qu-pcr 1.0.0

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+ *.gem
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+ *.rbc
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+ .bundle
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+ .config
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+ .yardoc
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+ Gemfile.lock
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+ InstalledFiles
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+ _yardoc
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+ coverage
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+ doc/
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+ lib/bundler/man
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+ pkg
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+ rdoc
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+ spec/reports
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+ test/tmp
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+ test/version_tmp
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+ tmp
data/Gemfile ADDED
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+ source 'https://rubygems.org'
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+
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+ # Specify your gem's dependencies in qu-pcr.gemspec
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+ gemspec
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+ gem 'qu/utils'
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+ gem 'qu/cmdwrapper'
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+ Copyright (c) 2013 Wubin Qu
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+
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+ MIT License
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+
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+ Permission is hereby granted, free of charge, to any person obtaining
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+ a copy of this software and associated documentation files (the
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+ "Software"), to deal in the Software without restriction, including
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+ without limitation the rights to use, copy, modify, merge, publish,
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+ distribute, sublicense, and/or sell copies of the Software, and to
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+ permit persons to whom the Software is furnished to do so, subject to
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+ the following conditions:
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+
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+ The above copyright notice and this permission notice shall be
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+ included in all copies or substantial portions of the Software.
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+
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+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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+ EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
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+ MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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+ NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
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+ LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
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+ OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
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+ WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
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+ # Qu::Pcr
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+
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+ A package for PCR, including primers, products, primer3 parser, virtual electrophoresis, etc.
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+
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+ ## Installation
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+
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+ Add this line to your application's Gemfile:
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+
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+ gem 'qu-pcr'
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+
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+ And then execute:
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+
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+ $ bundle
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+
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+ Or install it yourself as:
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+
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+ $ gem install qu-pcr
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+
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+ ## Usage
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+
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+ mobility = Qu::Pcr::VirtualGel.cal_mobility(size)
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+
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+ ## Contributing
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+
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+ 1. Fork it
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+ 2. Create your feature branch (`git checkout -b my-new-feature`)
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+ 3. Commit your changes (`git commit -am 'Add some feature'`)
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+ 4. Push to the branch (`git push origin my-new-feature`)
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+ 5. Create new Pull Request
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+ require "bundler/gem_tasks"
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+ require 'qu/utils'
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+ require 'qu/cmdwrapper'
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+
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+ require_relative "pcr/version"
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+ require_relative "pcr/primer3"
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+ require_relative "pcr/primer3_parameters"
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+
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+ module Qu
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+ module Pcr
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+ class Primer
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+ attr_reader :type, :tm, :penalty, :pos, :seq, :gc
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+ def initialize(seq = nil,
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+ type = nil,
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+ gc = nil,
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+ tm = nil,
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+ penalty = nil,
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+ pos = nil)
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+
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+
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+ # type should be "forward" or "reverse"
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+ @type = type
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+
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+ @gc = gc.to_f
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+ @tm = tm.to_f
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+ @penalty = penalty.to_f
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+ # position of primer's 5' end
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+ @pos = pos.to_i
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+ @seq = Bio::Sequence::NA.new(seq)
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+ end
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+ end
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+
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+ class Product
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+ attr_reader :tm, :opt_a, :seq, :size, :id, :penalty
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+ def initialize(seq = nil,
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+ tm = nil,
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+ opt_a = nil,
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+ size = nil,
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+ id = nil,
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+ penalty = nil)
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+ @tm = tm.to_f
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+ @size = size.to_i
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+ @opt_a = opt_a.to_f
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+ @seq = Bio::Sequence::NA.new(seq)
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+ @id = id.to_s
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+ @penalty = penalty.to_f
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+ end
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+
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+ end
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+
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+ class VirtualGel
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+ PARA = {
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+ 0.5 => {
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+ 'a' => 2.7094,
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+ 'b' => 0.2691,
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+ 'k' => 464.4412
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+ },
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+ 1.0 => {
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+ 'a' => 2.3977,
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+ 'b' => 0.2700,
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+ 'k' => 73.9788
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+ },
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+ 1.5 => {
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+ 'a' => 2.3221,
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+ 'b' => 0.2634,
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+ 'k' => 48.0873
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+ },
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+ 2.0 => {
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+ 'a' => 2.1333,
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+ 'b' => 0.2561,
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+ 'k' => 18.5417
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+ }}
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+
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+ def self.get_para(gel_conc)
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+ a = PARA[gel_conc]['a']
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+ b = PARA[gel_conc]['b']
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+ k = PARA[gel_conc]['k']
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+ return a, b, k
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+ end
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+
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+ def self.cal_mobility(size, gel_conc=1.0, ref_mobility=50)
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+ a, b, k = get_para(gel_conc)
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+ return ((a - b * Math.log(size + k)) * ref_mobility.to_f).round(2)
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+ end
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+
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+ def self.cal_size(mobility, gel_conc=1.0, ref_mobility=50)
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+ a, b, k = get_para(gel_conc)
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+ return (Math.exp((a - mobility / ref_mobility.to_f) / b) - k).round
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+ end
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+
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+ def self.cal_size_range(size, offset=2, gel_conc=1.0, ref_mobility=50)
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+ y = cal_mobility(size, gel_conc, ref_mobility)
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+ x_min = cal_size(y + offset, gel_conc, ref_mobility)
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+ x_max = cal_size(y - offset, gel_conc, ref_mobility)
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+ return x_min, x_max
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+ end
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+ end # VirtualGel
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+ end
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+ end
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+ #!/usr/bin/env ruby
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+
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+ require 'csv'
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+
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+ module Qu
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+ module Pcr
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+ class Primer3
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+ attr_accessor :para
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+
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+ def initialize(custom_para=nil)
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+ @para = {}
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+
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+ # set default values
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+ PRIMER3_OPTIONS.each_pair do |opt, value|
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+ @para[opt] = value
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+ end
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+
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+ # set custom value
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+ unless custom_para.nil?
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+ custom_para.each_pair do |opt, value|
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+ @para[opt] = value
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+ end
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+ end
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+
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+ end
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+
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+ def out
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+ p3_string = create_p3_input()
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+ p3_input_file = Tempfile.new('p3_input')
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+ p3_input_file.write(p3_string)
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+ p3_input_file.close
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+
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+ p3_out = Cmdwrapper::primer3_core(p3_input_file)
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+
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+ p3_input_file.unlink
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+
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+ return Primer3Parser.new(p3_out).records
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+ end
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+
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+ private
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+ def create_p3_input()
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+ lines = []
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+ @para.each_pair do |key, value|
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+ next if value.to_s.empty?
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+ lines << "#{key}=#{value}"
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+ end
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+ lines << "="
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+ return lines.join("\n")
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+ end
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+ end # End Primer3 class
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+
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+ class Amplicon
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+ attr_reader :fp, :rp, :product
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+ def initialize(record, i, type='primer3')
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+ if type == 'primer3'
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+ (fp_5_pos, fp_size) = record["PRIMER_LEFT_%s" %[i]].split(',')
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+ (rp_5_pos, rp_size) = record["PRIMER_RIGHT_%s" %[i]].split(',')
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+ fp_seq = record["PRIMER_LEFT_%s_SEQUENCE" % [i]]
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+ rp_seq = record["PRIMER_RIGHT_%s_SEQUENCE" % [i]]
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+ fp_gc = record["PRIMER_LEFT_%s_GC_PERCENT" % [i]].to_f
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+ rp_gc = record["PRIMER_RIGHT_%s_GC_PERCENT" % [i]].to_f
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+ fp_tm = record["PRIMER_LEFT_%s_TM" % [i]].to_f
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+ rp_tm = record["PRIMER_RIGHT_%s_TM" % [i]].to_f
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+ product_opt_a = record["PRIMER_PAIR_%s_T_OPT_A" % [i]].to_f
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+ product_size = record["PRIMER_PAIR_%s_PRODUCT_SIZE" % [i]].to_i
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+ product_tm = record["PRIMER_PAIR_%s_PRODUCT_TM" % [i]].to_f
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+ penalty = record["PRIMER_PAIR_%s_PENALTY" % [i]].to_f
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+ fp_penalty = record["PRIMER_LEFT_%s_PENALTY" % [i]].to_f
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+ rp_penalty = record["PRIMER_RIGHT_%s_PENALTY" % [i]].to_f
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+ id = record["SEQUENCE_ID"].to_s
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+ product_seq = record["SEQUENCE_TEMPLATE"].to_s[fp_5_pos.to_i..rp_5_pos.to_i]
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+
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+ @fp = Primer.new(seq = fp_seq,
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+ type = 'forward',
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+ gc = fp_gc,
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+ tm = fp_tm,
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+ penalty = fp_penalty,
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+ pos = fp_5_pos,
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+ )
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+
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+ @rp = Primer.new(seq = rp_seq,
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+ type = 'reverse',
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+ gc = rp_gc,
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+ tm = rp_tm,
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+ penalty = rp_penalty,
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+ pos = rp_5_pos,
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+ )
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+
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+ @product = Product.new(seq = product_seq,
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+ tm = product_tm,
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+ opt_a = product_opt_a,
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+ size = product_size,
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+ id = id,
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+ penalty = penalty,
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+ )
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+ end
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+ end
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+ end # Amplicon
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+
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+ class Primer3Parser
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+ def initialize(p3_out)
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+ if p3_out.class != String
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+ $stderr.puts "Need primer3 output file content (not file name) for parsing."
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+ end
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+ @p3_out = p3_out
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+ end
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+
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+ private
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+ def parse
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+ result = []
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+ if @p3_out.empty?
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+ return result
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+ end
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+ @p3_out.split(/\n=\n/).each do |record|
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+ record_result = {}
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+ record.each_line do |line|
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+ line.strip!
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+ items = line.split('=')
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+ record_result[items[0]] = items[1]
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+ end
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+ result << record_result
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+ end
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+
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+ return result
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+ end
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+
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+ public
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+ def records
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+ p3_hash = {}
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+ p3_record = parse
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+ p3_record.each do |record|
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+ seq_id = record['SEQUENCE_ID']
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+ if record.has_key?('PRIMER_ERROR')
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+ $stderr.puts "#{record['PRIMER_ERROR']}"
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+ return p3_hash
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+ end
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+ pp_num = record['PRIMER_PAIR_NUM_RETURNED'].to_i
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+ if pp_num < 1
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+ $stderr.puts "Failed design for %s" % [seq_id]
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+ $stderr.puts "Left: #{record['PRIMER_LEFT_EXPLAIN']}"
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+ $stderr.puts "Right: #{record['PRIMER_RIGHT_EXPLAIN']}"
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+ $stderr.puts "Pair: #{record['PRIMER_PAIR_EXPLAIN']}"
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+ #exit
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+ end
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+ p3_hash[seq_id] = []
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+ (0...pp_num).each do |i|
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+ p3_hash[seq_id] << Amplicon.new(record, i, type='primer3')
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+ end
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+ end
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+
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+ return p3_hash
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+ end
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+ end # Primer3Parser
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+
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+ end # end Pcr module
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+
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+ end # end Qu module
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+ # Primer3 Parameters
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+
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+ module Qu
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+ module Pcr
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+ PRIMER3_OPTIONS = {
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+ SEQUENCE_ID: "",
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+ SEQUENCE_TARGET: "",
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+ SEQUENCE_EXCLUDED_REGION: "",
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+ SEQUENCE_FORCE_LEFT_START: -1000000,
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+ SEQUENCE_FORCE_LEFT_END: -1000000,
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+ SEQUENCE_FORCE_RIGHT_START: -1000000,
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+ SEQUENCE_FORCE_RIGHT_END: -1000000,
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+ SEQUENCE_PRIMER: '',
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+ SEQUENCE_PRIMER_REVCOMP: '',
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+ PRIMER_PRODUCT_SIZE_RANGE: '100-200 200-300 300-400 400-500',
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+ PRIMER_MIN_SIZE: 18,
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+ PRIMER_OPT_SIZE: 22,
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+ PRIMER_MAX_SIZE: 28,
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+ PRIMER_MIN_TM: 55,
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+ PRIMER_OPT_TM: 60,
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+ PRIMER_MAX_TM: 65,
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+ PRIMER_MIN_GC: 40,
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+ PRIMER_OPT_GC: 50,
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+ PRIMER_MAX_GC: 60,
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+ PRIMER_MAX_POLY_X: 4,
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+ PRIMER_MAX_HAIRPIN_TH: 47,
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+ PRIMER_MAX_SELF_ANY_TH: 47,
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+ PRIMER_MAX_SELF_END_TH: 47,
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+ SEQUENCE_TEMPLATE: "",
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+ PRIMER_THERMODYNAMIC_PARAMETERS_PATH: Cmdwrapper::THERMO_PATH,
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+ PRIMER_PICK_LEFT_PRIMER: 1,
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+ PRIMER_PICK_INTERNAL_OLIGO: 0,
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+ PRIMER_PICK_RIGHT_PRIMER: 1,
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+ PRIMER_NUM_RETURN: 10,
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+ PRIMER_MAX_NS_ACCEPTED: 0,
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+ PRIMER_THERMODYNAMIC_ALIGNMENT: 1,
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+ PRIMER_TM_FORMULA: 1,
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+ PRIMER_SALT_CORRECTIONS: 1,
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+ PRIMER_SALT_MONOVALENT: 50.0,
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+ PRIMER_SALT_DIVALENT: 1.5,
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+ PRIMER_DNTP_CONC: 0.25,
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+ PRIMER_DNA_CONC: 50.0,
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+ P3_FILE_FLAG: 0,
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+ PRIMER_EXPLAIN_FLAG: 1,
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+ PRIMER_PRODUCT_MAX_TM: 100000,
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+ PRIMER_PICK_ANYWAY: 0,
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+ PRIMER_TASK: "generic",
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+ SEQUENCE_PRIMER_PAIR_OK_REGION_LIST: "",
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+ PRIMER_MIN_LEFT_THREE_PRIME_DISTANCE: 2,
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+ PRIMER_LOWERCASE_MASKING: 1,
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+ }
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+
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+ # Parameters not shown to users for editing
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+ USER_SPECIFIC_OPTIONS = [
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+ :SEQUENCE_ID,
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+ :SEQUENCE_TARGET,
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+ :SEQUENCE_EXCLUDED_REGION,
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+ :SEQUENCE_FORCE_LEFT_START,
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+ :SEQUENCE_FORCE_LEFT_END,
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+ :SEQUENCE_FORCE_RIGHT_START,
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+ :SEQUENCE_FORCE_RIGHT_END,
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+ :SEQUENCE_PRIMER,
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+ :SEQUENCE_PRIMER_REVCOMP,
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+ :PRIMER_PRODUCT_SIZE_RANGE,
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+ :PRIMER_MIN_SIZE,
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+ :PRIMER_OPT_SIZE,
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+ :PRIMER_MAX_SIZE,
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+ :PRIMER_MIN_TM,
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+ :PRIMER_OPT_TM,
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+ :PRIMER_MAX_TM,
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+ :PRIMER_MIN_GC,
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+ :PRIMER_OPT_GC,
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+ :PRIMER_MAX_GC,
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+ :PRIMER_MAX_POLY_X,
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+ :PRIMER_MAX_HAIRPIN_TH,
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+ :PRIMER_MAX_SELF_ANY_TH,
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+ :PRIMER_MAX_SELF_END_TH,
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+ ]
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+ end
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+ end
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+ module Qu
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+ module Pcr
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+ VERSION = "1.0.0"
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+ end
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+ end
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+ # coding: utf-8
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+ lib = File.expand_path('../lib', __FILE__)
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+ $LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
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+ require 'qu/pcr/version'
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+
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+ Gem::Specification.new do |spec|
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+ spec.name = "qu-pcr"
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+ spec.version = Qu::Pcr::VERSION
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+ spec.authors = ["Wubin Qu"]
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+ spec.email = ["quwubin@gmail.com"]
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+ spec.description = %q{A package for PCR, including primers, products, primer3 parser, virtual electrophoresis, etc.}
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+ spec.summary = %q{A ruby library for PCR}
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+ spec.homepage = "https://github.com/quwubin/qu-pcr"
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+ spec.license = "MIT"
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+
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+ spec.files = `git ls-files`.split($/)
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+ spec.executables = spec.files.grep(%r{^bin/}) { |f| File.basename(f) }
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+ spec.test_files = spec.files.grep(%r{^(test|spec|features)/})
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+ spec.require_paths = ["lib"]
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+
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+ spec.add_runtime_dependency 'qu-utils', '~> 1.0'
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+ spec.add_runtime_dependency 'qu-cmdwrapper', '~> 1.0'
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+
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+ spec.add_development_dependency "bundler", "~> 1.3"
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+ spec.add_development_dependency "rake"
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+ end
metadata ADDED
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+ --- !ruby/object:Gem::Specification
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+ name: qu-pcr
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+ version: !ruby/object:Gem::Version
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+ version: 1.0.0
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+ platform: ruby
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+ authors:
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+ - Wubin Qu
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+ autorequire:
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+ bindir: bin
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+ cert_chain: []
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+ date: 2014-04-28 00:00:00.000000000 Z
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+ dependencies:
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+ - !ruby/object:Gem::Dependency
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+ name: qu-utils
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+ requirement: !ruby/object:Gem::Requirement
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+ requirements:
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+ - - "~>"
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+ - !ruby/object:Gem::Version
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+ version: '1.0'
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+ type: :runtime
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+ prerelease: false
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+ version_requirements: !ruby/object:Gem::Requirement
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+ requirements:
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+ - - "~>"
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+ - !ruby/object:Gem::Version
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+ version: '1.0'
27
+ - !ruby/object:Gem::Dependency
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+ name: qu-cmdwrapper
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+ requirement: !ruby/object:Gem::Requirement
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+ requirements:
31
+ - - "~>"
32
+ - !ruby/object:Gem::Version
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+ version: '1.0'
34
+ type: :runtime
35
+ prerelease: false
36
+ version_requirements: !ruby/object:Gem::Requirement
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+ requirements:
38
+ - - "~>"
39
+ - !ruby/object:Gem::Version
40
+ version: '1.0'
41
+ - !ruby/object:Gem::Dependency
42
+ name: bundler
43
+ requirement: !ruby/object:Gem::Requirement
44
+ requirements:
45
+ - - "~>"
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+ - !ruby/object:Gem::Version
47
+ version: '1.3'
48
+ type: :development
49
+ prerelease: false
50
+ version_requirements: !ruby/object:Gem::Requirement
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+ requirements:
52
+ - - "~>"
53
+ - !ruby/object:Gem::Version
54
+ version: '1.3'
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+ - !ruby/object:Gem::Dependency
56
+ name: rake
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+ requirement: !ruby/object:Gem::Requirement
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+ requirements:
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+ - - ">="
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+ - !ruby/object:Gem::Version
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+ version: '0'
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+ type: :development
63
+ prerelease: false
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+ version_requirements: !ruby/object:Gem::Requirement
65
+ requirements:
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+ - - ">="
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+ - !ruby/object:Gem::Version
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+ version: '0'
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+ description: A package for PCR, including primers, products, primer3 parser, virtual
70
+ electrophoresis, etc.
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+ email:
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+ - quwubin@gmail.com
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+ executables: []
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+ extensions: []
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+ extra_rdoc_files: []
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+ files:
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+ - ".gitignore"
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+ - Gemfile
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+ - LICENSE.txt
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+ - README.md
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+ - Rakefile
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+ - lib/qu/pcr.rb
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+ - lib/qu/pcr/primer3.rb
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+ - lib/qu/pcr/primer3_parameters.rb
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+ - lib/qu/pcr/version.rb
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+ - qu-pcr.gemspec
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+ homepage: https://github.com/quwubin/qu-pcr
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+ licenses:
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+ - MIT
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+ metadata: {}
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+ post_install_message:
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+ rdoc_options: []
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+ require_paths:
94
+ - lib
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+ required_ruby_version: !ruby/object:Gem::Requirement
96
+ requirements:
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+ - - ">="
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+ - !ruby/object:Gem::Version
99
+ version: '0'
100
+ required_rubygems_version: !ruby/object:Gem::Requirement
101
+ requirements:
102
+ - - ">="
103
+ - !ruby/object:Gem::Version
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+ version: '0'
105
+ requirements: []
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+ rubyforge_project:
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+ rubygems_version: 2.2.0
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+ signing_key:
109
+ specification_version: 4
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+ summary: A ruby library for PCR
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+ test_files: []