bio-ipcress 0.0.1

data/.document

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

data/.travis.yml

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

data/Gemfile

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+source "http://rubygems.org"
+# Add dependencies required to use your gem here.
+# Example:
+#   gem "activesupport", ">= 2.3.5"
+gem 'bio', '>=1.4.2'
+
+# Add dependencies to develop your gem here.
+# Include everything needed to run rake, tests, features, etc.
+group :development do
+  gem "shoulda", ">= 0"
+  gem "rdoc", "~> 3.12"
+  gem "jeweler", "~> 1.8.3"
+  gem "bundler", ">= 1.0.21"
+  gem "bio", ">= 1.4.2"
+  gem "rdoc", "~> 3.12"
+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

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+# bio-ipcress
+
+```bio-ipcress``` is a programmatic interface to the ```ipcress``` in-silico PCR software, which
+is bundled with [exonerate](http://www.ebi.ac.uk/~guy/exonerate/).
+
+You can run a PCR:
+```ruby
+require 'bio-ipcress'
+
+#hits the first and last bits of the Methanocella_conradii_16s.fa
+primer_set = Bio::Ipcress::PrimerSet.new(
+  'GGTCACTGCTA','GGCTACCTTGTTACGACTTAAC'
+  )
+
+# Run ipcress on a template sequence, specified in as a FASTA file
+results = Bio::Ipcress.run(
+  primer_set,
+  'Methanocella_conradii_16s.fa', #this file is in the test/data/Ipcress directory
+  {:min_distance => 2, :max_distance => 10000})
+#=> A Bio::Ipcress::Result object, parsed from
+#
+#Ipcress result
+#--------------
+# Experiment: AE12_pmid21856836_16S
+#    Primers: A B
+#     Target: gi|335929284|gb|JN048683.1|:filter(unmasked) Methanocella conradii HZ254 16S ribosomal RNA gene, partial sequence
+#    Matches: 19/20 14/15
+#    Product: 502 bp (range 2-10000)
+#Result type: forward
+#
+#...AAACTTAAAGGAATTGGCGG......................... # forward
+#   ||||| ||| |||||| |||-->
+#5'-AAACTYAAAKGAATTGRCGG-3' 3'-CRTGTGTGGCGGGCA-5' # primers
+#                           <--| |||||||||||||
+#..............................CGTGTGTGGCGGGCA... # revcomp
+#--
+#ipcress: gi|335929284|gb|JN048683.1|:filter(unmasked) AE12_pmid21856836_16S 502 A 826 1 B 1313 1 forward
+#-- completed ipcress analysis"
+
+
+
+# This Bio::Ipcress::Result object now holds info about the result:
+results.length #=> 1
+
+res = results[0]
+res.experiment_name #=> 'AE12_pmid21856836_16S' 
+res.primers #=> 'A B' 
+res.target #=> 'gi|335929284|gb|JN048683.1|:filter(unmasked) Methanocella conradii HZ254 16S ribosomal RNA gene, partial sequence'
+res.matches #=> '19/20 14/15' 
+res.product #=> '502 bp (range 2-10000)' 
+res.result_type #=> 'forward' 
+res.forward_matching_sequence #=> 'AAACTTAAAGGAATTGGCGG' 
+res.forward_primer_sequence #=> 'AAACTYAAAKGAATTGRCGG' 
+res.reverse_primer_sequence #=> 'CRTGTGTGGCGGGCA' 
+res.reverse_matching_sequence #=> 'CGTGTGTGGCGGGCA' 
+res.length #=> 502
+res.start #=> 826
+res.forward_mismatches #=> 1 
+res.reverse_mismatches #=> 1
+```
+
+There appears to be a slight bug in iPCRess, in the way it handles primers with 'wobble' bases like AAACT*Y*,
+which indicates that both AAACT*C* and AAACT*T* are added as primers.
+IPCress always suggests that there is at least a single mismatch,
+when this is not always the case. To workaround this, the
+```Result#recalculate_mismatches_from_alignments``` method re-computes the 
+number of forward and reverse mismatches.
+
+```ruby
+#...AAACTTAAAGGAATTGGCGG......................... # forward
+#   ||||| ||| |||||| |||-->
+#5'-AAACTYAAAKGAATTGRCGG-3' 3'-CRTGTGTGGCGGGCA-5' # primers
+#                           <--| |||||||||||||
+#..............................CGTGTGTGGCGGGCA... # revcomp
+res = Bio::Ipcress::Result.new
+res.forward_matching_sequence = 'AAACTTAAAGGAATTGGCGG'
+res.forward_primer_sequence = 'AAACTYAAAKGAATTGRCGG'
+res.reverse_matching_sequence = 'CGTGTGTGGCGGGCA'
+res.reverse_primer_sequence = 'CRTGTGTGGCGGGCA'
+
+res.recalculate_mismatches_from_alignments #=> [0,0]
+```
+
+## Installation
+
+```sh
+gem install bio-ipcress
+```
+
+You'll also need to install [exonerate](http://www.ebi.ac.uk/~guy/exonerate/)
+        
+## Project home page
+
+Information on the source tree, documentation, examples, issues and
+how to contribute, see
+
+  http://github.com/wwood/bioruby-ipcress
+
+The BioRuby community is on IRC server: irc.freenode.org, channel: #bioruby.
+
+## Cite
+
+If you use this software, please cite exonerate
+
+## Biogems.info
+
+This Biogem is published at [#bio-ipcress](http://biogems.info/index.html)
+
+## 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-ipcress"
+  gem.homepage = "http://github.com/wwood/bioruby-ipcress"
+  gem.license = "MIT"
+  gem.summary = %Q{a programmatic interface to the iPCRess in-silico PCR software}
+  gem.description = %Q{a programmatic interface to the iPCRess in-silico PCR software. iPCRess is part of the exonerate suite.}
+  gem.email = "gmail.com after donttrustben"
+  gem.authors = ["Ben J Woodcroft"]
+  # dependencies defined in Gemfile
+end
+Jeweler::RubygemsDotOrgTasks.new
+
+require 'rake/testtask'
+Rake::TestTask.new(:test) do |test|
+  test.libs << 'lib' << 'test'
+  test.pattern = 'test/**/test_*.rb'
+  test.verbose = true
+end
+
+task :default => :test
+
+require 'rdoc/task'
+Rake::RDocTask.new do |rdoc|
+  version = File.exist?('VERSION') ? File.read('VERSION') : ""
+
+  rdoc.rdoc_dir = 'rdoc'
+  rdoc.title = "bio-ipcress #{version}"
+  rdoc.rdoc_files.include('README*')
+  rdoc.rdoc_files.include('lib/**/*.rb')
+end

data/VERSION

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+0.0.1

data/lib/bio-ipcress.rb

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+require 'bio'
+require 'bio/appl/ipcress.rb'
+

data/lib/bio/appl/ipcress.rb

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+require 'bio'
+require 'tempfile'
+
+module Bio
+  class Ipcress
+    # A full Ipcress result looks something like this. Parse it into an array of Ipcress::Result objects
+    #
+    # ** Message: Loaded [1] experiments
+    # 
+    # Ipcress result
+    # --------------
+    #  Experiment: AE12_pmid21856836_16S
+    #     Primers: A B
+    #      Target: gi|335929284|gb|JN048683.1|:filter(unmasked) Methanocella conradii HZ254 16S ribosomal RNA gene, partial sequence
+    #     Matches: 19/20 14/15
+    #     Product: 502 bp (range 2-10000)
+    # Result type: forward
+    # 
+    # ...AAACTTAAAGGAATTGGCGG......................... # forward
+    #    ||||| ||| |||||| |||-->
+    # 5'-AAACTYAAAKGAATTGRCGG-3' 3'-CRTGTGTGGCGGGCA-5' # primers
+    #                            <--| |||||||||||||
+    # ..............................CGTGTGTGGCGGGCA... # revcomp
+    # --
+    # ipcress: gi|335929284|gb|JN048683.1|:filter(unmasked) AE12_pmid21856836_16S 502 A 826 1 B 1313 1 forward
+    # -- completed ipcress analysis
+    def self.parse(ipcress_output_string)
+      results = Results.new
+      
+      ipcress_output_string.split(/\nIpcress result\n--------------\n/m).each_with_index do |result_chunk, index|
+        next if index == 0 # ignore the first chunk since that isn't a result
+        
+        lines = result_chunk.split("\n").collect{|l| l.strip}
+        
+        result = Result.new
+        i=0
+        result.experiment_name  = lines[i].match(/^Experiment: (.+)$/)[1]; i+=1
+        result.primers     = lines[i].match(/^Primers: (.+)$/)[1]; i+=1
+        result.target      = lines[i].match(/^Target: (.+)$/)[1]; i+=1
+        result.matches     = lines[i].match(/^Matches: (.+)$/)[1]; i+=1
+        result.product     = lines[i].match(/^Product: (.+)$/)[1]; i+=1
+        result.result_type = lines[i].match(/^Result type: (.+)$/)[1]
+        
+        i+= 2
+        result.forward_matching_sequence = lines[i].match(/^\.\.\.(\w+)\.+ \# forward$/)[1]
+        i+= 2
+        matching = lines[i].match(/^5'\-(\w+)-3' 3'\-(\w+)-5' \# primers$/)
+        result.forward_primer_sequence = matching[1]
+        result.reverse_primer_sequence = matching[2]
+        i+= 2
+        result.reverse_matching_sequence = lines[i].match(/^\.+(\w+)\.\.\. \# revcomp$/)[1]
+        
+        i+= 2
+        matching = lines[i].match(/^ipcress: (\S+) (\S+) (\d+) [AB] (\d+) (\d+) [AB] (\d+) (\d+) (\S+)$/)
+        result.length = matching[3].to_i
+        result.start = matching[4].to_i
+        result.forward_mismatches = matching[5].to_i
+        result.reverse_mismatches = matching[7].to_i
+        
+        results.push result
+      end
+      return results
+    end
+    
+    # Run ipcress
+    #
+    # * primer_set: a PrimerSet object with defined forward and reverse primers
+    # * fasta_file: a String path to a fasta file that will be used as template
+    # * options hash: contains less-used parameters
+    # ** :min_distance: the minimum length of product to be amplified (default 100)
+    # ** :max_distance: the maxmimum length of product to be amplified (default 1000)
+    # ** :ipcress_path: path the ipcress executable (default 'ipcress')
+    # ** :mismatches: number of mismatches allowable (-m parameter to ipcress binary, default 0)
+    #
+    # Return an array of parsed Result objects
+    def self.run(primer_set, fasta_file, options={})
+      raise unless primer_set.kind_of?(PrimerSet)
+      raise unless fasta_file.kind_of?(String)
+      options[:ipcress_path] ||= 'ipcress'
+      
+      Tempfile.open('ipcress') do |tempfile|
+        # Write a tempfile that contains the primer set to be queried
+        primers = primer_set.to_ipcress_format(options)
+        tempfile.puts primers
+        tempfile.close
+        
+        command = [
+          options[:ipcress_path],
+        ]
+        if options[:mismatches]
+          command.push '-m'
+          command.push options[:mismatches].to_s
+        end
+        command.push tempfile.path
+        command.push fasta_file
+
+        Bio::Command.call_command_open3(command) do |stdin, stdout, stderr|
+          out = stdout.read
+          raise stderr.read if out == '' #if there is a problem running ipcress e.g. the fasta file isn't found
+          
+          return parse(out)
+        end
+      end
+    end
+    
+    # A class to represent a pair of primers that will be used by Ipcress
+    # to amplify from template DNA in-silico
+    class PrimerSet
+      attr_accessor :forward_primer, :reverse_primer
+      
+      def initialize(forward_primer, reverse_primer)
+        @forward_primer = forward_primer
+        @reverse_primer = reverse_primer
+      end
+      
+      # To a string in the "ipcress file" format required for ipcress usage
+      def to_ipcress_format(options={})
+        options ||= {}
+        options[:min_distance] ||= 100
+        options[:max_distance] ||= 1000
+        "ID1 #{@forward_primer} #{@reverse_primer} #{options[:min_distance]} #{options[:max_distance]}"
+      end
+    end
+
+    # A collection of Ipcress Result objects for a given run
+    class Results < Array
+    end
+    
+    # Ipcress single result (single primer pair match)
+    #
+    # Attributes of this class should be largely obvious by inspecting the Ipcress output
+    class Result
+      attr_accessor :experiment_name
+      
+      attr_accessor :primers, :target, :matches, :product, :result_type
+      
+      # A String representing the matching part of the sequence
+      attr_accessor :forward_matching_sequence
+      
+      # A String representing the matching primer
+      attr_accessor :forward_primer_sequence
+      
+      # A String representing the matching primer
+      attr_accessor :reverse_primer_sequence
+      
+      # A String representing the matching part of the sequence
+      attr_accessor :reverse_matching_sequence
+      
+      attr_accessor :length, :forward_mismatches, :start, :reverse_mismatches
+      
+      # When there are wobbles in the primers, Ipcress always reports at
+      # least 1 mismatch (1 for all matching wobbles plus regular mismatches).
+      #
+      # This method recalculates the mismatches by re-aligning the primers
+      # against the sequences that they hit in this Result.
+      #
+      # Returns an array of 2 values corresponding to the number of mismatches
+      # in the forward and revcomp primers, respectively.
+      #
+      # Assumes that there is only wobbles in the primers, not the sequence
+      # (Does ipcress itself assume this?)
+      def recalculate_mismatches_from_alignments
+        calculate_mismatches = lambda do |seq, primer|
+          mismatches = 0
+          (0..(seq.length-1)).each do |position|
+            regex = Bio::Sequence::NA.new(primer[position].downcase).to_re
+            seqp = seq[position].downcase
+            mismatches += 1 unless regex.match(seqp)
+          end
+          mismatches
+        end
+        
+        return [
+          calculate_mismatches.call(@forward_matching_sequence, @forward_primer_sequence),
+          calculate_mismatches.call(@reverse_matching_sequence, @reverse_primer_sequence)
+        ]
+      end
+    end
+  end
+end

data/test/data/Ipcress/Methanocella_conradii_16s.fa

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+>gi|335929284|gb|JN048683.1| Methanocella conradii HZ254 16S ribosomal RNA gene, partial sequence
+GGTCACTGCTATCGGTGTCCGATTAAGCCATGCGAGTCGTGAGGGGTGAGCCCTCGGCGTACTGCTCAGT
+AACACGTGGACAATCTGCCCAAAAGTCCGGGATAACCCCGGGAAACTGGGGATAATACCGGATAGGCCAC
+CAATTGCTGGAATGGCCTGGTGGTTGAAACGAGAGGCTTTTGGATGGGTCTGCGGCGGATTAGGTTGACG
+CCGGTGTAACGTACCGGCGTGCCTGTAATCCGTACGGGTTGTGGGAGCAAGAGCCCGGAGATGGATTCTG
+AGACACGAATCCAGGCCCTACGGGGCGCAGCAGGCGCGAAAACTCTACAATGCAGGCAATCTGCGATAGG
+GGGACATCGAGTGGCATCTTCTTAAGGTGCCTGTCCAACCGTCTAAAAAACGGTTGTTAGCAAGGGCCGG
+GTAAGACCGGTGCCAGCCGCCGCGGTAATACCGGCGGCTCGAGTGGTGGCCGATATTATTGAGTCTAAAG
+GGTCCGTAGCCGGCTTTGCAAGTCCCCTGGGAAATCCAGCGGCTTAACCGTTGGGCGCCCATGGGATACT
+ACATTGCTTGGGACTGGGAGAGGCGAGAGGTACTCGAGGGGTAGGGGTGAAATCCTGTAATCCTTCGGGG
+ACCACCGGTGGCGAAGGCGTCTCGCCAGAACAGGTCCGACGGTGAGGGACGAAAGCTAGGGGCACGAACC
+GGATTAGATACCCGGGTAGTCCTAGCCGTAAACGATGCCCGCTAGGTGTCACGATAATCGTGAATTATCG
+TGGTGCCGTAGGGAAGCCGCGAAGCGGGCCACTTGGGAAGTACGACCGCAAGGTTGAAACTTAAAGGAAT
+TGGCGGGGGAGCACCACAACGGGTGGAGCCTGCGGTTTAATTGGATTCAACGCCGGGAAGCTTACCGGGA
+TCGACAGTTGAATGAAGGCCAGGCCGAAGACCTTGCCGGACTAGCTGAGAGGAGGTGCATGGCCGTCGTC
+AGTTCGTACCGTGAGGCGTCCTGTTAAGTCAGGCAACGAGCGAGACCCATGTCCACTGTTGCTAACGCGT
+CCGCGAGGACGGCGAGTACACTGTGGAGACTGCTGGCGCTAAGTCAGAGGAAGGGTTGGTCGACGGTAGG
+TCAGTATGCCCCGAATATCCCGGGCTACACGCGGGCTACAATGGACAGGACAATGGGTAACAACACCGAG
+AGGTGAAGTTAATCTCTTAAACCTGTCCCTAGTTCGGATTGAGGGCTGAAACCCGCCCTCATGAAGATGG
+AATCCGTAGTAATCGCATTTCAAAACAGTGCGGTGAATACGTCCCTGCTCCTTGCACACACCGCCCGTCA
+AACCACCCGAGCGGGGCGTGAATAAGGACTCTTTTCCTTGAAGAGCTCGAATTCACGTTCTGTAAGGGGG
+GTTAAGTCGTAACAAGGTAGCC

data/test/data/Ipcress/Methanocella_conradii_16s_2_sequences.fa

@@ -0,0 +1,44 @@
+>gi|335929284|gb|JN048683.1| Methanocella conradii HZ254 16S ribosomal RNA gene, partial sequence
+GGTCACTGCTATCGGTGTCCGATTAAGCCATGCGAGTCGTGAGGGGTGAGCCCTCGGCGTACTGCTCAGT
+AACACGTGGACAATCTGCCCAAAAGTCCGGGATAACCCCGGGAAACTGGGGATAATACCGGATAGGCCAC
+CAATTGCTGGAATGGCCTGGTGGTTGAAACGAGAGGCTTTTGGATGGGTCTGCGGCGGATTAGGTTGACG
+CCGGTGTAACGTACCGGCGTGCCTGTAATCCGTACGGGTTGTGGGAGCAAGAGCCCGGAGATGGATTCTG
+AGACACGAATCCAGGCCCTACGGGGCGCAGCAGGCGCGAAAACTCTACAATGCAGGCAATCTGCGATAGG
+GGGACATCGAGTGGCATCTTCTTAAGGTGCCTGTCCAACCGTCTAAAAAACGGTTGTTAGCAAGGGCCGG
+GTAAGACCGGTGCCAGCCGCCGCGGTAATACCGGCGGCTCGAGTGGTGGCCGATATTATTGAGTCTAAAG
+GGTCCGTAGCCGGCTTTGCAAGTCCCCTGGGAAATCCAGCGGCTTAACCGTTGGGCGCCCATGGGATACT
+ACATTGCTTGGGACTGGGAGAGGCGAGAGGTACTCGAGGGGTAGGGGTGAAATCCTGTAATCCTTCGGGG
+ACCACCGGTGGCGAAGGCGTCTCGCCAGAACAGGTCCGACGGTGAGGGACGAAAGCTAGGGGCACGAACC
+GGATTAGATACCCGGGTAGTCCTAGCCGTAAACGATGCCCGCTAGGTGTCACGATAATCGTGAATTATCG
+TGGTGCCGTAGGGAAGCCGCGAAGCGGGCCACTTGGGAAGTACGACCGCAAGGTTGAAACTTAAAGGAAT
+TGGCGGGGGAGCACCACAACGGGTGGAGCCTGCGGTTTAATTGGATTCAACGCCGGGAAGCTTACCGGGA
+TCGACAGTTGAATGAAGGCCAGGCCGAAGACCTTGCCGGACTAGCTGAGAGGAGGTGCATGGCCGTCGTC
+AGTTCGTACCGTGAGGCGTCCTGTTAAGTCAGGCAACGAGCGAGACCCATGTCCACTGTTGCTAACGCGT
+CCGCGAGGACGGCGAGTACACTGTGGAGACTGCTGGCGCTAAGTCAGAGGAAGGGTTGGTCGACGGTAGG
+TCAGTATGCCCCGAATATCCCGGGCTACACGCGGGCTACAATGGACAGGACAATGGGTAACAACACCGAG
+AGGTGAAGTTAATCTCTTAAACCTGTCCCTAGTTCGGATTGAGGGCTGAAACCCGCCCTCATGAAGATGG
+AATCCGTAGTAATCGCATTTCAAAACAGTGCGGTGAATACGTCCCTGCTCCTTGCACACACCGCCCGTCA
+AACCACCCGAGCGGGGCGTGAATAAGGACTCTTTTCCTTGAAGAGCTCGAATTCACGTTCTGTAAGGGGG
+GTTAAGTCGTAACAAGGTAGCC
+>2nd
+GGTCACTGCTATCGGTGTCCGATTAAGCCATGCGAGTCGTGAGGGGTGAGCCCTCGGCGTACTGCTCAGT
+AACACGTGGACAATCTGCCCAAAAGTCCGGGATAACCCCGGGAAACTGGGGATAATACCGGATAGGCCAC
+CAATTGCTGGAATGGCCTGGTGGTTGAAACGAGAGGCTTTTGGATGGGTCTGCGGCGGATTAGGTTGACG
+CCGGTGTAACGTACCGGCGTGCCTGTAATCCGTACGGGTTGTGGGAGCAAGAGCCCGGAGATGGATTCTG
+AGACACGAATCCAGGCCCTACGGGGCGCAGCAGGCGCGAAAACTCTACAATGCAGGCAATCTGCGATAGG
+GGGACATCGAGTGGCATCTTCTTAAGGTGCCTGTCCAACCGTCTAAAAAACGGTTGTTAGCAAGGGCCGG
+GTAAGACCGGTGCCAGCCGCCGCGGTAATACCGGCGGCTCGAGTGGTGGCCGATATTATTGAGTCTAAAG
+GGTCCGTAGCCGGCTTTGCAAGTCCCCTGGGAAATCCAGCGGCTTAACCGTTGGGCGCCCATGGGATACT
+ACATTGCTTGGGACTGGGAGAGGCGAGAGGTACTCGAGGGGTAGGGGTGAAATCCTGTAATCCTTCGGGG
+ACCACCGGTGGCGAAGGCGTCTCGCCAGAACAGGTCCGACGGTGAGGGACGAAAGCTAGGGGCACGAACC
+GGATTAGATACCCGGGTAGTCCTAGCCGTAAACGATGCCCGCTAGGTGTCACGATAATCGTGAATTATCG
+TGGTGCCGTAGGGAAGCCGCGAAGCGGGCCACTTGGGAAGTACGACCGCAAGGTTGAAACTTAAAGGAAT
+TGGCGGGGGAGCACCACAACGGGTGGAGCCTGCGGTTTAATTGGATTCAACGCCGGGAAGCTTACCGGGA
+TCGACAGTTGAATGAAGGCCAGGCCGAAGACCTTGCCGGACTAGCTGAGAGGAGGTGCATGGCCGTCGTC
+AGTTCGTACCGTGAGGCGTCCTGTTAAGTCAGGCAACGAGCGAGACCCATGTCCACTGTTGCTAACGCGT
+CCGCGAGGACGGCGAGTACACTGTGGAGACTGCTGGCGCTAAGTCAGAGGAAGGGTTGGTCGACGGTAGG
+TCAGTATGCCCCGAATATCCCGGGCTACACGCGGGCTACAATGGACAGGACAATGGGTAACAACACCGAG
+AGGTGAAGTTAATCTCTTAAACCTGTCCCTAGTTCGGATTGAGGGCTGAAACCCGCCCTCATGAAGATGG
+AATCCGTAGTAATCGCATTTCAAAACAGTGCGGTGAATACGTCCCTGCTCCTTGCACACACCGCCCGTCA
+AACCACCCGAGCGGGGCGTGAATAAGGACTCTTTTCCTTGAAGAGCTCGAATTCACGTTCTGTAAGGGGG
+GTTAAGTCGTAACAAGGTAGCC

data/test/data/Ipcress/Methanocella_conradii_16s_twice.fa

@@ -0,0 +1,43 @@
+>gi|335929284|gb|JN048683.1| Methanocella conradii HZ254 16S ribosomal RNA gene, partial sequence
+GGTCACTGCTATCGGTGTCCGATTAAGCCATGCGAGTCGTGAGGGGTGAGCCCTCGGCGTACTGCTCAGT
+AACACGTGGACAATCTGCCCAAAAGTCCGGGATAACCCCGGGAAACTGGGGATAATACCGGATAGGCCAC
+CAATTGCTGGAATGGCCTGGTGGTTGAAACGAGAGGCTTTTGGATGGGTCTGCGGCGGATTAGGTTGACG
+CCGGTGTAACGTACCGGCGTGCCTGTAATCCGTACGGGTTGTGGGAGCAAGAGCCCGGAGATGGATTCTG
+AGACACGAATCCAGGCCCTACGGGGCGCAGCAGGCGCGAAAACTCTACAATGCAGGCAATCTGCGATAGG
+GGGACATCGAGTGGCATCTTCTTAAGGTGCCTGTCCAACCGTCTAAAAAACGGTTGTTAGCAAGGGCCGG
+GTAAGACCGGTGCCAGCCGCCGCGGTAATACCGGCGGCTCGAGTGGTGGCCGATATTATTGAGTCTAAAG
+GGTCCGTAGCCGGCTTTGCAAGTCCCCTGGGAAATCCAGCGGCTTAACCGTTGGGCGCCCATGGGATACT
+ACATTGCTTGGGACTGGGAGAGGCGAGAGGTACTCGAGGGGTAGGGGTGAAATCCTGTAATCCTTCGGGG
+ACCACCGGTGGCGAAGGCGTCTCGCCAGAACAGGTCCGACGGTGAGGGACGAAAGCTAGGGGCACGAACC
+GGATTAGATACCCGGGTAGTCCTAGCCGTAAACGATGCCCGCTAGGTGTCACGATAATCGTGAATTATCG
+TGGTGCCGTAGGGAAGCCGCGAAGCGGGCCACTTGGGAAGTACGACCGCAAGGTTGAAACTTAAAGGAAT
+TGGCGGGGGAGCACCACAACGGGTGGAGCCTGCGGTTTAATTGGATTCAACGCCGGGAAGCTTACCGGGA
+TCGACAGTTGAATGAAGGCCAGGCCGAAGACCTTGCCGGACTAGCTGAGAGGAGGTGCATGGCCGTCGTC
+AGTTCGTACCGTGAGGCGTCCTGTTAAGTCAGGCAACGAGCGAGACCCATGTCCACTGTTGCTAACGCGT
+CCGCGAGGACGGCGAGTACACTGTGGAGACTGCTGGCGCTAAGTCAGAGGAAGGGTTGGTCGACGGTAGG
+TCAGTATGCCCCGAATATCCCGGGCTACACGCGGGCTACAATGGACAGGACAATGGGTAACAACACCGAG
+AGGTGAAGTTAATCTCTTAAACCTGTCCCTAGTTCGGATTGAGGGCTGAAACCCGCCCTCATGAAGATGG
+AATCCGTAGTAATCGCATTTCAAAACAGTGCGGTGAATACGTCCCTGCTCCTTGCACACACCGCCCGTCA
+AACCACCCGAGCGGGGCGTGAATAAGGACTCTTTTCCTTGAAGAGCTCGAATTCACGTTCTGTAAGGGGG
+GTTAAGTCGTAACAAGGTAGCC
+GGTCACTGCTATCGGTGTCCGATTAAGCCATGCGAGTCGTGAGGGGTGAGCCCTCGGCGTACTGCTCAGT
+AACACGTGGACAATCTGCCCAAAAGTCCGGGATAACCCCGGGAAACTGGGGATAATACCGGATAGGCCAC
+CAATTGCTGGAATGGCCTGGTGGTTGAAACGAGAGGCTTTTGGATGGGTCTGCGGCGGATTAGGTTGACG
+CCGGTGTAACGTACCGGCGTGCCTGTAATCCGTACGGGTTGTGGGAGCAAGAGCCCGGAGATGGATTCTG
+AGACACGAATCCAGGCCCTACGGGGCGCAGCAGGCGCGAAAACTCTACAATGCAGGCAATCTGCGATAGG
+GGGACATCGAGTGGCATCTTCTTAAGGTGCCTGTCCAACCGTCTAAAAAACGGTTGTTAGCAAGGGCCGG
+GTAAGACCGGTGCCAGCCGCCGCGGTAATACCGGCGGCTCGAGTGGTGGCCGATATTATTGAGTCTAAAG
+GGTCCGTAGCCGGCTTTGCAAGTCCCCTGGGAAATCCAGCGGCTTAACCGTTGGGCGCCCATGGGATACT
+ACATTGCTTGGGACTGGGAGAGGCGAGAGGTACTCGAGGGGTAGGGGTGAAATCCTGTAATCCTTCGGGG
+ACCACCGGTGGCGAAGGCGTCTCGCCAGAACAGGTCCGACGGTGAGGGACGAAAGCTAGGGGCACGAACC
+GGATTAGATACCCGGGTAGTCCTAGCCGTAAACGATGCCCGCTAGGTGTCACGATAATCGTGAATTATCG
+TGGTGCCGTAGGGAAGCCGCGAAGCGGGCCACTTGGGAAGTACGACCGCAAGGTTGAAACTTAAAGGAAT
+TGGCGGGGGAGCACCACAACGGGTGGAGCCTGCGGTTTAATTGGATTCAACGCCGGGAAGCTTACCGGGA
+TCGACAGTTGAATGAAGGCCAGGCCGAAGACCTTGCCGGACTAGCTGAGAGGAGGTGCATGGCCGTCGTC
+AGTTCGTACCGTGAGGCGTCCTGTTAAGTCAGGCAACGAGCGAGACCCATGTCCACTGTTGCTAACGCGT
+CCGCGAGGACGGCGAGTACACTGTGGAGACTGCTGGCGCTAAGTCAGAGGAAGGGTTGGTCGACGGTAGG
+TCAGTATGCCCCGAATATCCCGGGCTACACGCGGGCTACAATGGACAGGACAATGGGTAACAACACCGAG
+AGGTGAAGTTAATCTCTTAAACCTGTCCCTAGTTCGGATTGAGGGCTGAAACCCGCCCTCATGAAGATGG
+AATCCGTAGTAATCGCATTTCAAAACAGTGCGGTGAATACGTCCCTGCTCCTTGCACACACCGCCCGTCA
+AACCACCCGAGCGGGGCGTGAATAAGGACTCTTTTCCTTGAAGAGCTCGAATTCACGTTCTGTAAGGGGG
+GTTAAGTCGTAACAAGGTAGCC

data/test/data/Ipcress/input1.txt

@@ -0,0 +1 @@
+AE12_pmid21856836_16S AAACTYAAAKGAATTGRCGG ACGGGCGGTGTGTRC 2 10000

data/test/data/Ipcress/input1_with_insert.txt

@@ -0,0 +1 @@
+AE12_pmid21856836_16S AAACTYAAAAKGAATTGRCGG ACGGGCGGTGTGTRC 2 10000

data/test/data/Ipcress/input2.txt

@@ -0,0 +1,2 @@
+AE12_pmid21856836_16S_1 AAACTYAAAKGAATTGRCGG ACGGGCGGTGTGTRC 2 10000
+AE12_pmid21856836_16S_mismatch AATCTYAAAKGAATTGRCGG ACGGGCGGTGTGTRC 2 10000

data/test/helper.rb

@@ -0,0 +1,21 @@
+require 'rubygems'
+require 'bundler'
+begin
+  Bundler.setup(:default, :development)
+rescue Bundler::BundlerError => e
+  $stderr.puts e.message
+  $stderr.puts "Run `bundle install` to install missing gems"
+  exit e.status_code
+end
+require 'test/unit'
+require 'shoulda'
+
+$LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
+$LOAD_PATH.unshift(File.dirname(__FILE__))
+require 'bio-ipcress'
+
+class Test::Unit::TestCase
+end
+
+
+DATA_DIR = File.join(File.dirname(__FILE__), 'data','Ipcress')

data/test/test_bio-ipcress.rb

@@ -0,0 +1,178 @@
+require 'helper'
+require 'stringio'
+
+class TestBioIpcress < Test::Unit::TestCase
+  should "test 1 result" do
+    ipcress = "
+Ipcress result
+--------------
+ Experiment: AE12_pmid21856836_16S
+    Primers: A B
+     Target: gi|335929284|gb|JN048683.1|:filter(unmasked) Methanocella conradii HZ254 16S ribosomal RNA gene, partial sequence
+    Matches: 19/20 14/15
+    Product: 502 bp (range 2-10000)
+Result type: forward
+
+...AAACTTAAAGGAATTGGCGG......................... # forward
+   ||||| ||| |||||| |||-->
+5'-AAACTYAAAKGAATTGRCGG-3' 3'-CRTGTGTGGCGGGCA-5' # primers
+                           <--| |||||||||||||
+..............................CGTGTGTGGCGGGCA... # revcomp
+--
+ipcress: gi|335929284|gb|JN048683.1|:filter(unmasked) AE12_pmid21856836_16S 502 A 826 1 B 1313 1 forward
+-- completed ipcress analysis"
+    results = Bio::Ipcress.parse(ipcress)
+    assert_equal 1, results.length
+    res = results[0]
+    assert_equal 'AE12_pmid21856836_16S', res.experiment_name
+    assert_equal 'A B', res.primers
+    assert_equal 'gi|335929284|gb|JN048683.1|:filter(unmasked) Methanocella conradii HZ254 16S ribosomal RNA gene, partial sequence',
+      res.target
+    assert_equal '19/20 14/15', res.matches
+    assert_equal '502 bp (range 2-10000)', res.product
+    assert_equal 'forward', res.result_type
+    assert_equal 'AAACTTAAAGGAATTGGCGG', res.forward_matching_sequence
+    assert_equal 'AAACTYAAAKGAATTGRCGG', res.forward_primer_sequence
+    assert_equal 'CRTGTGTGGCGGGCA', res.reverse_primer_sequence
+    assert_equal 'CGTGTGTGGCGGGCA', res.reverse_matching_sequence
+    assert_equal 502, res.length
+    assert_equal 826, res.start
+    assert_equal 1, res.forward_mismatches
+    assert_equal 1, res.reverse_mismatches
+  end
+
+  should "test multi-experiment results" do
+    ipcress = "
+Ipcress result
+--------------
+ Experiment: AE12_pmid21856836_16S
+    Primers: B B
+     Target: gi|335929284|gb|JN048683.1|:filter(unmasked) Methanocella conradii HZ254 16S ribosomal RNA gene, partial sequence
+    Matches: 10/15 14/15
+    Product: 1085 bp (range 2-10000)
+Result type: single_B
+
+...ACGGGTTGTGGGAGC......................... # forward
+   |||||  ||| |  |-->
+5'-ACGGGCGGTGTGTRC-3' 3'-CRTGTGTGGCGGGCA-5' # primers
+                      <--| |||||||||||||
+.........................CGTGTGTGGCGGGCA... # revcomp
+--
+ipcress: gi|335929284|gb|JN048683.1|:filter(unmasked) AE12_pmid21856836_16S 1085 B 243 5 B 1313 1 single_B
+
+Ipcress result
+--------------
+ Experiment: AE12_pmid21856836_16S
+    Primers: A B
+     Target: gi|335929284|gb|JN048683.1|:filter(unmasked) Methanocella conradii HZ254 16S ribosomal RNA gene, partial sequence
+    Matches: 16/21 14/15
+    Product: 503 bp (range 2-10000)
+Result type: forward
+
+...GAAACTTAAAGGAATTGGCGG......................... # forward
+    ||    ||| |||||| |||-->
+5'-AAACTYAAAAKGAATTGRCGG-3' 3'-CRTGTGTGGCGGGCA-5' # primers
+                            <--| |||||||||||||
+...............................CGTGTGTGGCGGGCA... # revcomp
+--
+ipcress: gi|335929284|gb|JN048683.1|:filter(unmasked) AE12_pmid21856836_16S 503 A 825 5 B 1313 1 forward
+
+Ipcress result
+--------------
+ Experiment: AE12_pmid21856836_16S
+    Primers: B B
+     Target: gi|335929284|gb|JN048683.1|:filter(unmasked) Methanocella conradii HZ254 16S ribosomal RNA gene, partial sequence
+    Matches: 10/15 14/15
+    Product: 470 bp (range 2-10000)
+Result type: single_B
+
+...ACGGGTGGAGCCTGC......................... # forward
+   ||||| || |  | |-->
+5'-ACGGGCGGTGTGTRC-3' 3'-CRTGTGTGGCGGGCA-5' # primers
+                      <--| |||||||||||||
+.........................CGTGTGTGGCGGGCA... # revcomp
+--
+ipcress: gi|335929284|gb|JN048683.1|:filter(unmasked) AE12_pmid21856836_16S 470 B 858 5 B 1313 1 single_B
+-- completed ipcress analysis
+"
+    results = Bio::Ipcress.parse(ipcress)
+    assert_equal 3, results.length
+    assert_equal 5, results[0].forward_mismatches
+  end
+
+  should "test recalculation of matches" do
+    res = Bio::Ipcress::Result.new
+
+    #...AAACTTAAAGGAATTGGCGG......................... # forward
+    #   ||||| ||| |||||| |||-->
+    #5'-AAACTYAAAKGAATTGRCGG-3' 3'-CRTGTGTGGCGGGCA-5' # primers
+    #                           <--| |||||||||||||
+    #..............................CGTGTGTGGCGGGCA... # revcomp
+    res.forward_matching_sequence = 'AAACTTAAAGGAATTGGCGG'
+    res.forward_primer_sequence = 'AAACTYAAAKGAATTGRCGG'
+    res.reverse_matching_sequence = 'CGTGTGTGGCGGGCA'
+    res.reverse_primer_sequence = 'CRTGTGTGGCGGGCA'
+    assert_equal [0,0], res.recalculate_mismatches_from_alignments
+
+    res.reverse_primer_sequence = 'CRTGTGTGGCGGGCT'
+    assert_equal [0,1], res.recalculate_mismatches_from_alignments
+
+    res.forward_primer_sequence = 'AAACTRAAAKGAATTGRCGG'
+    res.reverse_primer_sequence = 'CRTGTGTGGCGGGCA'
+    assert_equal [1,0], res.recalculate_mismatches_from_alignments, "mismatching wobble R"
+  end
+
+  should "primer set to ipcress format" do
+    primer_set = Bio::Ipcress::PrimerSet.new('AAT','GTG')
+
+    assert_equal 'ID1 AAT GTG 100 1000', primer_set.to_ipcress_format
+    assert_equal 'ID1 AAT GTG 3 700', primer_set.to_ipcress_format({:min_distance => 3, :max_distance => 700})
+  end
+
+  should "run ipcress ok" do
+    primer_set = Bio::Ipcress::PrimerSet.new('GGTCACTGCTA','GGCTACCTTGTTACGACTTAAC') #the first and last bits of the Methanocella_conradii_16s.fa
+    results = Bio::Ipcress.run(primer_set, File.join(DATA_DIR, 'Methanocella_conradii_16s.fa'), {:min_distance => 2, :max_distance => 10000})
+    assert_equal 1, results.length
+    assert_equal 'ID1', results[0].experiment_name
+  end
+
+  should "return empty array when ipcress finds nadda" do
+    primer_set = Bio::Ipcress::PrimerSet.new('AAAAAAAAAAAAAAAA','TTTTTTTTTTTTTTTTT') #the first and last bits of the Methanocella_conradii_16s.fa
+    results = Bio::Ipcress.run(primer_set, File.join(DATA_DIR, 'Methanocella_conradii_16s.fa'))
+    assert_kind_of Array, results
+    assert_equal 0, results.length
+  end
+
+  # This test is handled by bioruby's Bio::Command, so eh
+  # should "raise exception when there is a problem running ipcress" do
+  # primer_set = Bio::Ipcress::PrimerSet.new('AAAAAAAAAAAAAAAA','TTTTTTTTTTTTTTTTT') #the first and last bits of the Methanocella_conradii_16s.fa
+  # assert_raise RuntimeError do
+  # Bio::Ipcress.run(primer_set, File.join(DATA_DIR, 'Methanocella_conradii_16s.fa'), :ipcress_path => 'not_ipcress')
+  # end
+  # end
+  
+  should "run should complain about bad inputs" do
+    assert_raise RuntimeError do
+      Bio::Ipcress.run(nil, 'abc.fa')
+    end
+    assert_raise RuntimeError do
+      Bio::Ipcress.run(Bio::Ipcress::PrimerSet.new('GGTCACTGCTA','GGCTACCTTGTTACGACTTAAC'), [])
+    end
+  end
+  
+  should "run sensibly when the fasta file is not found" do
+    assert_raise RuntimeError do
+      Bio::Ipcress.run(Bio::Ipcress::PrimerSet.new('GGTCACTGCTA','GGCTACCTTGTTACGACTTAAC'), 'notafasta_file_fo_so.fa')
+    end
+  end
+  
+  should "run with multiple hits" do
+    primer_set = Bio::Ipcress::PrimerSet.new('GGTCACTGCTA','GGCTACCTTGTTACGACTTAAC') #the first and last bits of the Methanocella_conradii_16s.fa
+    results = Bio::Ipcress.run(primer_set, File.join(DATA_DIR, 'Methanocella_conradii_16s_2_sequences.fa'), {:min_distance => 2, :max_distance => 10000})
+    assert_equal 2, results.length
+    assert_equal 'ID1', results[0].experiment_name
+    assert_equal 'gi|335929284|gb|JN048683.1|:filter(unmasked) Methanocella conradii HZ254 16S ribosomal RNA gene, partial sequence', results[0].target
+    assert_equal '2nd:filter(unmasked)', results[1].target
+  end
+
+end

metadata

@@ -0,0 +1,145 @@
+--- !ruby/object:Gem::Specification
+name: bio-ipcress
+version: !ruby/object:Gem::Version
+  version: 0.0.1
+  prerelease: 
+platform: ruby
+authors:
+- Ben J Woodcroft
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2012-08-08 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: bio
+  requirement: &72407200 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 1.4.2
+  type: :runtime
+  prerelease: false
+  version_requirements: *72407200
+- !ruby/object:Gem::Dependency
+  name: shoulda
+  requirement: &72406750 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: *72406750
+- !ruby/object:Gem::Dependency
+  name: rdoc
+  requirement: &72406370 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '3.12'
+  type: :development
+  prerelease: false
+  version_requirements: *72406370
+- !ruby/object:Gem::Dependency
+  name: jeweler
+  requirement: &72406020 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.8.3
+  type: :development
+  prerelease: false
+  version_requirements: *72406020
+- !ruby/object:Gem::Dependency
+  name: bundler
+  requirement: &72405780 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 1.0.21
+  type: :development
+  prerelease: false
+  version_requirements: *72405780
+- !ruby/object:Gem::Dependency
+  name: bio
+  requirement: &72405540 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 1.4.2
+  type: :development
+  prerelease: false
+  version_requirements: *72405540
+- !ruby/object:Gem::Dependency
+  name: rdoc
+  requirement: &72405300 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '3.12'
+  type: :development
+  prerelease: false
+  version_requirements: *72405300
+description: a programmatic interface to the iPCRess in-silico PCR software. iPCRess
+  is part of the exonerate suite.
+email: gmail.com after donttrustben
+executables: []
+extensions: []
+extra_rdoc_files:
+- LICENSE.txt
+- README.md
+files:
+- .document
+- .travis.yml
+- Gemfile
+- LICENSE.txt
+- README.md
+- Rakefile
+- VERSION
+- lib/bio-ipcress.rb
+- lib/bio/appl/ipcress.rb
+- test/data/Ipcress/Methanocella_conradii_16s.fa
+- test/data/Ipcress/Methanocella_conradii_16s_2_sequences.fa
+- test/data/Ipcress/Methanocella_conradii_16s_twice.fa
+- test/data/Ipcress/input1.txt
+- test/data/Ipcress/input1_with_insert.txt
+- test/data/Ipcress/input2.txt
+- test/helper.rb
+- test/test_bio-ipcress.rb
+homepage: http://github.com/wwood/bioruby-ipcress
+licenses:
+- MIT
+post_install_message: 
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  none: false
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+      segments:
+      - 0
+      hash: 237777805
+required_rubygems_version: !ruby/object:Gem::Requirement
+  none: false
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubyforge_project: 
+rubygems_version: 1.8.17
+signing_key: 
+specification_version: 3
+summary: a programmatic interface to the iPCRess in-silico PCR software
+test_files: []