bio-synreport 0.1.0

data/Gemfile

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+source "http://rubygems.org"
+# Add dependencies required to use your gem here.
+# Example:
+#   gem "activesupport", ">= 2.3.5"
+
+# Add dependencies to develop your gem here.
+# Include everything needed to run rake, tests, features, etc.
+group :development do
+  gem "shoulda", ">= 0"
+  gem "bundler", "~> 1.0.0"
+  gem "jeweler", "~> 1.6.4"
+  gem "rcov", ">= 0"
+  gem "bio", ">= 1.4.2"
+end

data/Gemfile.lock

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+GEM
+  remote: http://rubygems.org/
+  specs:
+    activesupport (3.2.9)
+      i18n (~> 0.6)
+      multi_json (~> 1.0)
+    bio (1.4.3)
+    git (1.2.5)
+    i18n (0.6.1)
+    jeweler (1.6.4)
+      bundler (~> 1.0)
+      git (>= 1.2.5)
+      rake
+    multi_json (1.3.7)
+    rake (10.0.2)
+    rcov (1.0.0)
+    shoulda (3.3.2)
+      shoulda-context (~> 1.0.1)
+      shoulda-matchers (~> 1.4.1)
+    shoulda-context (1.0.1)
+    shoulda-matchers (1.4.1)
+      activesupport (>= 3.0.0)
+
+PLATFORMS
+  ruby
+
+DEPENDENCIES
+  bio (>= 1.4.2)
+  bundler (~> 1.0.0)
+  jeweler (~> 1.6.4)
+  rcov
+  shoulda

data/LICENSE.txt

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+Copyright (c) 2012 Dan MacLean
+
+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.rdoc

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+= bio-synreport
+
+Description goes here.
+
+== Contributing to bio-synreport
+ 
+* Check out the latest master to make sure the feature hasn't been implemented or the bug hasn't been fixed yet
+* Check out the issue tracker to make sure someone already hasn't requested it and/or contributed it
+* Fork the project
+* Start a feature/bugfix branch
+* Commit and push until you are happy with your contribution
+* Make sure to add tests for it. This is important so I don't break it in a future version unintentionally.
+* Please try not to mess with the Rakefile, version, or history. If you want to have your own version, or is otherwise necessary, that is fine, but please isolate to its own commit so I can cherry-pick around it.
+
+== Copyright
+
+Copyright (c) 2012 Dan MacLean. 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-synreport"
+  gem.homepage = "http://github.com/danmaclean/bioruby-synreport"
+  gem.license = "MIT"
+  gem.summary = %Q{Reports whether a nucleotide change results in synonymous or non-synonymous mutations}
+  gem.description = %Q{Takes a GFF and genomic sequence file, constructs CDS and when given a position and alternative base will report whether this change is in a coding region and if it results in a synonymous or non-synonymous mutation.}
+  gem.email = "maclean.daniel@gmail.com"
+  gem.authors = ["Dan MacLean"]
+  # 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
+
+require 'rcov/rcovtask'
+Rcov::RcovTask.new do |test|
+  test.libs << 'test'
+  test.pattern = 'test/**/test_*.rb'
+  test.verbose = true
+  test.rcov_opts << '--exclude "gems/*"'
+end
+
+task :default => :test
+
+require 'rake/rdoctask'
+Rake::RDocTask.new do |rdoc|
+  version = File.exist?('VERSION') ? File.read('VERSION') : ""
+
+  rdoc.rdoc_dir = 'rdoc'
+  rdoc.title = "bio-synreport #{version}"
+  rdoc.rdoc_files.include('README*')
+  rdoc.rdoc_files.include('lib/**/*.rb')
+end

data/VERSION

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+0.1.0

data/bio-synreport.gemspec

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+# Generated by jeweler
+# DO NOT EDIT THIS FILE DIRECTLY
+# Instead, edit Jeweler::Tasks in Rakefile, and run 'rake gemspec'
+# -*- encoding: utf-8 -*-
+
+Gem::Specification.new do |s|
+  s.name = "bio-synreport"
+  s.version = "0.1.0"
+
+  s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
+  s.authors = ["Dan MacLean"]
+  s.date = "2012-11-21"
+  s.description = "Takes a GFF and genomic sequence file, constructs CDS and when given a position and alternative base will report whether this change is in a coding region and if it results in a synonymous or non-synonymous mutation."
+  s.email = "maclean.daniel@gmail.com"
+  s.extra_rdoc_files = [
+    "LICENSE.txt",
+    "README.rdoc"
+  ]
+  s.files = [
+    "Gemfile",
+    "Gemfile.lock",
+    "LICENSE.txt",
+    "README.rdoc",
+    "Rakefile",
+    "VERSION",
+    "bio-synreport.gemspec",
+    "examples/test.rb",
+    "lib/bio-synreport.rb",
+    "lib/bio/utils/bio-synreport.rb",
+    "test/helper.rb",
+    "test/test_bio-synreport.rb"
+  ]
+  s.homepage = "http://github.com/danmaclean/bioruby-synreport"
+  s.licenses = ["MIT"]
+  s.require_paths = ["lib"]
+  s.rubygems_version = "1.8.11"
+  s.summary = "Reports whether a nucleotide change results in synonymous or non-synonymous mutations"
+
+  if s.respond_to? :specification_version then
+    s.specification_version = 3
+
+    if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
+      s.add_development_dependency(%q<shoulda>, [">= 0"])
+      s.add_development_dependency(%q<bundler>, ["~> 1.0.0"])
+      s.add_development_dependency(%q<jeweler>, ["~> 1.6.4"])
+      s.add_development_dependency(%q<rcov>, [">= 0"])
+      s.add_development_dependency(%q<bio>, [">= 1.4.2"])
+    else
+      s.add_dependency(%q<shoulda>, [">= 0"])
+      s.add_dependency(%q<bundler>, ["~> 1.0.0"])
+      s.add_dependency(%q<jeweler>, ["~> 1.6.4"])
+      s.add_dependency(%q<rcov>, [">= 0"])
+      s.add_dependency(%q<bio>, [">= 1.4.2"])
+    end
+  else
+    s.add_dependency(%q<shoulda>, [">= 0"])
+    s.add_dependency(%q<bundler>, ["~> 1.0.0"])
+    s.add_dependency(%q<jeweler>, ["~> 1.6.4"])
+    s.add_dependency(%q<rcov>, [">= 0"])
+    s.add_dependency(%q<bio>, [">= 1.4.2"])
+  end
+end
+

data/examples/test.rb

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+$LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
+$LOAD_PATH.unshift(File.dirname(__FILE__))
+
+
+  
+  require 'bio-synreport'
+  require 'pp'
+  
+  #this is how you use it... no really! 
+  
+  db = Bio::Util::SynReport.new(:gff => ARGV[0], :fasta => ARGV[1], :verbose => true)
+  chr, pos, ref,alt = 'Chr2',7634495, 'a', 't'
+  pp db.mutation_info(chr,pos,alt) 
+  
+  chr, pos, ref,alt = 'Chr3',123456, 'a', 't'
+  pp db.mutation_info(chr,pos,alt)
+  
+    chr, pos, ref,alt = 'Chr2',7626518, 'a', 't'
+  pp db.mutation_info(chr,pos,alt) 

data/lib/bio-synreport.rb

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+# Please require your code below, respecting the bioruby directory tree. 
+# For instance, perhaps the only uncommented line in this file might 
+# be something like this:
+#
+#   require 'bio/sequence/awesome_sequence_plugin_thingy'
+#
+# and then create the ruby file 'lib/bio/sequence/awesome_sequence_thingy.rb'
+# and put your plugin's code there. It is bad practice to write other code 
+# directly into this file, because doing so causes confusion if this biogem 
+# was ever to get merged into the main bioruby tree.
+
+require 'bio/utils/bio-synreport'

data/lib/bio/utils/bio-synreport.rb

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+require 'rubygems'
+require 'pp'
+require 'bio'
+
+module Bio
+  class Util
+    
+    class MrnaModel
+      attr_accessor :seqname, :gff_id, :strand, :cds, :sequences
+  
+      def initialize(chr, id, strand, cds_arr, seq_arr)
+        @seqname, @gff_id, @strand, @cds, @sequences = chr, id, strand, cds_arr, seq_arr
+      end
+  
+      def includes?(seq, point)
+        @cds.each {|start, stop| return true if @seqname == seq and point.to_i >= start and point.to_i <= stop}
+        false
+      end
+  
+      def seq
+        @sequences.join
+      end
+  
+      def substitution_info(chr,point,alt)
+        cds_start = @cds.first.first
+        running_total = 0
+        @cds.each do |start,stop|
+          if point.to_i >= start and point.to_i <= stop
+            offset = case @strand
+            when "+"
+              #offset = 
+              (point.to_i - start) + running_total
+            when "-"
+              (stop - point.to_i) + running_total 
+            end  #offset = how far into cds SNP is
+            codon_number = offset / 3
+            position_in_codon = offset % 3
+            #pp [offset, codon_number, position_in_codon] 
+            codon_array = []; Bio::Sequence::NA.new(self.seq).window_search(3,3) {|b| codon_array << b}
+            codon = codon_array[codon_number]
+            nt = codon[position_in_codon]
+            new_codon = codon.dup
+            new_codon[position_in_codon] = alt.downcase
+            #pp [codon, position_in_codon, nt, new_codon]
+            a = Bio::Sequence::NA.new(codon).translate.codes.first
+            b =  Bio::Sequence::NA.new(new_codon).translate.codes.first
+            sub_type = a == b ? "SYN" : "NON_SYN"
+            return {:id => @gff_id, 
+                    :chr => @seqname, 
+                    :strand => @strand, 
+                    :position => point,
+                    :original_codon => codon, 
+                    :original_residue => a || 'stop', 
+                    :mutant_codon => new_codon, 
+                    :mutant_residue =>b || 'stop', 
+                    :position_in_codon => position_in_codon + 1, 
+                    :substitution_type => sub_type
+                    }
+          end
+          running_total += (stop - start)
+          running_total += 1 if @strand == '-' #how far we are into the cds
+        end
+      end
+      
+    end#class end
+    
+    
+    class SynReport
+      #attr_accessor :cdshash, :cds_list, :mRNAhash, :seqhash
+      
+      def initialize(opts)
+        @gene_array = []
+        @cdshash = Hash.new {|h,k| h[k] = Hash.new {|a,b| a[b] = [] } }
+        @mRNAhash = Hash.new {|h,k| h[k] = Hash.new {|a,b| a[b] = [] } }
+        File.open(opts[:gff], "r").each do |gffline|
+          record=Bio::GFF::GFF3::Record.new(gffline)
+          if(record.feature_type == 'gene')
+              @gene_array << [record.seqname, record.id]
+          elsif(record.feature_type == 'CDS' or record.feature_type == 'mRNA')
+            parents = record.get_attributes('Parent')
+            parents.each do |parent|  
+              if record.feature_type == 'CDS'
+                @cdshash[record.seqname][parent] << record
+              else
+                @mRNAhash[record.seqname][parent] << record
+              end
+            end
+          end
+        end
+        $stderr.puts "Loaded GFF..." if opts[:verbose]
+        @seqhash = {}
+        Bio::FastaFormat.open(opts[:fasta]).each { |seq| @seqhash[seq.entry_id] = seq.to_seq }
+        $stderr.puts "Loaded Seq..." if opts[:verbose]
+        
+        @models = Hash.new {|h,k| h[k] =  []  }
+        $stderr.puts "Building models..." if opts[:verbose] 
+        @gene_array.each do |gene|
+
+          mRNAs=@mRNAhash[gene.first][gene.last]
+          mRNAs.each do |mRNA|
+            next if @seqhash[gene.first].nil?
+            cdsa = []
+            seqs = []
+            cdsary=@cdshash[gene.first][mRNA.id]
+            cdsary.each {|c| cdsa << [c.start, c.end]} 
+            cdsa.sort!
+            cdsa.reverse! if mRNA.strand == '-'
+            
+            cdsa.each do |cds|
+
+              #cdsa << [cds.start, cds.end]
+              if mRNA.strand == '+'
+                seqs << Bio::Sequence::NA.new(@seqhash[mRNA.seqname].splicing("#{cds.first}..#{cds.last}") )
+              elsif mRNA.strand == "-"
+                seqs << Bio::Sequence::NA.new(@seqhash[mRNA.seqname].splicing("#{cds.first}..#{cds.last}") ).complement
+              end
+            end
+            @models[mRNA.seqname] << Bio::Util::MrnaModel.new(mRNA.seqname, mRNA.id, mRNA.strand, cdsa, seqs )
+            #pp @models[mRNA.seqname][-1].cds if mRNA.id == 'AT2G17530.1' or mRNA.id == 'AT2G17550.1'
+          end
+        end
+        $stderr.puts "Models built..." if opts[:verbose]
+      end#init end
+        
+        def is_in_cds?(chr,point)
+          @self.mutation_info(chr,point) ? true : false
+        end
+        
+        #returns mutation info if point in CDS, if not in CDS returns false
+        def mutation_info(chr,pos,alt)
+
+          @models[chr].each do |m|
+             if m.includes?(chr,pos)
+               return m.substitution_info(chr,pos,alt)   
+             end
+          end
+          false
+        end
+        
+        
+    end#class end
+  end#class util end
+end# module end

data/test/helper.rb

@@ -0,0 +1,18 @@
+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-synreport'
+
+class Test::Unit::TestCase
+end

data/test/test_bio-synreport.rb

@@ -0,0 +1,7 @@
+require 'helper'
+
+class TestBioSynreport < Test::Unit::TestCase
+  should "probably rename this file and start testing for real" do
+    flunk "hey buddy, you should probably rename this file and start testing for real"
+  end
+end

metadata

@@ -0,0 +1,152 @@
+--- !ruby/object:Gem::Specification 
+name: bio-synreport
+version: !ruby/object:Gem::Version 
+  hash: 27
+  prerelease: 
+  segments: 
+  - 0
+  - 1
+  - 0
+  version: 0.1.0
+platform: ruby
+authors: 
+- Dan MacLean
+autorequire: 
+bindir: bin
+cert_chain: []
+
+date: 2012-11-21 00:00:00 Z
+dependencies: 
+- !ruby/object:Gem::Dependency 
+  type: :development
+  prerelease: false
+  requirement: &id001 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        hash: 3
+        segments: 
+        - 0
+        version: "0"
+  version_requirements: *id001
+  name: shoulda
+- !ruby/object:Gem::Dependency 
+  type: :development
+  prerelease: false
+  requirement: &id002 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ~>
+      - !ruby/object:Gem::Version 
+        hash: 23
+        segments: 
+        - 1
+        - 0
+        - 0
+        version: 1.0.0
+  version_requirements: *id002
+  name: bundler
+- !ruby/object:Gem::Dependency 
+  type: :development
+  prerelease: false
+  requirement: &id003 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ~>
+      - !ruby/object:Gem::Version 
+        hash: 7
+        segments: 
+        - 1
+        - 6
+        - 4
+        version: 1.6.4
+  version_requirements: *id003
+  name: jeweler
+- !ruby/object:Gem::Dependency 
+  type: :development
+  prerelease: false
+  requirement: &id004 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        hash: 3
+        segments: 
+        - 0
+        version: "0"
+  version_requirements: *id004
+  name: rcov
+- !ruby/object:Gem::Dependency 
+  type: :development
+  prerelease: false
+  requirement: &id005 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        hash: 3
+        segments: 
+        - 1
+        - 4
+        - 2
+        version: 1.4.2
+  version_requirements: *id005
+  name: bio
+description: Takes a GFF and genomic sequence file, constructs CDS and when given a position and alternative base will report whether this change is in a coding region and if it results in a synonymous or non-synonymous mutation.
+email: maclean.daniel@gmail.com
+executables: []
+
+extensions: []
+
+extra_rdoc_files: 
+- LICENSE.txt
+- README.rdoc
+files: 
+- Gemfile
+- Gemfile.lock
+- LICENSE.txt
+- README.rdoc
+- Rakefile
+- VERSION
+- bio-synreport.gemspec
+- examples/test.rb
+- lib/bio-synreport.rb
+- lib/bio/utils/bio-synreport.rb
+- test/helper.rb
+- test/test_bio-synreport.rb
+homepage: http://github.com/danmaclean/bioruby-synreport
+licenses: 
+- MIT
+post_install_message: 
+rdoc_options: []
+
+require_paths: 
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement 
+  none: false
+  requirements: 
+  - - ">="
+    - !ruby/object:Gem::Version 
+      hash: 3
+      segments: 
+      - 0
+      version: "0"
+required_rubygems_version: !ruby/object:Gem::Requirement 
+  none: false
+  requirements: 
+  - - ">="
+    - !ruby/object:Gem::Version 
+      hash: 3
+      segments: 
+      - 0
+      version: "0"
+requirements: []
+
+rubyforge_project: 
+rubygems_version: 1.8.11
+signing_key: 
+specification_version: 3
+summary: Reports whether a nucleotide change results in synonymous or non-synonymous mutations
+test_files: []
+