bio-stockholm 0.0.1

data/.document

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

data/.rspec

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+--color

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"
+
+# Add dependencies to develop your gem here.
+# Include everything needed to run rake, tests, features, etc.
+group :development do
+  gem "rspec", "~> 2.8.0"
+  gem "rdoc", "~> 3.12"
+  gem "jeweler", "~> 1.8.4"
+  gem "bundler", ">= 1.0.21"
+  gem "bio", ">= 1.4.2"
+  gem "rdoc", "~> 3.12"
+end

data/LICENSE.txt

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+Copyright (c) 2013 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-stockholm
+
+[![Build Status](https://secure.travis-ci.org/wwood/bioruby-stockholm.png)](http://travis-ci.org/wwood/bioruby-stockholm)
+
+Stockholm format file parser for ruby.
+
+## Installation
+
+```sh
+gem install bio-stockholm
+```
+
+## Usage
+
+An example stockholm format file, from https://en.wikipedia.org/wiki/Stockholm_format
+```
+# STOCKHOLM 1.0
+#=GF ID CBS1
+#=GF AC PF00571
+#=GF DE CBS domain
+#=GF AU Bateman A
+#=GF CC CBS domains are small intracellular modules mostly found
+#=GF CC in 2 or four copies within a protein.
+#=GF SQ 5
+#=GS O31698/18-71 AC O31698
+#=GS O83071/192-246 AC O83071
+#=GS O83071/259-312 AC O83071
+#=GS O31698/88-139 AC O31698
+#=GS O31698/88-139 OS Bacillus subtilis
+O83071/192-246          MTCRAQLIAVPRASSLAEAIACAQKMRVSRVPVYERS
+#=GR O83071/192-246 SA  9998877564535242525515252536463774777
+O83071/259-312          MQHVSAPVFVFECTRLAYVQHKLRAHSRAVAIVLDEY
+#=GR O83071/259-312 SS  CCCCCHHHHHHHHHHHHHEEEEEEEEEEEEEEEEEEE
+O31698/18-71            MIEADKVAHVQVGNNLEHALLVLTKTGYTAIPVLDPS
+#=GR O31698/18-71 SS    CCCHHHHHHHHHHHHHHHEEEEEEEEEEEEEEEEHHH
+O31698/88-139           EVMLTDIPRLHINDPIMKGFGMVINN..GFVCVENDE
+#=GR O31698/88-139 SS   CCCCCCCHHHHHHHHHHHHEEEEEEEEEEEEEEEEEH
+#=GC SS_cons            CCCCCHHHHHHHHHHHHHEEEEEEEEEEEEEEEEEEH
+O31699/88-139           EVMLTDIPRLHINDPIMKGFGMVINN..GFVCVENDE
+#=GR O31699/88-139 AS   ________________*____________________
+#=GR O31699/88-139 IN   ____________1____________2______0____
+//
+```
+
+```ruby
+require 'bio-stockholm'
+
+entries = Bio::Stockholm::Reader.parse_from_file('spec/data/wikipedia.sto') #=> Array of 1
+
+cbs = entries[0] #=> Bio::Stockholm::Store object
+
+cbs.gf_features['ID'] #=> 'CBS'
+cbs.gf_features['AC'] #=> 'PF00571'
+
+# #=GS O31698/88-139 OS Bacillus subtilis
+cbs.records['O31698/88-139'].gs_features['OS'] #=> 'Bacillus subtilis'
+
+# O83071/192-246          MTCRAQLIAVPRASSLAEAIACAQKMRVSRVPVYERS
+cbs.records['O83071/192-246'].sequence #=> 'MTCRAQLIAVPRASSLAEAIACAQKMRVSRVPVYERS'
+```
+
+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-stockholm
+
+The BioRuby community is on IRC server: irc.freenode.org, channel: #bioruby.
+
+## Cite
+
+This software is currently unpublished.
+
+## Biogems.info
+
+This Biogem is published at (http://biogems.info/index.html#bio-stockholm)
+
+## Copyright
+
+Copyright (c) 2013 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-stockholm"
+  gem.homepage = "http://github.com/wwood/bioruby-stockholm"
+  gem.license = "MIT"
+  gem.summary = %Q{Parse stockholm sequence alignment format}
+  gem.description = %Q{Parses stockholm sequence alignment format}
+  gem.email = "donttrustben near 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(:rcov) do |spec|
+  spec.pattern = 'spec/**/*_spec.rb'
+  spec.rcov = true
+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-stockholm #{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-stockholm.rb

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+# Please require your code below, respecting the naming conventions in the
+# bioruby directory tree.
+#
+# For example, say you have a plugin named bio-plugin, the only uncommented
+# line in this file would be
+#
+#   require 'bio/bio-plugin/plugin'
+#
+# In this file only require other files. Avoid other source code.
+
+require 'bio-stockholm/stockholm.rb'
+

data/lib/bio-stockholm/stockholm.rb

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+
+module Bio
+  module Stockholm
+    class Reader
+      def self.parse_from_file(filename)
+        # # STOCKHOLM 1.0
+        #
+        # #=GS ABK77038.1 DE ammonia monooxygenase subunit A [Cenarchaeum symbiosum A]
+        #
+        # ABK77038.1         --------------------------------------LTMVWLRRCTHY
+        # #=GR ABK77038.1 PP ......................................67889999****
+        # #=GC PP_cons       ......................................67889999****
+        # #=GC RF            xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
+        #
+        # ABK77038.1         LFIAVVAVNSTLLTINAGDYIFYTDWAWTS--F..TVFSISQTLML....
+        # #=GR ABK77038.1 PP **************************9886..4..699********....
+        # #=GC PP_cons       **************************9886..4..699********....
+        # #=GC RF            xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxx....
+        # //
+        state = :first
+        returns = []
+        to_return = Bio::Stockholm::Store.new
+
+        File.open(filename).each_line do |line|
+          next if line.strip.empty? and state == :first_block
+
+          if state == :first
+            unless line == "\# STOCKHOLM 1.0\n"
+              raise FormatException, "Currently unable to parse stockholm format files unless they are version 1.0"
+            end
+            to_return.header = line.strip
+            state = :first_block
+
+          elsif state == :first_block
+            # Match a GR, GS, etc. "markup" line
+            if matches = line.match(/^\#=(..) (\S+)\s+(.*)/)
+              if matches[1] == 'GF'
+                to_return.gf_features ||= {}
+                if to_return.gf_features.key?(matches[2])
+                  to_return.gf_features[matches[2]] = to_return.gf_features[matches[2]]+' '+matches[3]
+                else
+                  to_return.gf_features[matches[2]] = matches[3]
+                end
+              elsif matches[1] == 'GC'
+                to_return.gc_features ||= {}
+                if to_return.gc_features.key?(matches[2])
+                  to_return.gc_features[matches[2]] = to_return.gc_features[matches[2]]+matches[3]
+                else
+                  to_return.gc_features[matches[2]] = matches[3]
+                end
+              else
+                # GS, GR, or bad parsing
+                unless matches2 = matches[3].match(/(.*?)\s+(.*)/)
+                  raise FormatException, "Unable to parse stockholm GS or GR format line: #{line}"
+                end
+                sequence_identifier = matches[2]
+                to_return.records[sequence_identifier] ||= Record.new
+
+                if matches[1] == 'GS'
+                  to_return.records[sequence_identifier].gs_features ||= {}
+
+                  if to_return.records[sequence_identifier].gs_features[matches2[1]]
+                    to_return.records[sequence_identifier].gs_features[matches2[1]] += matches2[2]
+                  else
+                    to_return.records[sequence_identifier].gs_features[matches2[1]] = matches2[2]
+                  end
+                elsif matches[1] == 'GR'
+                  to_return.records[sequence_identifier].gr_features ||= {}
+
+                  if to_return.records[sequence_identifier].gr_features[matches2[1]]
+                    to_return.records[sequence_identifier].gr_features[matches2[1]] += matches2[2]
+                  else
+                    to_return.records[sequence_identifier].gr_features[matches2[1]] = matches2[2]
+                  end
+                else
+                  raise FormatException, "Unable to parse stockholm format line: #{line}"
+                end
+              end
+            elsif line.match(/^\/\//)
+              returns.push to_return
+              to_return = Bio::Stockholm::Store.new
+            else
+              # Else this is just plain old sequence, aligned
+              unless matches = line.match(/^(\S+)\s+(.+)$/)
+                raise FormatException, "Unable to parse stockholm format line: #{line}"
+              end
+              to_return.records[matches[1]] ||= Record.new
+              to_return.records[matches[1]].sequence ||= ''
+              to_return.records[matches[1]].sequence += matches[2].rstrip
+            end
+          end
+        end
+
+        return returns
+      end
+    end
+
+    class Store
+      # '# STOCKHOLM 1.0'
+      attr_accessor :header
+
+      # Array of Record objects, which in turn store sequence, GR and GS features
+      attr_accessor :records
+
+      # GF and GC type features
+      attr_accessor :gc_features, :gf_features
+
+      def initialize
+        @records = {}
+      end
+    end
+
+    class Record
+      # Hash of feature field names to values
+      attr_accessor :gr_features, :gs_features
+
+      attr_accessor :sequence
+    end
+
+    class FormatException < Exception; end
+  end
+end

data/spec/bio-stockholm_spec.rb

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+require File.expand_path(File.dirname(__FILE__) + '/spec_helper')
+
+describe "BioStockholm" do
+  it "should parse a stockholm file 1" do
+    stocks = Bio::Stockholm::Reader.parse_from_file(File.expand_path "#{TEST_DATA_DIR}/test1.sto")
+    stocks.should be_kind_of(Array)
+    stocks.length.should == 1
+    stock = stocks[0]
+    stock.records.length.should == 1
+    stock.records.values[0].sequence.should == '--------------------------------------LTMVWLRRCTHYLFIAVVAVNSTLLTINAGDYIFYTDWAWTS--F..TVFSISQTLML....'
+  end
+
+  it 'should parse a version correctly' do
+    stocks = Bio::Stockholm::Reader.parse_from_file(File.expand_path "#{TEST_DATA_DIR}/test1.sto")
+    stock = stocks[0]
+    stock.header.should == '# STOCKHOLM 1.0'
+  end
+
+  it 'should parse the wikipedia stockholm format entry' do
+    #  # STOCKHOLM 1.0
+    #  #=GF ID CBS
+    #  #=GF AC PF00571
+    #  #=GF DE CBS domain
+    #  #=GF AU Bateman A
+    #  #=GF CC CBS domains are small intracellular modules mostly found
+    #  #=GF CC in 2 or four copies within a protein.
+    #  #=GF SQ 5
+    #  #=GS O31698/18-71 AC O31698
+    #  #=GS O83071/192-246 AC O83071
+    #  #=GS O83071/259-312 AC O83071
+    #  #=GS O31698/88-139 AC O31698
+    #  #=GS O31698/88-139 OS Bacillus subtilis
+    #  O83071/192-246          MTCRAQLIAVPRASSLAEAIACAQKMRVSRVPVYERS
+    #  #=GR O83071/192-246 SA  9998877564535242525515252536463774777
+    #  O83071/259-312          MQHVSAPVFVFECTRLAYVQHKLRAHSRAVAIVLDEY
+    #  #=GR O83071/259-312 SS  CCCCCHHHHHHHHHHHHHEEEEEEEEEEEEEEEEEEE
+    #  O31698/18-71            MIEADKVAHVQVGNNLEHALLVLTKTGYTAIPVLDPS
+    #  #=GR O31698/18-71 SS    CCCHHHHHHHHHHHHHHHEEEEEEEEEEEEEEEEHHH
+    #  O31698/88-139           EVMLTDIPRLHINDPIMKGFGMVINN..GFVCVENDE
+    #  #=GR O31698/88-139 SS   CCCCCCCHHHHHHHHHHHHEEEEEEEEEEEEEEEEEH
+    #  #=GC SS_cons            CCCCCHHHHHHHHHHHHHEEEEEEEEEEEEEEEEEEH
+    #  O31699/88-139           EVMLTDIPRLHINDPIMKGFGMVINN..GFVCVENDE
+    #  #=GR O31699/88-139 AS   ________________*____________________
+    #  #=GR O31699/88-139 IN   ____________1____________2______0____
+    #  //
+    stocks = Bio::Stockholm::Reader.parse_from_file(File.expand_path "#{TEST_DATA_DIR}/wikipedia_test.sto")
+    stocks.should be_kind_of(Array)
+    stocks.length.should == 1
+    stock = stocks[0]
+
+    stock.gf_features['ID'].should == 'CBS'
+    stock.gf_features['DE'].should == 'CBS domain'
+    stock.gf_features['SQ'].should == '5'
+    stock.gf_features.length.should == 6
+    stock.gf_features['CC'].should == 'CBS domains are small intracellular modules mostly found in 2 or four copies within a protein.'
+
+    stock.records['O31698/18-71'].should be_kind_of(Bio::Stockholm::Record)
+    stock.records['O31698/18-71'].gs_features.should be_kind_of(Hash)
+    stock.records['O31698/18-71'].gs_features['AC'].should == 'O31698'
+    stock.records['O31698/88-139'].gs_features['AC'].should == 'O31698'
+    stock.records['O31698/88-139'].gs_features['OS'].should == 'Bacillus subtilis'
+    stock.records['O31698/88-139'].gs_features.length.should == 2
+
+    stock.records.length.should == 5
+    stock.records['O83071/259-312'].sequence.should == 'MQHVSAPVFVFECTRLAYVQHKLRAHSRAVAIVLDEY'
+    stock.records['O83071/259-312'].gr_features['SS'].should == 'CCCCCHHHHHHHHHHHHHEEEEEEEEEEEEEEEEEEE'
+    stock.gc_features.should == {'SS_cons' => 'CCCCCHHHHHHHHHHHHHEEEEEEEEEEEEEEEEEEH'}
+    stock.gc_features.should be_kind_of(Hash)
+  end
+
+  it 'should parse multiple ones' do
+    stocks = Bio::Stockholm::Reader.parse_from_file(File.expand_path "#{TEST_DATA_DIR}/2wikipedias.sto")
+    stocks.length.should == 2
+    stocks[0].gf_features['ID'].should == 'CBS1'
+    stocks[1].gf_features['ID'].should == 'CBS2'
+  end
+end

data/spec/data/2wikipedias.sto

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+# STOCKHOLM 1.0
+#=GF ID CBS1
+#=GF AC PF00571
+#=GF DE CBS domain
+#=GF AU Bateman A
+#=GF CC CBS domains are small intracellular modules mostly found
+#=GF CC in 2 or four copies within a protein.
+#=GF SQ 5
+#=GS O31698/18-71 AC O31698
+#=GS O83071/192-246 AC O83071
+#=GS O83071/259-312 AC O83071
+#=GS O31698/88-139 AC O31698
+#=GS O31698/88-139 OS Bacillus subtilis
+O83071/192-246          MTCRAQLIAVPRASSLAEAIACAQKMRVSRVPVYERS
+#=GR O83071/192-246 SA  9998877564535242525515252536463774777
+O83071/259-312          MQHVSAPVFVFECTRLAYVQHKLRAHSRAVAIVLDEY
+#=GR O83071/259-312 SS  CCCCCHHHHHHHHHHHHHEEEEEEEEEEEEEEEEEEE
+O31698/18-71            MIEADKVAHVQVGNNLEHALLVLTKTGYTAIPVLDPS
+#=GR O31698/18-71 SS    CCCHHHHHHHHHHHHHHHEEEEEEEEEEEEEEEEHHH
+O31698/88-139           EVMLTDIPRLHINDPIMKGFGMVINN..GFVCVENDE
+#=GR O31698/88-139 SS   CCCCCCCHHHHHHHHHHHHEEEEEEEEEEEEEEEEEH
+#=GC SS_cons            CCCCCHHHHHHHHHHHHHEEEEEEEEEEEEEEEEEEH
+O31699/88-139           EVMLTDIPRLHINDPIMKGFGMVINN..GFVCVENDE
+#=GR O31699/88-139 AS   ________________*____________________
+#=GR O31699/88-139 IN   ____________1____________2______0____
+//
+#=GF ID CBS2
+#=GF AC PF00571
+#=GF DE CBS domain
+#=GF AU Bateman A
+#=GF CC CBS domains are small intracellular modules mostly found
+#=GF CC in 2 or four copies within a protein.
+#=GF SQ 5
+#=GS O31698/18-71 AC O31698
+#=GS O83071/192-246 AC O83071
+#=GS O83071/259-312 AC O83071
+#=GS O31698/88-139 AC O31698
+#=GS O31698/88-139 OS Bacillus subtilis
+O83071/192-246          MTCRAQLIAVPRASSLAEAIACAQKMRVSRVPVYERS
+#=GR O83071/192-246 SA  9998877564535242525515252536463774777
+O83071/259-312          MQHVSAPVFVFECTRLAYVQHKLRAHSRAVAIVLDEY
+#=GR O83071/259-312 SS  CCCCCHHHHHHHHHHHHHEEEEEEEEEEEEEEEEEEE
+O31698/18-71            MIEADKVAHVQVGNNLEHALLVLTKTGYTAIPVLDPS
+#=GR O31698/18-71 SS    CCCHHHHHHHHHHHHHHHEEEEEEEEEEEEEEEEHHH
+O31698/88-139           EVMLTDIPRLHINDPIMKGFGMVINN..GFVCVENDE
+#=GR O31698/88-139 SS   CCCCCCCHHHHHHHHHHHHEEEEEEEEEEEEEEEEEH
+#=GC SS_cons            CCCCCHHHHHHHHHHHHHEEEEEEEEEEEEEEEEEEH
+O31699/88-139           EVMLTDIPRLHINDPIMKGFGMVINN..GFVCVENDE
+#=GR O31699/88-139 AS   ________________*____________________
+#=GR O31699/88-139 IN   ____________1____________2______0____
+//

data/spec/data/test1.sto

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+# STOCKHOLM 1.0
+
+#=GS ABK77038.1 DE ammonia monooxygenase subunit A [Cenarchaeum symbiosum A]
+
+ABK77038.1         --------------------------------------LTMVWLRRCTHY
+#=GR ABK77038.1 PP ......................................67889999****
+#=GC PP_cons       ......................................67889999****
+#=GC RF            xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
+
+ABK77038.1         LFIAVVAVNSTLLTINAGDYIFYTDWAWTS--F..TVFSISQTLML....
+#=GR ABK77038.1 PP **************************9886..4..699********....
+#=GC PP_cons       **************************9886..4..699********....
+#=GC RF            xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxx....
+//

data/spec/data/wikipedia_test.sto

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+# STOCKHOLM 1.0
+#=GF ID CBS
+#=GF AC PF00571
+#=GF DE CBS domain
+#=GF AU Bateman A
+#=GF CC CBS domains are small intracellular modules mostly found
+#=GF CC in 2 or four copies within a protein.
+#=GF SQ 5
+#=GS O31698/18-71 AC O31698
+#=GS O83071/192-246 AC O83071
+#=GS O83071/259-312 AC O83071
+#=GS O31698/88-139 AC O31698
+#=GS O31698/88-139 OS Bacillus subtilis
+O83071/192-246          MTCRAQLIAVPRASSLAEAIACAQKMRVSRVPVYERS
+#=GR O83071/192-246 SA  9998877564535242525515252536463774777
+O83071/259-312          MQHVSAPVFVFECTRLAYVQHKLRAHSRAVAIVLDEY
+#=GR O83071/259-312 SS  CCCCCHHHHHHHHHHHHHEEEEEEEEEEEEEEEEEEE
+O31698/18-71            MIEADKVAHVQVGNNLEHALLVLTKTGYTAIPVLDPS
+#=GR O31698/18-71 SS    CCCHHHHHHHHHHHHHHHEEEEEEEEEEEEEEEEHHH
+O31698/88-139           EVMLTDIPRLHINDPIMKGFGMVINN..GFVCVENDE
+#=GR O31698/88-139 SS   CCCCCCCHHHHHHHHHHHHEEEEEEEEEEEEEEEEEH
+#=GC SS_cons            CCCCCHHHHHHHHHHHHHEEEEEEEEEEEEEEEEEEH
+O31699/88-139           EVMLTDIPRLHINDPIMKGFGMVINN..GFVCVENDE
+#=GR O31699/88-139 AS   ________________*____________________
+#=GR O31699/88-139 IN   ____________1____________2______0____
+//

data/spec/spec_helper.rb

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+$LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
+$LOAD_PATH.unshift(File.dirname(__FILE__))
+require 'rspec'
+require 'bio-stockholm'
+
+# 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
+
+TEST_DATA_DIR = File.join(File.dirname(__FILE__),'data')

metadata

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+--- !ruby/object:Gem::Specification
+name: bio-stockholm
+version: !ruby/object:Gem::Version
+  version: 0.0.1
+  prerelease: 
+platform: ruby
+authors:
+- Ben J. Woodcroft
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2013-06-19 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: rspec
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 2.8.0
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 2.8.0
+- !ruby/object:Gem::Dependency
+  name: rdoc
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '3.12'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '3.12'
+- !ruby/object:Gem::Dependency
+  name: jeweler
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.8.4
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.8.4
+- !ruby/object:Gem::Dependency
+  name: bundler
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 1.0.21
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 1.0.21
+- !ruby/object:Gem::Dependency
+  name: bio
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 1.4.2
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 1.4.2
+- !ruby/object:Gem::Dependency
+  name: rdoc
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '3.12'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '3.12'
+description: Parses stockholm sequence alignment format
+email: donttrustben near gmail.com
+executables: []
+extensions: []
+extra_rdoc_files:
+- LICENSE.txt
+- README.md
+files:
+- .document
+- .rspec
+- .travis.yml
+- Gemfile
+- LICENSE.txt
+- README.md
+- Rakefile
+- VERSION
+- lib/bio-stockholm.rb
+- lib/bio-stockholm/stockholm.rb
+- spec/bio-stockholm_spec.rb
+- spec/data/2wikipedias.sto
+- spec/data/test1.sto
+- spec/data/wikipedia_test.sto
+- spec/spec_helper.rb
+homepage: http://github.com/wwood/bioruby-stockholm
+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: 602560815
+required_rubygems_version: !ruby/object:Gem::Requirement
+  none: false
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubyforge_project: 
+rubygems_version: 1.8.25
+signing_key: 
+specification_version: 3
+summary: Parse stockholm sequence alignment format
+test_files: []