SilkSlider 0.1.0

checksums.yaml

@@ -0,0 +1,7 @@
+---
+SHA1:
+  metadata.gz: f46fdc69dee531983bef5fa6c99b460693f4d74f
+  data.tar.gz: 17e84f801770f8e6acede7f750f1514d12fc6ae5
+SHA512:
+  metadata.gz: 347c0cb9b39eb0ffa6bc04aaf1fa3198789e4b9cec1f6a90adc6da36da57fb1401d3123a0e734c543ae6705d785daf5d881e1ed33a0bbfd4a919f3858c7ebc91
+  data.tar.gz: ec2b31727a8ec2bc4fc30c13ba67544c94c26db42364bbb610c8dc7e19748036d69b2432af071e00b195f67268a53057e3ecd7da3340db777d20010a2a839451

data/.document

@@ -0,0 +1,5 @@
+lib/**/*.rb
+bin/*
+- 
+features/**/*.feature
+LICENSE.txt

data/.rspec

@@ -0,0 +1 @@
+--color

data/.travis.yml

@@ -0,0 +1,13 @@
+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 +1,20 @@
+source "http://rubygems.org"
+# Add dependencies required to use your gem here.
+# Example:
+#   gem "activesupport", ">= 2.3.5"
+gem 'bio-signalp', '~>0.3'
+gem 'bio-tm_hmm', '~>0.2.2', '>=0.2.2'
+gem 'bio', '~>1.4', '>=1.4.2'
+gem 'bio-logger', '~>1.0'
+
+# Add dependencies to develop your gem here.
+# Include everything needed to run rake, tests, features, etc.
+group :development do
+  gem 'bio-commandeer', '~>0.1'
+  gem 'pry', '~>0.1'
+
+  gem "rspec", "~> 2.8"
+  gem "jeweler", "~> 2.0"
+  gem "bundler", '~>1.0', ">= 1.0.21"
+  gem "rdoc", "~> 3.12"
+end

data/LICENSE.txt

@@ -0,0 +1,20 @@
+Copyright (c) 2014 Carmel McDougall, Ben Woodcroft, and Bernard Degnan.
+
+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 +1,48 @@
+# SilkSlider
+
+[![Build Status](https://secure.travis-ci.org/wwood/bioruby-SilkSlider.png)](http://travis-ci.org/wwood/bioruby-SilkSlider)
+
+A bioinformatic program for predicting whether proteins are 'silk-like' or not.
+
+This program was developed by Carmel McDougall and Ben Woodcroft at the [Degnan Laboratory](http://www.biology.uq.edu.au/staff/bernie-degnan) at the University of Queensland.
+
+## Installation
+
+After installing Ruby (SilkSlider is tested on Ruby 2.1.2):
+```sh
+gem install SilkSlider
+```
+
+Also required is the [SignalP](http://www.cbs.dtu.dk/services/SignalP/) and [TMHMM](http://www.cbs.dtu.dk/services/TMHMM/) programs, which need to be installed separately and available to silk_slider on the `$PATH`. SilkSlider is only tested on linux systems.
+
+## Usage
+
+To run the program:
+```sh
+silk_slider my.fasta
+```
+The program outputs a 
+To see the help:
+```sh
+silk_slider -h
+```
+
+## Project home page
+
+Information on the source tree, documentation, examples, issues and
+how to contribute, see
+
+  http://github.com/wwood/SilkSlider
+
+## Cite
+
+Currently unpublished - a journal article is in preparation.
+
+## Biogems.info
+
+This Biogem is published at (http://biogems.info/index.html#SilkSlider)
+
+## Copyright
+
+Copyright (c) 2014 Carmel McDougall, Ben Woodcroft, and Bernard Degnan. See LICENSE.txt for further details.
+

data/Rakefile

@@ -0,0 +1,50 @@
+# 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://guides.rubygems.org/specification-reference/ for more options
+  gem.name = "SilkSlider"
+  gem.homepage = "http://github.com/wwood/SilkSlider"
+  gem.license = "MIT"
+  gem.summary = %Q{Predict silk-like proteins from its amino acid sequence}
+  gem.description = %Q{Predict silk-like proteins from its amino acid sequence.}
+  gem.email = "donttrustben near gmail.com"
+  gem.authors = ["Carmel McDougall", "Ben J. Woodcroft", "Bernard Degnan"]
+  # 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
+
+desc "Code coverage detail"
+task :simplecov do
+  ENV['COVERAGE'] = "true"
+  Rake::Task['spec'].execute
+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 = "SilkSlider #{version}"
+  rdoc.rdoc_files.include('README*')
+  rdoc.rdoc_files.include('lib/**/*.rb')
+end

data/VERSION

@@ -0,0 +1 @@
+0.1.0

data/bin/silk_slider

@@ -0,0 +1,81 @@
+#!/usr/bin/env ruby
+
+require 'bio'
+require 'bio-logger'
+require 'optparse'
+
+require 'bio-signalp'
+require 'bio-tm_hmm'
+
+$LOAD_PATH.unshift File.join(File.dirname(__FILE__), *%w[.. lib])
+require 'sequence_window_descriptor'
+
+
+# Parse command line options into the options hash
+SCRIPT_NAME = File.basename(__FILE__); LOG_NAME = SCRIPT_NAME.gsub('.rb','')
+options = {
+  :logger => 'stderr',
+  :log_level => 'info',
+  :window_size => 80,
+  :min_glycines => 20,
+}
+o = OptionParser.new do |opts|
+  opts.banner = "
+    Usage: #{SCRIPT_NAME} my.fasta
+
+    Predict proteins as being silk-like or not.
+
+    my.fasta is the name of the fasta file you want to analyse. Output is all sequences predicted to be silk-like.
+      \n\n"
+
+  opts.separator "\nOptional parameters:\n\n"
+  opts.on("--window-size NUM", Integer, "Size of the window to determine glycine percentage over [default: #{options[:window_size] }]") do |arg|
+    options[:window_size] = arg
+  end
+  opts.on("--min-glycines NUM", Integer, "Number of glycines in a window for the protein to be considered silk-like, as an absolute number (not percentage) [default: #{options[:min_glycines] }]") do |arg|
+    options[:min_glycines] = arg
+  end
+  opts.separator "\nVerbosity:\n\n"
+  opts.on("-q", "--quiet", "Run quietly, set logging to ERROR level [default INFO]") {options[:log_level] = 'error'}
+  opts.on("--logger filename",String,"Log to file [default #{options[:logger]}]") { |name| options[:logger] = name}
+  opts.on("--trace options",String,"Set log level [default INFO]. e.g. '--trace debug' to set logging level to DEBUG"){|s| options[:log_level] = s}
+
+  opts.separator "\n\n"
+end
+o.parse!
+if ARGV.length != 1
+  $stderr.puts o
+  exit 1
+end
+Bio::Log::CLI.logger(options[:logger]); Bio::Log::CLI.trace(options[:log_level]); log = Bio::Log::LoggerPlus.new(LOG_NAME); Bio::Log::CLI.configure(LOG_NAME)
+
+signalp_runner = Bio::SignalP::Wrapper.new
+tmhmm_runner = Bio::TMHMM::TmHmmWrapper.new
+
+Bio::FlatFile.open(Bio::FastaFormat, ARGF).each do |seq|
+  signalp_result = signalp_runner.calculate(seq.seq)
+  if signalp_result.nil?
+    $stderr.puts "Unexpected empty sequence detected, ignoring: #{seq.definition}"
+    next
+  end
+
+  log.debug "Sequence #{seq.definition} predicted by SignalP? #{signalp_result.prediction}" if log.debug?
+  if signalp_result.prediction
+    sequence_without_signal_peptide = signalp_result.cleave(seq.seq)
+
+    tmhmm_protein = tmhmm_runner.calculate sequence_without_signal_peptide
+    log.debug "Sequence #{seq.definition} predicted by TMHMM2? #{tmhmm_protein.has_domain?}" if log.debug?
+
+    if !tmhmm_protein.has_domain?
+      # Does it pass the sliding window test?
+      slider = Bio::SequenceWindowDescriptor.new
+      slider.calculate sequence_without_signal_peptide, options[:window_size]
+      log.debug "Found maximal glycine count of #{slider.maximum_counts[:gly] } in window size #{options[:window_size] }" if log.debug?
+      if slider.maximum_counts[:gly] >= options[:min_glycines]
+        # We have a winner. Output.
+        puts ">#{seq.definition}"
+        puts seq.seq
+      end
+    end
+  end
+end

data/lib/sequence_window_descriptor.rb

@@ -0,0 +1,25 @@
+require 'bio'
+
+module Bio
+  class SequenceWindowDescriptor
+    attr_reader :maximum_counts, :maximum_sequences
+    def calculate(sequence_object, window_size)
+      # initialise maximums
+      @maximum_counts = {}
+      @maximum_sequences = {}
+      [:gly].each do |sym|
+        @maximum_counts[sym] = 0
+        @maximum_sequences[sym] = ''
+      end
+
+      sequence_object.window_search(window_size) do |str|
+        num = 0
+        str.scan(/g/i) {num += 1}
+        if num >= @maximum_counts[:gly]
+          @maximum_counts[:gly] = num
+          @maximum_sequences[:gly] = str
+        end
+      end
+    end
+  end
+end

data/spec/sequence_window_descriptor_spec.rb

@@ -0,0 +1,26 @@
+require File.expand_path(File.dirname(__FILE__) + '/spec_helper')
+
+require 'sequence_window_descriptor'
+
+describe "SequenceWindowDescriptor" do
+  it 'test_first' do
+    desc = Bio::SequenceWindowDescriptor.new
+    desc.calculate(Bio::Sequence::AA.new('GGY'), 2)
+    desc.maximum_counts[:gly].should == 2
+    desc.maximum_sequences[:gly].should == 'GG'
+  end
+
+  it 'test_not_first' do
+    desc = Bio::SequenceWindowDescriptor.new
+    desc.calculate(Bio::Sequence::AA.new('GGYYYGGYGY'), 4)
+    desc.maximum_counts[:gly].should == 3
+    desc.maximum_sequences[:gly].should == 'GGYG'
+  end
+
+  it 'test_not_big_enough' do
+    desc = Bio::SequenceWindowDescriptor.new
+    desc.calculate(Bio::Sequence::AA.new('GG'), 4)
+    desc.maximum_counts[:gly].should == 0
+    desc.maximum_sequences[:gly].should == ''
+  end
+end

data/spec/silk_slider_spec.rb

@@ -0,0 +1,107 @@
+require File.expand_path(File.dirname(__FILE__) + '/spec_helper')
+require 'bio-commandeer'
+require 'pry'
+
+describe "SilkSlider" do
+  PATH_TO_SCRIPT = File.join(File.dirname(__FILE__),'..','bin','silk_slider')
+
+  it "should work with a positive" do
+    # This is a malarial protein known to have a signal peptide
+    acp = 'MKILLLCIIFLYYVNAFKNTQKDGVSLQILKKKRSNQVNFLNRKNDYNLIKNKNPSSSLKSTFDDIKKIISKQLSVEEDK'+
+      'IQMNSNFTKDLGADSLDLVELIMALEEKFNVTISDQDALKINTVQDAIDYIEKNNKQ'
+    acp_gly = acp + 'G'*30
+    fasta = [
+      '>positive',
+      acp_gly
+      ].join("\n")+"\n"
+    command = "#{PATH_TO_SCRIPT} --quiet /dev/stdin"
+    res = Bio::Commandeer.run command, :stdin => fasta
+    res.should == fasta
+  end
+
+  it "should work with a negative" do
+    # This is a malarial protein known to have a signal peptide
+    acp = 'MKILLLCIIFLYYVNAFKNTQKDGVSLQILKKKRSNQVNFLNRKNDYNLIKNKNPSSSLKSTFDDIKKIISKQLSVEEDK'+
+      'IQMNSNFTKDLGADSLDLVELIMALEEKFNVTISDQDALKINTVQDAIDYIEKNNKQ'
+    fasta = [
+      '>positive',
+      acp
+      ].join("\n")+"\n"
+    command = "#{PATH_TO_SCRIPT} --quiet /dev/stdin"
+    res = Bio::Commandeer.run command, :stdin => fasta
+    res.should == ''
+  end
+
+  it 'should screen out non-signal peptide proteins' do
+    # This is a malarial protein known to have a signal peptide
+    acp_without_start_sp = 'SLQILKKKRSNQVNFLNRKNDYNLIKNKNPSSSLKSTFDDIKKIISKQLSVEEDK'+
+      'IQMNSNFTKDLGADSLDLVELIMALEEKFNVTISDQDALKINTVQDAIDYIEKNNKQ'
+    acp_gly = acp_without_start_sp + 'G'*30
+    fasta = [
+      '>positive',
+      acp_gly
+      ].join("\n")+"\n"
+    command = "#{PATH_TO_SCRIPT} --quiet /dev/stdin"
+    res = Bio::Commandeer.run command, :stdin => fasta
+    res.should == ''
+  end
+
+  it 'should screen out TMD proteins' do
+    # This is a malarial protein known to have several TMDs (but no SP)
+    pfcrt = 'MKFASKKNNQKNSSKNDERYRELDNLVQEGNGSRLGGGSCLGKCAHVFKLIFKEIKDNIFIYILSIIYLSVCVMNKIFAK
+RTLNKIGNYSFVTSETHNFICMIMFFIVYSLFGNKKGNSKERHRSFNLQFFAISMLDACSVILAFIGLTRTTGNIQSFVL
+QLSIPINMFFCFLILRYRYHLYNYLGAVIIVVTIALVEMKLSFETQEENSIIFNLVLISALIPVCFSNMTREIVFKKYKI
+DILRLNAMVSFFQLFTSCLILPVYTLPFLKQLHLPYNEIWTNIKNGFACLFLGRNTVVENCGLGMAKLCDDCDGAWKTFA
+LFSFFNICDNLITSYIIDKFSTMTYTIVSCIQGPAIAIAYYFKFLAGDVVREPRLLDFVTLFGYLFGSIIYRVGNIILER
+KKMRNEENEDSEGELTNVDSIITQ'
+    acp = 'MKILLLCIIFLYYVNAFKNTQKDGVSLQILKKKRSNQVNFLNRKNDYNLIKNKNPSSSLKSTFDDIKKIISKQLSVEEDK'+
+      'IQMNSNFTKDLGADSLDLVELIMALEEKFNVTISDQDALKINTVQDAIDYIEKNNKQ'
+    acp_pfcrt_gly = acp + pfcrt + 'G'*30 #put a SP on the start of a TMD protein, then a passing window
+    fasta = [
+      '>positive',
+      acp_pfcrt_gly
+      ].join("\n")+"\n"
+    command = "#{PATH_TO_SCRIPT} --quiet /dev/stdin"
+    res = Bio::Commandeer.run command, :stdin => fasta
+    res.should == ''
+  end
+
+  it 'should work with multiple sequences' do
+    acp = 'MKILLLCIIFLYYVNAFKNTQKDGVSLQILKKKRSNQVNFLNRKNDYNLIKNKNPSSSLKSTFDDIKKIISKQLSVEEDK'+
+      'IQMNSNFTKDLGADSLDLVELIMALEEKFNVTISDQDALKINTVQDAIDYIEKNNKQ'
+    acp_without_start_sp = 'SLQILKKKRSNQVNFLNRKNDYNLIKNKNPSSSLKSTFDDIKKIISKQLSVEEDK'+
+      'IQMNSNFTKDLGADSLDLVELIMALEEKFNVTISDQDALKINTVQDAIDYIEKNNKQ'
+
+    fasta = [
+      '>positive1',
+      acp + 'G'*30,
+      '>neg',
+      acp_without_start_sp,
+      '>pos2 yeh',
+      acp + 'G'*25,
+      ].join("\n")+"\n"
+    command = "#{PATH_TO_SCRIPT} --quiet /dev/stdin"
+    res = Bio::Commandeer.run command, :stdin => fasta
+    res.should == [
+      '>positive1',
+      acp + 'G'*30,
+      '>pos2 yeh',
+      acp + 'G'*25,
+      ].join("\n")+"\n"
+  end
+
+  it 'shoudl work with changed min gly' do
+    acp = 'MKILLLCIIFLYYVNAFKNTQKDGVSLQILKKKRSNQVNFLNRKNDYNLIKNKNPSSSLKSTFDDIKKIISKQLSVEEDK'+
+      'IQMNSNFTKDLGADSLDLVELIMALEEKFNVTISDQDALKINTVQDAIDYIEKNNKQ'
+    fasta = [
+      '>positive1',
+      acp + 'G'*15,
+      ].join("\n")+"\n"
+    command = "#{PATH_TO_SCRIPT} --quiet /dev/stdin"
+    res = Bio::Commandeer.run command, :stdin => fasta
+    res.should == ''
+    command = "#{PATH_TO_SCRIPT} --quiet /dev/stdin --min-glycines 5"
+    res = Bio::Commandeer.run command, :stdin => fasta
+    res.should == fasta
+  end
+end

data/spec/spec_helper.rb

@@ -0,0 +1,13 @@
+
+$LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
+$LOAD_PATH.unshift(File.dirname(__FILE__))
+
+require 'rspec'
+
+# 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 +1,219 @@
+--- !ruby/object:Gem::Specification
+name: SilkSlider
+version: !ruby/object:Gem::Version
+  version: 0.1.0
+platform: ruby
+authors:
+- Carmel McDougall
+- Ben J. Woodcroft
+- Bernard Degnan
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2014-07-02 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: bio-signalp
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.3'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.3'
+- !ruby/object:Gem::Dependency
+  name: bio-tm_hmm
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 0.2.2
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 0.2.2
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 0.2.2
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 0.2.2
+- !ruby/object:Gem::Dependency
+  name: bio
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 1.4.2
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.4'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 1.4.2
+    - - "~>"
+      - !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: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.1'
+- !ruby/object:Gem::Dependency
+  name: pry
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.1'
+  type: :development
+  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: 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: 1.0.21
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 1.0.21
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.0'
+- !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'
+description: Predict silk-like proteins from its amino acid sequence.
+email: donttrustben near gmail.com
+executables:
+- silk_slider
+extensions: []
+extra_rdoc_files:
+- LICENSE.txt
+- README.md
+files:
+- ".document"
+- ".rspec"
+- ".travis.yml"
+- Gemfile
+- LICENSE.txt
+- README.md
+- Rakefile
+- VERSION
+- bin/silk_slider
+- lib/sequence_window_descriptor.rb
+- spec/sequence_window_descriptor_spec.rb
+- spec/silk_slider_spec.rb
+- spec/spec_helper.rb
+homepage: http://github.com/wwood/SilkSlider
+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: '0'
+requirements: []
+rubyforge_project: 
+rubygems_version: 2.2.2
+signing_key: 
+specification_version: 4
+summary: Predict silk-like proteins from its amino acid sequence
+test_files: []