bio-tm_hmm 0.2.0 → 0.2.1

data/.travis.yml

@@ -0,0 +1,12 @@
+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

@@ -2,12 +2,13 @@ source "http://rubygems.org"
 # Add dependencies required to use your gem here.
 # Example:
 #   gem "activesupport", ">= 2.3.5"
-gem "bio", ">= 1.4.1"
 
 # Add dependencies to develop your gem here.
 # Include everything needed to run rake, tests, features, etc.
 group :development do
-  gem "bundler", "~> 1.0.0"
-  gem "jeweler", "~> 1.5.2"
-  gem "rcov", ">= 0"
+  gem "shoulda", ">= 0"
+  gem "rdoc", "~> 3.12"
+  gem "jeweler", "~> 1.8.3"
+  gem "bundler", ">= 1.0.21"
+  gem "bio", ">= 1.4.2"
 end

data/LICENSE.txt

@@ -1,4 +1,4 @@
-Copyright (c) 2011 Ben J. Woodcroft
+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

data/README.rdoc

@@ -1,21 +1,56 @@
 = bio-tm_hmm
 
+{<img
+src="https://secure.travis-ci.org/wwood/bioruby-tm_hmm.png"
+/>}[http://travis-ci.org/#!/wwood/bioruby-tm_hmm]
+
 A bioruby plugin for running TMHMM automatically on multiple sequences in a FASTA file and manipulation of the results
 
-  biotm_hmm -f proteome.fasta
+Note: this software is under active development!
+
+== Installation
+
+        gem install bio-tm_hmm
+
+== Usage
+
+  bio-tm_hmm my.fasta
+
+Where my.fasta is a FASTA file with one or more protein sequences in it. Output will be a description of the transmembrane domains predicted by TMHMM.
+
+Other options include -f for printing out the fasta sequences that have some number of transmembrane domains in them, and ignoring those that done (converse is -g)
+
+  bio-tm_hmm -f 2 <my.fasta
+
+== Developers
 
-== Contributing to bio-tm_hmm
+To use the library 
+
+        require 'bio-tm_hmm'
+
+The API doc is online. For more code examples see also the test files in
+the source tree.
+        
+== Project home page
+
+Information on the source tree, documentation, issues and how to contribute, see
+
+  http://github.com/wwood/bioruby-tm_hmm
+
+The BioRuby community is on IRC server: irc.freenode.org, channel: #bioruby.
+
+== Cite
+
+  If you use this software, please cite one of
  
-* 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.
+* [BioRuby: bioinformatics software for the Ruby programming language](http://dx.doi.org/10.1093/bioinformatics/btq475)
+* [Biogem: an effective tool-based approach for scaling up open source software development in bioinformatics](http://dx.doi.org/10.1093/bioinformatics/bts080)
+
+== Biogems.info
+
+This Biogem is published at http://biogems.info/index.html#bio-tm_hmm
 
 == Copyright
 
-Copyright (c) 2011 Ben J. Woodcroft. See LICENSE.txt for
-further details.
+Copyright (c) 2012 Ben J Woodcroft. See LICENSE.txt for further details.
 

data/Rakefile

@@ -1,3 +1,5 @@
+# encoding: utf-8
+
 require 'rubygems'
 require 'bundler'
 begin
@@ -19,10 +21,7 @@ Jeweler::Tasks.new do |gem|
   gem.description = %Q{A bioruby plugin for interaction with the transmembrane predictor TMHMM}
   gem.email = "donttrustben@gmail.com"
   gem.authors = ["Ben J. Woodcroft"]
-  # Include your dependencies below. Runtime dependencies are required when using your gem,
-  # and development dependencies are only needed for development (ie running rake tasks, tests, etc)
-  #  gem.add_runtime_dependency 'jabber4r', '> 0.1'
-  #  gem.add_development_dependency 'rspec', '> 1.2.3'
+  # dependencies defined in Gemfile
 end
 Jeweler::RubygemsDotOrgTasks.new
 
@@ -33,16 +32,9 @@ Rake::TestTask.new(:test) do |test|
   test.verbose = true
 end
 
-require 'rcov/rcovtask'
-Rcov::RcovTask.new do |test|
-  test.libs << 'test'
-  test.pattern = 'test/**/test_*.rb'
-  test.verbose = true
-end
-
 task :default => :test
 
-require 'rake/rdoctask'
+require 'rdoc/task'
 Rake::RDocTask.new do |rdoc|
   version = File.exist?('VERSION') ? File.read('VERSION') : ""
 

data/VERSION

@@ -1 +1 @@
-0.2.0
+0.2.1

data/bin/bio-tm_hmm

@@ -0,0 +1,69 @@
+#!/usr/bin/env ruby
+
+# Author:: Ben J. Woodcroft
+# Copyright:: 2011
+# License:: The Ruby License
+
+require 'rubygems'
+require 'bio'
+require 'bio-tm_hmm'
+require 'optparse'
+
+# If being run directly instead of being require'd,
+# output one transmembrane per line, and
+# indicate that a particular protein has no transmembrane domain
+options = {
+  :filter_in => false,
+  :filter_out => false,
+}
+o = OptionParser.new do |opts|
+  opts.banner = ['',
+    'Usage: tm_hmm_wrapper.rb [-fg] [fasta_filename]','',
+    "\tfasta file can also be piped in on STDIN.",
+    "\twithout arguments, a description of the transmembranes is printed out for each input sequence",''
+  ].join("\n")
+  opts.on('-f','--filter-in [MIN_TRANSMEMBRANE_DOMAINS]','Print those sequences that have a transmembrane domain. If MIN_TRANSMEMBRANE_DOMAINS is defined, only those proteins with that many TMDs or more are printed out') do |m|
+    options[:filter_in] = m.to_i #gets set to 0 when optional MIN_TRANSMEMBRANE_DOMAINS is omitted
+  end
+  opts.on('-g','--filter-out [MIN_TRANSMEMBRANE_DOMAINS]','Print those sequences that do NOT have a transmembrane domain. If MIN_TRANSMEMBRANE_DOMAINS is defined, only those proteins with that many TMDs or more are filtered out') do |m|
+    options[:filter_out] = m.to_i #gets set to 0 when optional MIN_TRANSMEMBRANE_DOMAINS is omitted
+  end
+end
+o.parse!
+
+runner = Bio::TMHMM::TmHmmWrapper.new
+
+Bio::FlatFile.auto(ARGF).each do |seq|
+  result = runner.calculate(seq.seq)
+  name = seq.definition
+
+  # Default output - a description of the TMDs for each input aaseq
+  if options[:filter_in] == false and options[:filter_out] == false
+    if result.has_domain?
+      # At least one TMD found. Output each on a separate line
+      result.transmembrane_domains.each do |tmd|
+        puts [
+        name,
+        result.transmembrane_type,
+        tmd.start,
+        tmd.stop,
+        tmd.orientation
+      ].join("\t")
+      end
+    else
+      puts [
+      name,
+      'No Transmembrane Domain Found'
+    ].join("\t")
+    end
+
+  elsif options[:filter_in] != false
+  	if result.transmembrane_domains.length >= options[:filter_in]
+  		puts seq
+  	end
+  elsif options[:filter_out] != false
+  	unless result.transmembrane_domains.length >= options[:filter_out]
+  		puts seq
+  	end
+  end
+end

data/bio-tm_hmm.gemspec

@@ -4,28 +4,28 @@
 # -*- encoding: utf-8 -*-
 
 Gem::Specification.new do |s|
-  s.name = %q{bio-tm_hmm}
-  s.version = "0.2.0"
+  s.name = "bio-tm_hmm"
+  s.version = "0.2.1"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Ben J. Woodcroft"]
-  s.date = %q{2011-04-06}
-  s.default_executable = %q{biotm_hmm}
-  s.description = %q{A bioruby plugin for interaction with the transmembrane predictor TMHMM}
-  s.email = %q{donttrustben@gmail.com}
-  s.executables = ["biotm_hmm"]
+  s.date = "2012-05-03"
+  s.description = "A bioruby plugin for interaction with the transmembrane predictor TMHMM"
+  s.email = "donttrustben@gmail.com"
+  s.executables = ["bio-tm_hmm"]
   s.extra_rdoc_files = [
     "LICENSE.txt",
     "README.rdoc"
   ]
   s.files = [
     ".document",
+    ".travis.yml",
     "Gemfile",
     "LICENSE.txt",
     "README.rdoc",
     "Rakefile",
     "VERSION",
-    "bin/biotm_hmm",
+    "bin/bio-tm_hmm",
     "bio-tm_hmm.gemspec",
     "lib/bio-tm_hmm.rb",
     "lib/bio/appl/tmhmm/tmhmm_runner.rb",
@@ -35,36 +35,34 @@ Gem::Specification.new do |s|
     "test/test_tm_hmm_wrapper.rb",
     "test/test_transmembrane.rb"
   ]
-  s.homepage = %q{http://github.com/wwood/bioruby-tm_hmm}
+  s.homepage = "http://github.com/wwood/bioruby-tm_hmm"
   s.licenses = ["MIT"]
   s.require_paths = ["lib"]
-  s.rubygems_version = %q{1.6.2}
-  s.summary = %q{A bioruby plugin for interaction with the transmembrane predictor TMHMM}
-  s.test_files = [
-    "test/helper.rb",
-    "test/test_tm_hmm_wrapper.rb",
-    "test/test_transmembrane.rb"
-  ]
+  s.rubygems_version = "1.8.21"
+  s.summary = "A bioruby plugin for interaction with the transmembrane predictor TMHMM"
 
   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_runtime_dependency(%q<bio>, [">= 1.4.1"])
-      s.add_development_dependency(%q<bundler>, ["~> 1.0.0"])
-      s.add_development_dependency(%q<jeweler>, ["~> 1.5.2"])
-      s.add_development_dependency(%q<rcov>, [">= 0"])
+      s.add_development_dependency(%q<shoulda>, [">= 0"])
+      s.add_development_dependency(%q<rdoc>, ["~> 3.12"])
+      s.add_development_dependency(%q<jeweler>, ["~> 1.8.3"])
+      s.add_development_dependency(%q<bundler>, [">= 1.0.21"])
+      s.add_development_dependency(%q<bio>, [">= 1.4.2"])
     else
-      s.add_dependency(%q<bio>, [">= 1.4.1"])
-      s.add_dependency(%q<bundler>, ["~> 1.0.0"])
-      s.add_dependency(%q<jeweler>, ["~> 1.5.2"])
-      s.add_dependency(%q<rcov>, [">= 0"])
+      s.add_dependency(%q<shoulda>, [">= 0"])
+      s.add_dependency(%q<rdoc>, ["~> 3.12"])
+      s.add_dependency(%q<jeweler>, ["~> 1.8.3"])
+      s.add_dependency(%q<bundler>, [">= 1.0.21"])
+      s.add_dependency(%q<bio>, [">= 1.4.2"])
     end
   else
-    s.add_dependency(%q<bio>, [">= 1.4.1"])
-    s.add_dependency(%q<bundler>, ["~> 1.0.0"])
-    s.add_dependency(%q<jeweler>, ["~> 1.5.2"])
-    s.add_dependency(%q<rcov>, [">= 0"])
+    s.add_dependency(%q<shoulda>, [">= 0"])
+    s.add_dependency(%q<rdoc>, ["~> 3.12"])
+    s.add_dependency(%q<jeweler>, ["~> 1.8.3"])
+    s.add_dependency(%q<bundler>, [">= 1.0.21"])
+    s.add_dependency(%q<bio>, [">= 1.4.2"])
   end
 end
 

data/lib/bio/transmembrane.rb

@@ -1,3 +1,35 @@
+
+# Monkey-patch Array#pair in
+class Array
+  # Return an array of all pairs of elements from this array (each is an array).
+  # If another_array is not nil, then do pairwise between this array and that (but not within each)
+  #
+  # NOT thread safe.
+  def pairs(another_array = nil)
+    pairs = []
+    
+    if another_array #between this array and the next
+     (0..length-1).each do |index1|
+     (0..another_array.length-1).each do |index2|
+          pairs.push [self[index1], another_array[index2]]
+        end
+      end
+    else # within this array only
+     (0..length-1).each do |index1|
+        index2 = index1+1
+        while index2 < length
+          pairs.push [self[index1], self[index2]]
+          index2 += 1
+        end
+      end
+    end
+    
+    return pairs
+  end
+end  
+
+
+
 # a simple class to represent a transmembrane domain, and a transmembrane domain containing protein
 module Bio
   module Transmembrane
@@ -51,6 +83,16 @@ module Bio
       def each
         @transmembrane_domains.each{|t| yield t}
       end
+    
+      def residue_number_contained?(residue_number)
+        contained = false
+        @transmembrane_domains.each do |tmd|
+          if tmd.start <= residue_number and tmd.stop >= residue_number
+            contained = true
+          end
+        end
+        contained
+      end
     end
     
     class OrientedTransmembraneDomainProtein<TransmembraneProtein
@@ -138,8 +180,16 @@ module Bio
       end
     end
     
+    # From Predicting transmembrane protein topology with a hidden markov model: application to complete g
+    #
+    # Another signal shown to be associated with transmembrane helices is
+    # the abundance of positively charged residues in the part of the
+    # sequence on the cytoplasmic side of the membrane, “the positive inside
+    # rule” (von Heijne 1986) and (von Heijne 1994).
+    #
+    # So, inside means cytosolic. So outside_in means type I transmembrane domain protein
     class OrientedTransmembraneDomain<TransmembraneDomainDefinition
-      # The orientation can either be inside out (like a type II transmembrane domain protein)
+     # The orientation can either be inside out (like a type II transmembrane domain protein)
       INSIDE_OUT = 'inside_out'
       # Or outside in, like a type I transmembrane domain protein)
       OUTSIDE_IN = 'outside_in'

data/test/test_transmembrane.rb

@@ -116,5 +116,31 @@ module Transmembrane
       assert_equal 1, tmd1.overlap_length(tmd2)
       assert_equal((3..3), tmd1.intersection(tmd2))
     end
+    
+    def test_residue_contained?
+      p = TransmembraneProtein.new
+      
+      # test none
+      p.transmembrane_domains = []
+      assert_equal false, p.residue_number_contained?(5)
+      
+      # test one
+      p.transmembrane_domains = [TransmembraneDomainDefinition.new(5,8)]
+      assert p.residue_number_contained?(5)
+      assert p.residue_number_contained?(6)
+      assert p.residue_number_contained?(8)
+      assert_equal false, p.residue_number_contained?(4)
+      assert_equal false, p.residue_number_contained?(9)
+      
+      # test 3
+      p.transmembrane_domains = [
+      TransmembraneDomainDefinition.new(1,10),
+      TransmembraneDomainDefinition.new(90,100),
+      TransmembraneDomainDefinition.new(16,24),
+      ]
+      assert p.residue_number_contained?(5)
+      assert p.residue_number_contained?(95)
+      assert_equal false, p.residue_number_contained?(150)
+    end
   end
 end

metadata

@@ -1,102 +1,113 @@
---- !ruby/object:Gem::Specification 
+--- !ruby/object:Gem::Specification
 name: bio-tm_hmm
-version: !ruby/object:Gem::Version 
-  hash: 23
+version: !ruby/object:Gem::Version
+  version: 0.2.1
   prerelease: 
-  segments: 
-  - 0
-  - 2
-  - 0
-  version: 0.2.0
 platform: ruby
-authors: 
+authors:
 - Ben J. Woodcroft
 autorequire: 
 bindir: bin
 cert_chain: []
-
-date: 2011-04-06 00:00:00 +10:00
-default_executable: biotm_hmm
-dependencies: 
-- !ruby/object:Gem::Dependency 
-  type: :runtime
-  requirement: &id001 !ruby/object:Gem::Requirement 
+date: 2012-05-03 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: shoulda
+  requirement: !ruby/object:Gem::Requirement
     none: false
-    requirements: 
-    - - ">="
-      - !ruby/object:Gem::Version 
-        hash: 5
-        segments: 
-        - 1
-        - 4
-        - 1
-        version: 1.4.1
-  name: bio
-  version_requirements: *id001
-  prerelease: false
-- !ruby/object:Gem::Dependency 
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
   type: :development
-  requirement: &id002 !ruby/object:Gem::Requirement 
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
     none: false
-    requirements: 
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: rdoc
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
     - - ~>
-      - !ruby/object:Gem::Version 
-        hash: 23
-        segments: 
-        - 1
-        - 0
-        - 0
-        version: 1.0.0
-  name: bundler
-  version_requirements: *id002
-  prerelease: false
-- !ruby/object:Gem::Dependency 
+      - !ruby/object:Gem::Version
+        version: '3.12'
   type: :development
-  requirement: &id003 !ruby/object:Gem::Requirement 
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
     none: false
-    requirements: 
+    requirements:
     - - ~>
-      - !ruby/object:Gem::Version 
-        hash: 7
-        segments: 
-        - 1
-        - 5
-        - 2
-        version: 1.5.2
+      - !ruby/object:Gem::Version
+        version: '3.12'
+- !ruby/object:Gem::Dependency
   name: jeweler
-  version_requirements: *id003
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.8.3
+  type: :development
   prerelease: false
-- !ruby/object:Gem::Dependency 
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.8.3
+- !ruby/object:Gem::Dependency
+  name: bundler
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 1.0.21
   type: :development
-  requirement: &id004 !ruby/object:Gem::Requirement 
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
     none: false
-    requirements: 
-    - - ">="
-      - !ruby/object:Gem::Version 
-        hash: 3
-        segments: 
-        - 0
-        version: "0"
-  name: rcov
-  version_requirements: *id004
+    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
 description: A bioruby plugin for interaction with the transmembrane predictor TMHMM
 email: donttrustben@gmail.com
-executables: 
-- biotm_hmm
+executables:
+- bio-tm_hmm
 extensions: []
-
-extra_rdoc_files: 
+extra_rdoc_files:
 - LICENSE.txt
 - README.rdoc
-files: 
+files:
 - .document
+- .travis.yml
 - Gemfile
 - LICENSE.txt
 - README.rdoc
 - Rakefile
 - VERSION
-- bin/biotm_hmm
+- bin/bio-tm_hmm
 - bio-tm_hmm.gemspec
 - lib/bio-tm_hmm.rb
 - lib/bio/appl/tmhmm/tmhmm_runner.rb
@@ -105,41 +116,32 @@ files:
 - test/helper.rb
 - test/test_tm_hmm_wrapper.rb
 - test/test_transmembrane.rb
-has_rdoc: true
 homepage: http://github.com/wwood/bioruby-tm_hmm
-licenses: 
+licenses:
 - MIT
 post_install_message: 
 rdoc_options: []
-
-require_paths: 
+require_paths:
 - lib
-required_ruby_version: !ruby/object:Gem::Requirement 
+required_ruby_version: !ruby/object:Gem::Requirement
   none: false
-  requirements: 
-  - - ">="
-    - !ruby/object:Gem::Version 
-      hash: 3
-      segments: 
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+      segments:
       - 0
-      version: "0"
-required_rubygems_version: !ruby/object:Gem::Requirement 
+      hash: 1004564205
+required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
-  requirements: 
-  - - ">="
-    - !ruby/object:Gem::Version 
-      hash: 3
-      segments: 
-      - 0
-      version: "0"
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
 requirements: []
-
 rubyforge_project: 
-rubygems_version: 1.6.2
+rubygems_version: 1.8.21
 signing_key: 
 specification_version: 3
 summary: A bioruby plugin for interaction with the transmembrane predictor TMHMM
-test_files: 
-- test/helper.rb
-- test/test_tm_hmm_wrapper.rb
-- test/test_transmembrane.rb
+test_files: []

data/bin/biotm_hmm

@@ -1,72 +0,0 @@
-#!/usr/bin/env ruby
-
-# Author:: Ben J. Woodcroft
-# Copyright:: 2011
-# License:: The Ruby License
-
-require 'rubygems'
-require 'bio'
-require 'bio-tm_hmm'
-require 'optparse'
-
-# If being run directly instead of being require'd,
-# output one transmembrane per line, and
-# indicate that a particular protein has no transmembrane domain
-if $0 == __FILE__
-  options = {
-    :filter_in => false,
-    :filter_out => false,
-  }
-  o = OptionParser.new do |opts|
-    opts.banner = [
-      'Usage: tm_hmm_wrapper.rb [-fg] [fasta_filename]',
-      "\tfasta file can also be piped in on STDIN.",
-      "\twithout arguments, a description of the transmembranes is printed out for each input sequence"
-    ]
-    opts.on('-f','--filter-in [MIN_TRANSMEMBRANE_DOMAINS]','Print those sequences that have a transmembrane domain. If MIN_TRANSMEMBRANE_DOMAINS is defined, only those proteins with that many TMDs or more are printed out') do |m|
-      options[:filter_in] = m.to_i #gets set to 0 when optional MIN_TRANSMEMBRANE_DOMAINS is omitted
-    end
-    opts.on('-g','--filter-out [MIN_TRANSMEMBRANE_DOMAINS]','Print those sequences that do NOT have a transmembrane domain. If MIN_TRANSMEMBRANE_DOMAINS is defined, only those proteins with that many TMDs or more are filtered out') do |m|
-      options[:filter_out] = m.to_i #gets set to 0 when optional MIN_TRANSMEMBRANE_DOMAINS is omitted
-    end
-  end
-  o.parse!
-
-  runner = Bio::TMHMM::TmHmmWrapper.new
-
-  Bio::FlatFile.auto(ARGF).each do |seq|
-    result = runner.calculate(seq.seq)
-    name = seq.definition
-
-    # Default output - a description of the TMDs for each input aaseq
-    if options[:filter_in] == false and options[:filter_out] == false
-      if result.has_domain?
-        # At least one TMD found. Output each on a separate line
-        result.transmembrane_domains.each do |tmd|
-          puts [
-          name,
-          result.transmembrane_type,
-          tmd.start,
-          tmd.stop,
-          tmd.orientation
-        ].join("\t")
-        end
-      else
-        puts [
-        name,
-        'No Transmembrane Domain Found'
-      ].join("\t")
-      end
-
-    elsif options[:filter_in] != false
-    	if result.transmembrane_domains.length >= options[:filter_in]
-    		puts seq
-    	end
-    elsif options[:filter_out] != false
-    	unless result.transmembrane_domains.length >= options[:filter_out]
-    		puts seq
-    	end
-    end
-  end
-end
-