qu-pcr 1.0.0
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- checksums.yaml +7 -0
- data/.gitignore +17 -0
- data/Gemfile +6 -0
- data/LICENSE.txt +22 -0
- data/README.md +29 -0
- data/Rakefile +1 -0
- data/lib/qu/pcr.rb +98 -0
- data/lib/qu/pcr/primer3.rb +157 -0
- data/lib/qu/pcr/primer3_parameters.rb +80 -0
- data/lib/qu/pcr/version.rb +5 -0
- data/qu-pcr.gemspec +26 -0
- metadata +111 -0
checksums.yaml
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---
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SHA1:
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metadata.gz: d79948924f1faf4f40f3adc19249a7c848aca707
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data.tar.gz: 2d14089102d1bfc60de4efc5f3c6dc1113621f2a
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SHA512:
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metadata.gz: 1418a4f81f721d1ed5145f70e030c019f8c6d37be36668f51f4fc8346a87d1b52222ca9efd05126960976b8381cc97d3cd67a115767e36e71caa50048c9b0ead
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data.tar.gz: 1de67df5c43b23fc4bdb370fc30787b4b32dde56e1e59a2344aa18e3dddf52afb465d8bcac0f6054e058e9ffafb13dba36880352ebfe2c4578ee233d94400f53
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data/.gitignore
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data/Gemfile
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data/LICENSE.txt
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Copyright (c) 2013 Wubin Qu
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MIT License
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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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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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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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data/README.md
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# Qu::Pcr
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A package for PCR, including primers, products, primer3 parser, virtual electrophoresis, etc.
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## Installation
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Add this line to your application's Gemfile:
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gem 'qu-pcr'
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And then execute:
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$ bundle
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Or install it yourself as:
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$ gem install qu-pcr
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## Usage
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mobility = Qu::Pcr::VirtualGel.cal_mobility(size)
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## Contributing
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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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data/Rakefile
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require "bundler/gem_tasks"
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data/lib/qu/pcr.rb
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require 'qu/utils'
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require 'qu/cmdwrapper'
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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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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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# type should be "forward" or "reverse"
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@type = type
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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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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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end
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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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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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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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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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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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require 'csv'
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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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def initialize(custom_para=nil)
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@para = {}
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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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# 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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end
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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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p3_out = Cmdwrapper::primer3_core(p3_input_file)
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p3_input_file.unlink
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return Primer3Parser.new(p3_out).records
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end
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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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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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@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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@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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@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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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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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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return result
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end
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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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return p3_hash
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end
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end # Primer3Parser
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end # end Pcr module
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end # end Qu module
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# Primer3 Parameters
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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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34
|
+
PRIMER_NUM_RETURN: 10,
|
35
|
+
PRIMER_MAX_NS_ACCEPTED: 0,
|
36
|
+
PRIMER_THERMODYNAMIC_ALIGNMENT: 1,
|
37
|
+
PRIMER_TM_FORMULA: 1,
|
38
|
+
PRIMER_SALT_CORRECTIONS: 1,
|
39
|
+
PRIMER_SALT_MONOVALENT: 50.0,
|
40
|
+
PRIMER_SALT_DIVALENT: 1.5,
|
41
|
+
PRIMER_DNTP_CONC: 0.25,
|
42
|
+
PRIMER_DNA_CONC: 50.0,
|
43
|
+
P3_FILE_FLAG: 0,
|
44
|
+
PRIMER_EXPLAIN_FLAG: 1,
|
45
|
+
PRIMER_PRODUCT_MAX_TM: 100000,
|
46
|
+
PRIMER_PICK_ANYWAY: 0,
|
47
|
+
PRIMER_TASK: "generic",
|
48
|
+
SEQUENCE_PRIMER_PAIR_OK_REGION_LIST: "",
|
49
|
+
PRIMER_MIN_LEFT_THREE_PRIME_DISTANCE: 2,
|
50
|
+
PRIMER_LOWERCASE_MASKING: 1,
|
51
|
+
}
|
52
|
+
|
53
|
+
# Parameters not shown to users for editing
|
54
|
+
USER_SPECIFIC_OPTIONS = [
|
55
|
+
:SEQUENCE_ID,
|
56
|
+
:SEQUENCE_TARGET,
|
57
|
+
:SEQUENCE_EXCLUDED_REGION,
|
58
|
+
:SEQUENCE_FORCE_LEFT_START,
|
59
|
+
:SEQUENCE_FORCE_LEFT_END,
|
60
|
+
:SEQUENCE_FORCE_RIGHT_START,
|
61
|
+
:SEQUENCE_FORCE_RIGHT_END,
|
62
|
+
:SEQUENCE_PRIMER,
|
63
|
+
:SEQUENCE_PRIMER_REVCOMP,
|
64
|
+
:PRIMER_PRODUCT_SIZE_RANGE,
|
65
|
+
:PRIMER_MIN_SIZE,
|
66
|
+
:PRIMER_OPT_SIZE,
|
67
|
+
:PRIMER_MAX_SIZE,
|
68
|
+
:PRIMER_MIN_TM,
|
69
|
+
:PRIMER_OPT_TM,
|
70
|
+
:PRIMER_MAX_TM,
|
71
|
+
:PRIMER_MIN_GC,
|
72
|
+
:PRIMER_OPT_GC,
|
73
|
+
:PRIMER_MAX_GC,
|
74
|
+
:PRIMER_MAX_POLY_X,
|
75
|
+
:PRIMER_MAX_HAIRPIN_TH,
|
76
|
+
:PRIMER_MAX_SELF_ANY_TH,
|
77
|
+
:PRIMER_MAX_SELF_END_TH,
|
78
|
+
]
|
79
|
+
end
|
80
|
+
end
|
data/qu-pcr.gemspec
ADDED
@@ -0,0 +1,26 @@
|
|
1
|
+
# coding: utf-8
|
2
|
+
lib = File.expand_path('../lib', __FILE__)
|
3
|
+
$LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
|
4
|
+
require 'qu/pcr/version'
|
5
|
+
|
6
|
+
Gem::Specification.new do |spec|
|
7
|
+
spec.name = "qu-pcr"
|
8
|
+
spec.version = Qu::Pcr::VERSION
|
9
|
+
spec.authors = ["Wubin Qu"]
|
10
|
+
spec.email = ["quwubin@gmail.com"]
|
11
|
+
spec.description = %q{A package for PCR, including primers, products, primer3 parser, virtual electrophoresis, etc.}
|
12
|
+
spec.summary = %q{A ruby library for PCR}
|
13
|
+
spec.homepage = "https://github.com/quwubin/qu-pcr"
|
14
|
+
spec.license = "MIT"
|
15
|
+
|
16
|
+
spec.files = `git ls-files`.split($/)
|
17
|
+
spec.executables = spec.files.grep(%r{^bin/}) { |f| File.basename(f) }
|
18
|
+
spec.test_files = spec.files.grep(%r{^(test|spec|features)/})
|
19
|
+
spec.require_paths = ["lib"]
|
20
|
+
|
21
|
+
spec.add_runtime_dependency 'qu-utils', '~> 1.0'
|
22
|
+
spec.add_runtime_dependency 'qu-cmdwrapper', '~> 1.0'
|
23
|
+
|
24
|
+
spec.add_development_dependency "bundler", "~> 1.3"
|
25
|
+
spec.add_development_dependency "rake"
|
26
|
+
end
|
metadata
ADDED
@@ -0,0 +1,111 @@
|
|
1
|
+
--- !ruby/object:Gem::Specification
|
2
|
+
name: qu-pcr
|
3
|
+
version: !ruby/object:Gem::Version
|
4
|
+
version: 1.0.0
|
5
|
+
platform: ruby
|
6
|
+
authors:
|
7
|
+
- Wubin Qu
|
8
|
+
autorequire:
|
9
|
+
bindir: bin
|
10
|
+
cert_chain: []
|
11
|
+
date: 2014-04-28 00:00:00.000000000 Z
|
12
|
+
dependencies:
|
13
|
+
- !ruby/object:Gem::Dependency
|
14
|
+
name: qu-utils
|
15
|
+
requirement: !ruby/object:Gem::Requirement
|
16
|
+
requirements:
|
17
|
+
- - "~>"
|
18
|
+
- !ruby/object:Gem::Version
|
19
|
+
version: '1.0'
|
20
|
+
type: :runtime
|
21
|
+
prerelease: false
|
22
|
+
version_requirements: !ruby/object:Gem::Requirement
|
23
|
+
requirements:
|
24
|
+
- - "~>"
|
25
|
+
- !ruby/object:Gem::Version
|
26
|
+
version: '1.0'
|
27
|
+
- !ruby/object:Gem::Dependency
|
28
|
+
name: qu-cmdwrapper
|
29
|
+
requirement: !ruby/object:Gem::Requirement
|
30
|
+
requirements:
|
31
|
+
- - "~>"
|
32
|
+
- !ruby/object:Gem::Version
|
33
|
+
version: '1.0'
|
34
|
+
type: :runtime
|
35
|
+
prerelease: false
|
36
|
+
version_requirements: !ruby/object:Gem::Requirement
|
37
|
+
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
|
+
- - "~>"
|
46
|
+
- !ruby/object:Gem::Version
|
47
|
+
version: '1.3'
|
48
|
+
type: :development
|
49
|
+
prerelease: false
|
50
|
+
version_requirements: !ruby/object:Gem::Requirement
|
51
|
+
requirements:
|
52
|
+
- - "~>"
|
53
|
+
- !ruby/object:Gem::Version
|
54
|
+
version: '1.3'
|
55
|
+
- !ruby/object:Gem::Dependency
|
56
|
+
name: rake
|
57
|
+
requirement: !ruby/object:Gem::Requirement
|
58
|
+
requirements:
|
59
|
+
- - ">="
|
60
|
+
- !ruby/object:Gem::Version
|
61
|
+
version: '0'
|
62
|
+
type: :development
|
63
|
+
prerelease: false
|
64
|
+
version_requirements: !ruby/object:Gem::Requirement
|
65
|
+
requirements:
|
66
|
+
- - ">="
|
67
|
+
- !ruby/object:Gem::Version
|
68
|
+
version: '0'
|
69
|
+
description: A package for PCR, including primers, products, primer3 parser, virtual
|
70
|
+
electrophoresis, etc.
|
71
|
+
email:
|
72
|
+
- quwubin@gmail.com
|
73
|
+
executables: []
|
74
|
+
extensions: []
|
75
|
+
extra_rdoc_files: []
|
76
|
+
files:
|
77
|
+
- ".gitignore"
|
78
|
+
- Gemfile
|
79
|
+
- LICENSE.txt
|
80
|
+
- README.md
|
81
|
+
- Rakefile
|
82
|
+
- lib/qu/pcr.rb
|
83
|
+
- lib/qu/pcr/primer3.rb
|
84
|
+
- lib/qu/pcr/primer3_parameters.rb
|
85
|
+
- lib/qu/pcr/version.rb
|
86
|
+
- qu-pcr.gemspec
|
87
|
+
homepage: https://github.com/quwubin/qu-pcr
|
88
|
+
licenses:
|
89
|
+
- MIT
|
90
|
+
metadata: {}
|
91
|
+
post_install_message:
|
92
|
+
rdoc_options: []
|
93
|
+
require_paths:
|
94
|
+
- lib
|
95
|
+
required_ruby_version: !ruby/object:Gem::Requirement
|
96
|
+
requirements:
|
97
|
+
- - ">="
|
98
|
+
- !ruby/object:Gem::Version
|
99
|
+
version: '0'
|
100
|
+
required_rubygems_version: !ruby/object:Gem::Requirement
|
101
|
+
requirements:
|
102
|
+
- - ">="
|
103
|
+
- !ruby/object:Gem::Version
|
104
|
+
version: '0'
|
105
|
+
requirements: []
|
106
|
+
rubyforge_project:
|
107
|
+
rubygems_version: 2.2.0
|
108
|
+
signing_key:
|
109
|
+
specification_version: 4
|
110
|
+
summary: A ruby library for PCR
|
111
|
+
test_files: []
|