- lib/qu/pcr/version.rb
+- qu-pcr.gemspec
+homepage: https://github.com/quwubin/qu-pcr
+licenses:
+- MIT
+metadata: {}
+post_install_message: 
+rdoc_options: []
+require_paths:
+- lib
+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: 2.2.0
+signing_key: 
+specification_version: 4
+summary: A ruby library for PCR
+test_files: []