bio-primer3 0.0.1.pre

checksums.yaml

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+---
+SHA1:
+  metadata.gz: c135a6e6af65f1d5835a5016222aea290d37094b
+  data.tar.gz: 0b19ee1cf88372fba5615a5c261125a88e4be050
+SHA512:
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data/.document

@@ -0,0 +1,5 @@
+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

@@ -0,0 +1,15 @@
+source "http://rubygems.org"
+
+gem 'bio', '~>1.4'
+gem 'bio-logger', '~>1.0'
+gem 'bio-commandeer', '~>0.1'
+
+# Add dependencies to develop your gem here.
+# Include everything needed to run rake, tests, features, etc.
+group :development do
+  gem "rspec", "~> 2.8"
+  gem "yard", "~> 0.7"
+  gem "rdoc", "~> 3.12"
+  gem "jeweler", "~> 2.0"
+  gem "bundler", "~> 1.3"
+end

data/LICENSE.txt

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+Copyright (c) 2012 Ben J Woodcroft
+
+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

@@ -0,0 +1,47 @@
+# bio-primer3
+
+[![Build Status](https://secure.travis-ci.org/wwood/bioruby-primer3.png)](http://travis-ci.org/wwood/bioruby-primer3)
+
+Full description goes here
+
+Note: this software is under active development!
+
+## Installation
+
+```sh
+gem install bio-primer3
+```
+
+## Usage
+
+```ruby
+require 'bio-primer3'
+```
+
+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/wwood/bioruby-primer3
+
+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-primer3)
+
+## Copyright
+
+Copyright (c) 2012 Ben J Woodcroft. See LICENSE.txt for further details.
+

data/README.rdoc

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+= bio-primer3
+
+{<img
+src="https://secure.travis-ci.org/wwood/bioruby-primer3.png"
+/>}[http://travis-ci.org/#!/wwood/bioruby-primer3]
+
+Full description goes here
+
+Note: this software is under active development!
+
+== Installation
+
+        gem install bio-primer3
+
+== Usage
+
+== Developers
+
+To use the library 
+
+        require 'bio-primer3'
+
+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/wwood/bioruby-primer3
+
+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-primer3
+
+== Copyright
+
+Copyright (c) 2012 Ben J Woodcroft. 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-primer3"
+  gem.homepage = "http://github.com/wwood/bioruby-primer3"
+  gem.license = "MIT"
+  gem.summary = %Q{Primer3-related Ruby code}
+  gem.description = %Q{Primer3-related Ruby code - wrappers, Boulder IO, etc.}
+  gem.email = "donttrustben@gmail.com"
+  gem.authors = ["Ben J Woodcroft"]
+  # dependencies defined in Gemfile
+end
+Jeweler::RubygemsDotOrgTasks.new
+
+require 'rspec/core'
+require 'rspec/core/rake_task'
+RSpec::Core::RakeTask.new(:spec) do |spec|
+  spec.pattern = FileList['spec/**/*_spec.rb']
+end
+RSpec::Core::RakeTask.new(:test_without_wrapper) do |spec|
+  spec.pattern = FileList['spec/**/*_spec.rb'].reject{|f| f=='spec/bio-primer3_wrapper_spec.rb'}
+end
+
+task :default => :spec
+
+require 'rdoc/task'
+Rake::RDocTask.new do |rdoc|
+  version = File.exist?('VERSION') ? File.read('VERSION') : ""
+
+  rdoc.rdoc_dir = 'rdoc'
+  rdoc.title = "bio-primer3 #{version}"
+  rdoc.rdoc_files.include('README*')
+  rdoc.rdoc_files.include('lib/**/*.rb')
+end

data/VERSION

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+0.0.1.pre

data/lib/bio-primer3.rb

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+
+require 'bio-logger'
+Bio::Log::LoggerPlus.new('bio-primer3')
+module Bio::Primer3Logging
+  def log
+    Bio::Log::LoggerPlus['bio-primer3']
+  end
+end
+
+require 'bio/primer3/boulder_io.rb'
+require 'bio/primer3/wrapper.rb'
+require 'bio/primer3/result.rb'
+

data/lib/bio/primer3/boulder_io.rb

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+# A class for input and output of Boulder I/O files, for instance as used in
+# primer3. This (I don't think) is a full implementation of the Boulder I/O
+# format, but serves for my purposes.
+class BoulderIO
+  include Enumerable
+
+  class ParseException<Exception; end
+
+  class Record
+    include Enumerable
+    attr_accessor :attributes # a hash of key-value pairs
+    
+    # Initialise, setting the hash optionally. If no hash is specified, then the
+    # attributes will be an empty hash
+    def initialize(hash=nil)
+      @attributes = hash
+      @attributes ||= {}
+    end
+
+    def to_s
+      ats = @attributes.collect do |key,value|
+        "#{key}=#{value}\n"
+      end
+      "#{ats.join("")}="
+    end
+
+    # Given a Boulder I/O formatted string, parse into a record
+    def self.create(boulder_io_string)
+      baby = self.new
+
+      boulder_io_string.split("\n").each do |line|
+        line.strip!
+        break if line=='=' #break on the final record
+
+        splits = line.split('=')
+
+        # error checking
+        if splits.length != 2
+          raise ParseException, "Could not parse Boulder I/O line: `#{line}', quitting"
+        end
+
+        baby[splits[0]] = splits[1]
+      end
+      baby #return the new'un for convenience
+    end
+
+    # for Enumerable-compatibility
+    def each
+      @attributes.each do |k,v|
+        yield k,v
+      end
+    end
+
+    # Equivalent to attributes[] - this is a convenient method, isn't it?
+    def [](key)
+      @attributes[key]
+    end
+
+    # Equivalent to attributes[]= - this is a convenient method, isn't it?
+    def []=(key,value)
+      @attributes[key] = value
+    end
+  end
+
+  # an array of records
+  attr_accessor :records
+
+  # Open a Boulder I/O file and parse it. It is possible to go through all the
+  # records:
+  #
+  #    BoulderIO.open('/path/to/boulderio_file').each {|record| record}
+  def self.open(filename)
+    record_strings = File.open(filename).read.split("\n=\n")
+    @records = record_strings.collect do |s|
+      Record.create(s)
+    end
+    @records # return the records for convenience
+  end
+
+  # for Enumerable-compatibility
+  def each
+    @records.each do |r|
+      yield r
+    end
+  end
+end

data/lib/bio/primer3/result.rb

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+# Methods for interacting with Primer3 output.
+class Bio::Primer3::Result
+  attr_accessor :output_hash
+  def initialize
+    @output_hash ||= {}
+  end
+
+  # Was there any primers found? Assumes you were looking for a left primer, with
+  # a right primer, which won't always be the case.
+  def primer_found?
+    @output_hash['PRIMER_PAIR_NUM_RETURNED'].to_i>0 or
+    (!@output_hash['PRIMER_LEFT_NUM_RETURNED'].nil? and 
+     @output_hash['PRIMER_LEFT_NUM_RETURNED'].to_i>0
+     !@output_hash['PRIMER_RIGHT_NUM_RETURNED'].nil? and 
+     @output_hash['PRIMER_RIGHT_NUM_RETURNED'].to_i>0)
+  end
+  alias_method :yeh?, :primer_found?
+
+  # Return the requested part of the result
+  def [](key)
+    @output_hash[key]
+  end
+
+  # set the requested part of the result
+  def []=(key,value)
+    @output_hash[key] = value
+  end
+end

data/lib/bio/primer3/wrapper.rb

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+require 'tmpdir'
+require 'bio'
+require 'pp'
+require 'bio-commandeer'
+
+class Bio::Primer3
+  include Bio::Primer3Logging
+  def self.log
+    Bio::Primer3.new.log
+  end
+
+  # Can only handle single records to be passed at one time to primer3
+  def self.run(primer3_options_hash)
+    default_options = {}
+    unless primer3_options_hash.key?('PRIMER_THERMODYNAMIC_PARAMETERS_PATH')
+      @@thermodynamic_parameters_path ||= Bio::Primer3.compute_thermodynamic_parameters_path
+      if @@thermodynamic_parameters_path.nil?
+        log.warn "No primer3_config directory found, things might go awry when running primer3."
+      else
+        default_options['PRIMER_THERMODYNAMIC_PARAMETERS_PATH'] = @@thermodynamic_parameters_path
+      end
+    end
+    merged_hash = default_options.merge(primer3_options_hash)
+
+    input = BoulderIO::Record.new(merged_hash)
+
+    log = Bio::Log::LoggerPlus['bio-primer3']
+    if log.debug?
+      log.debug "Primer3 input:"
+      log.debug input.to_s
+    end
+
+    result = Bio::Primer3::Result.new
+    Dir.mktmpdir do |dir|
+      Dir.chdir(dir) do
+        out = Bio::Commandeer.run 'primer3_core', {:stdin => input.to_s, :log => log}
+        result.output_hash = BoulderIO::Record.create(out).attributes
+      end
+    end
+
+    return result
+  end
+
+  # By default, primer3_core can't find it's own parameters path
+  # (parameter PRIMER_THERMODYNAMIC_PARAMETERS_PATH) unless it is
+  # specified. This method computes the correct path based on the location
+  # of the primer3 executable, and returns the parameters folder
+  # based on it, or nil if none can be found
+  def self.compute_thermodynamic_parameters_path
+    guessed_path = File.join(
+      File.dirname(Bio::Commandeer.run('which primer3_core', :log => log).strip),
+      'primer3_config/'
+      )
+    if File.exist?(guessed_path) and File.directory?(guessed_path)
+      return guessed_path
+    else
+      return nil
+    end
+  end
+
+  # Ask primer3 if 2 primers are compatible, without regard to the sequence
+  # that they PCR. i.e. work out if there is any primer dimer issue, for instance
+  # or whether they have disparate melting temperatures.
+  #
+  # Returns true/false and the Bio::Primer3::Result object.
+  # other_primer3_options_hash specifies options that are passed to primer3,
+  # and options gives Ruby options:
+  # * :return_result: Instead of true/false being returned, an array of [true/false, primer3_output_hash]
+  # is returned instead.
+  def self.test_primer_compatibility(primer1, primer2, other_primer3_options_hash={}, options={})
+    hash = {
+      'SEQUENCE_PRIMER'=>primer1,
+      'SEQUENCE_PRIMER_REVCOMP'=>primer2,
+      'PRIMER_TASK'=>'check_primers',
+    }.merge(other_primer3_options_hash)
+
+    result = Bio::Primer3.run(hash)
+
+    if options and options[:return_result]
+      return result.primer_found?, result
+    else
+      return result.primer_found?
+    end
+  end
+end

data/spec/bio-primer3_result_spec.rb

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+require File.expand_path(File.dirname(__FILE__) + '/spec_helper')
+
+describe "Result" do
+  fail
+end

data/spec/bio-primer3_wrapper_spec.rb

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+require File.expand_path(File.dirname(__FILE__) + '/spec_helper')
+
+describe "Primer3Wrapper" do
+  it "should run the example file fine" do
+
+# This is straight from the example code, except without the P3_FILE_FLAG=1 line
+example = <<EOF
+SEQUENCE_ID=example
+SEQUENCE_TEMPLATE=GTAGTCAGTAGACNATGACNACTGACGATGCAGACNACACACACACACACAGCACACAGGTATTAGTGGGCCATTCGATCCCGACCCAAATCGATAGCTACGATGACG
+SEQUENCE_TARGET=37,21
+PRIMER_TASK=generic
+PRIMER_PICK_LEFT_PRIMER=1
+PRIMER_PICK_INTERNAL_OLIGO=1
+PRIMER_PICK_RIGHT_PRIMER=1
+PRIMER_OPT_SIZE=18
+PRIMER_MIN_SIZE=15
+PRIMER_MAX_SIZE=21
+PRIMER_MIN_TM=56
+PRIMER_MAX_NS_ACCEPTED=2
+PRIMER_PRODUCT_SIZE_RANGE=75-100
+P3_FILE_FLAG=1
+SEQUENCE_INTERNAL_EXCLUDED_REGION=37,21
+PRIMER_EXPLAIN_FLAG=1
+=
+EOF
+
+    example_hash = {}
+    example.split("\n").reject{|s| s== '='}.each do |line|
+    splits = line.split('=')
+    example_hash[splits[0]]=splits[1]
+    end
+
+
+    result = Bio::Primer3.run(example_hash)
+    result.kind_of?(Bio::Primer3::Result).should eq(true)
+
+    result['SEQUENCE_ID'].should eq('example') #Something the same between the input and output
+    result['PRIMER_INTERNAL_0_PENALTY'].nil?.should eq(false) #Something only in the output
+  end
+
+  it 'should correctly work out the path to the primer3 config directory' do
+    found_path = Bio::Primer3.compute_thermodynamic_parameters_path
+    found_path.match(/primer3_config\/$/).nil?.should eq(false)
+    found_path.length.should > 15 #should give an actual path
+  end
+
+  it "should ok reasonable primers" do
+    Bio::Primer3.test_primer_compatibility('NATGACNACTGACGATGCAGA', 'TCGTAGCTATCGATTTGGGT', {'PRIMER_MIN_TM'=>56, 'PRIMER_MAX_NS_ACCEPTED'=>2}).should eq(true)
+  end
+
+  it "should return object checking primers" do
+    bool, result = Bio::Primer3.test_primer_compatibility('NATGACNACTGACGATGCAGA', 'TCGTAGCTATCGATTTGGGT', {'PRIMER_MIN_TM'=>56, 'PRIMER_MAX_NS_ACCEPTED'=>2}, :return_result => true)
+    bool.should eq(true)
+    result.kind_of?(Bio::Primer3::Result).should == true
+  end
+
+  it "should not ok reasonable primers" do
+    # Won't work because there is an N in the moddle of the right primer
+    Bio::Primer3.test_primer_compatibility('ATTGACACTGACGATGCAGA', 'ATACGATTTGNGGTCGGGAT', 'PRIMER_MAX_NS_ACCEPTED'=>0).should eq(false)
+  end
+end

data/spec/spec_helper.rb

@@ -0,0 +1,12 @@
+$LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
+$LOAD_PATH.unshift(File.dirname(__FILE__))
+require 'rspec'
+require 'bio-primer3'
+
+# Requires supporting files with custom matchers and macros, etc,
+# in ./support/ and its subdirectories.
+Dir["#{File.dirname(__FILE__)}/support/**/*.rb"].each {|f| require f}
+
+RSpec.configure do |config|
+  
+end

metadata

@@ -0,0 +1,173 @@
+--- !ruby/object:Gem::Specification
+name: bio-primer3
+version: !ruby/object:Gem::Version
+  version: 0.0.1.pre
+platform: ruby
+authors:
+- Ben J Woodcroft
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2014-03-18 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: bio
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.4'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.4'
+- !ruby/object:Gem::Dependency
+  name: bio-logger
+  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: bio-commandeer
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.1'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.1'
+- !ruby/object:Gem::Dependency
+  name: rspec
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '2.8'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '2.8'
+- !ruby/object:Gem::Dependency
+  name: yard
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.7'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.7'
+- !ruby/object:Gem::Dependency
+  name: rdoc
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '3.12'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '3.12'
+- !ruby/object:Gem::Dependency
+  name: jeweler
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '2.0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '2.0'
+- !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'
+description: Primer3-related Ruby code - wrappers, Boulder IO, etc.
+email: donttrustben@gmail.com
+executables: []
+extensions: []
+extra_rdoc_files:
+- LICENSE.txt
+- README.md
+- README.rdoc
+files:
+- ".document"
+- ".travis.yml"
+- Gemfile
+- LICENSE.txt
+- README.md
+- README.rdoc
+- Rakefile
+- VERSION
+- lib/bio-primer3.rb
+- lib/bio/primer3/boulder_io.rb
+- lib/bio/primer3/result.rb
+- lib/bio/primer3/wrapper.rb
+- spec/bio-primer3_result_spec.rb
+- spec/bio-primer3_wrapper_spec.rb
+- spec/spec_helper.rb
+homepage: http://github.com/wwood/bioruby-primer3
+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: 1.3.1
+requirements: []
+rubyforge_project: 
+rubygems_version: 2.2.0
+signing_key: 
+specification_version: 4
+summary: Primer3-related Ruby code
+test_files: []