bio-tm_hmm 0.2.1 → 0.2.2

data/.travis.yml

@@ -9,4 +9,4 @@ rvm:
 #  - rbx-18mode
 
 # uncomment this line if your project needs to run something other than `rake`:
-# script: bundle exec rspec spec
+script: bundle exec rake test_without_tmhmm

data/README.md

@@ -0,0 +1,70 @@
+# bio-tm_hmm
+
+[![Build Status](https://secure.travis-ci.org/wwood/bioruby-sra.png)](http://travis-ci.org/#!/wwood/bioruby-tm_hmm)
+
+A bioruby plugin for running the transmembrane domain predictor TMHMM automatically on multiple sequences in a FASTA file and manipulation of the results.
+
+## Installation
+
+```
+gem install bio-tm_hmm
+```
+
+## Usage
+
+```
+Usage: bio-tm_hmm [-f NUM] [-g NUM] [fasta_filename]
+
+	fasta file can also be piped in on STDIN.
+	without arguments, a description of the transmembrane domains is printed out for each input sequence
+    -f MIN_TRANSMEMBRANE_DOMAINS,    Print those sequences that have at _least_ MIN_TRANSMEMBRANE_DOMAINS transmembrane domain(s). Prints out the sequences in FASTA format.
+        --filter-in
+    -g MAX_TRANSMEMBRANE_DOMAINS,    Print those sequences that have at _most_ MAX_TRANSMEMBRANE_DOMAINS transmembrane domain(s). Prints out the sequences in FASTA format.
+        --filter-out
+```
+
+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 don't (converse is -g). For instance, to filter out all sequences that have less than 2 predicted transmembrane domains:
+
+```
+bio-tm_hmm -f 2 <my.fasta
+```
+
+## Developers
+
+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:
+
+[Organellar proteomics reveals hundreds of novel nuclear proteins in the malaria parasite Plasmodium falciparum](http://genomebiology.com/2012/13/11/R108)
+
+Sophie C Oehring, Ben J Woodcroft, Suzette Moes, Johanna Wetzel, Olivier Dietz, Andreas Pulfer, Chaitali Dekiwadia, Pascal Maeser, Christian Flueck, Kathrin Witmer, Nicolas MB Brancucci, Igor Niederwieser, Paul Jenoe, Stuart A Ralph and Till S Voss	
+
+Genome Biology 2012, 13:R108 doi:10.1186/gb-2012-13-11-r108
+
+## Biogems.info
+
+This Biogem is published at http://biogems.info/index.html#bio-tm_hmm
+
+## Copyright
+
+Copyright (c) 2012 Ben J Woodcroft. See LICENSE.txt for further details.
+

data/Rakefile

@@ -31,6 +31,11 @@ Rake::TestTask.new(:test) do |test|
   test.pattern = 'test/**/test_*.rb'
   test.verbose = true
 end
+Rake::TestTask.new(:test_without_tmhmm) do |test|
+  test.libs << 'lib' << 'test'
+  test.test_files = FileList['test/test*.rb'].reject{|f| f=='test/test_tm_hmm_wrapper.rb'}
+  test.verbose = true
+end
 
 task :default => :test
 

data/VERSION

@@ -1 +1 @@
-0.2.1
+0.2.2

data/bin/bio-tm_hmm

@@ -17,16 +17,22 @@ options = {
   :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|
+    opts.banner = "
+    Usage: #{File.basename __FILE__} [-f NUM] [-g NUM] [fasta_filename]
+
+      Fasta file can be piped in on STDIN, or specified as the first unqualified argument.
+
+      Without arguments, a description of the transmembrane domains is printed out for each input sequence\n\n"
+
+  opts.on('-f','--filter-in MIN_TRANSMEMBRANE_DOMAINS','Print those sequences that have at _least_ MIN_TRANSMEMBRANE_DOMAINS transmembrane domain(s). Prints out the sequences in FASTA format.') 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
+  opts.on('-g','--filter-out MAX_TRANSMEMBRANE_DOMAINS','Print those sequences that have at _most_ MAX_TRANSMEMBRANE_DOMAINS transmembrane domain(s). Prints out the sequences in FASTA format.') do |m|
+    if m.nil?
+      options[:filter_out] = 1
+    else
+      options[:filter_out] = m.to_i
+    end
   end
 end
 o.parse!
@@ -39,6 +45,7 @@ Bio::FlatFile.auto(ARGF).each do |seq|
 
   # Default output - a description of the TMDs for each input aaseq
   if options[:filter_in] == false and options[:filter_out] == false
+    p result
     if result.has_domain?
       # At least one TMD found. Output each on a separate line
       result.transmembrane_domains.each do |tmd|
@@ -62,7 +69,7 @@ Bio::FlatFile.auto(ARGF).each do |seq|
   		puts seq
   	end
   elsif options[:filter_out] != false
-  	unless result.transmembrane_domains.length >= options[:filter_out]
+  	unless result.transmembrane_domains.length > options[:filter_out]
   		puts seq
   	end
   end

data/bio-tm_hmm.gemspec

@@ -5,24 +5,24 @@
 
 Gem::Specification.new do |s|
   s.name = "bio-tm_hmm"
-  s.version = "0.2.1"
+  s.version = "0.2.2"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Ben J. Woodcroft"]
-  s.date = "2012-05-03"
+  s.date = "2012-12-01"
   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"
+    "README.md"
   ]
   s.files = [
     ".document",
     ".travis.yml",
     "Gemfile",
     "LICENSE.txt",
-    "README.rdoc",
+    "README.md",
     "Rakefile",
     "VERSION",
     "bin/bio-tm_hmm",
@@ -32,13 +32,14 @@ Gem::Specification.new do |s|
     "lib/bio/transmembrane.rb",
     "test/data/falciparum1.fa",
     "test/helper.rb",
+    "test/test_tm_hmm_parser.rb",
     "test/test_tm_hmm_wrapper.rb",
     "test/test_transmembrane.rb"
   ]
   s.homepage = "http://github.com/wwood/bioruby-tm_hmm"
   s.licenses = ["MIT"]
   s.require_paths = ["lib"]
-  s.rubygems_version = "1.8.21"
+  s.rubygems_version = "1.8.24"
   s.summary = "A bioruby plugin for interaction with the transmembrane predictor TMHMM"
 
   if s.respond_to? :specification_version then

data/test/test_tm_hmm_parser.rb

@@ -0,0 +1,57 @@
+require 'bio'
+require 'helper'
+
+class TmHmmParserTest < Test::Unit::TestCase
+  include Bio::Transmembrane
+  
+  def test_parser
+    result = Bio::TMHMM::TmHmmResult.create_from_short_line('PFA0635c	len=555	ExpAA=0.00	First60=0.00	PredHel=0	Topology=o')
+    assert result
+    assert_equal false, result.has_domain?
+    
+    # test a single TMD
+    result = Bio::TMHMM::TmHmmResult.create_from_short_line('PFA0685c	len=324	ExpAA=20.36	First60=0.00	PredHel=1	Topology=o281-303i')
+    assert result
+    assert_equal 1, result.transmembrane_domains.length
+    assert_equal 281, result.transmembrane_domains[0].start
+    assert_equal 303, result.transmembrane_domains[0].stop
+    assert_equal Bio::Transmembrane::OrientedTransmembraneDomain::OUTSIDE_IN,
+      result.transmembrane_domains[0].orientation
+    assert result.transmembrane_type_1?
+    assert_equal false, result.transmembrane_type_2?
+    
+    # test 2 TMD
+    result = Bio::TMHMM::TmHmmResult.create_from_short_line('PFA0680c	len=209	ExpAA=43.03	First60=0.02	PredHel=2	Topology=i137-159o164-183i')
+    assert result
+    assert_equal 2, result.transmembrane_domains.length
+    assert_equal 137, result.transmembrane_domains[0].start
+    assert_equal 159, result.transmembrane_domains[0].stop
+    assert_equal Bio::Transmembrane::OrientedTransmembraneDomain::INSIDE_OUT,
+      result.transmembrane_domains[0].orientation
+    assert_equal 164, result.transmembrane_domains[1].start
+    assert_equal 183, result.transmembrane_domains[1].stop
+    assert_equal Bio::Transmembrane::OrientedTransmembraneDomain::OUTSIDE_IN,
+      result.transmembrane_domains[1].orientation
+    assert_equal false, result.transmembrane_type_1?
+    assert_equal false, result.transmembrane_type_2?
+    
+    # test 3 TMD
+    result = Bio::TMHMM::TmHmmResult.create_from_short_line('PFA0705c	len=282	ExpAA=90.97	First60=22.20	PredHel=4	Topology=i22-44o185-207i212-234o259-281i')
+    assert result
+    assert_equal 4, result.transmembrane_domains.length
+    assert_equal 22, result.transmembrane_domains[0].start
+    assert_equal 44, result.transmembrane_domains[0].stop
+    assert_equal Bio::Transmembrane::OrientedTransmembraneDomain::INSIDE_OUT,
+      result.transmembrane_domains[0].orientation
+    assert_equal 185, result.transmembrane_domains[1].start
+    assert_equal 207, result.transmembrane_domains[1].stop
+    assert_equal Bio::Transmembrane::OrientedTransmembraneDomain::OUTSIDE_IN,
+      result.transmembrane_domains[1].orientation
+    assert_equal 259, result.transmembrane_domains[3].start
+    assert_equal 281, result.transmembrane_domains[3].stop
+    assert_equal Bio::Transmembrane::OrientedTransmembraneDomain::OUTSIDE_IN,
+      result.transmembrane_domains[3].orientation
+    assert_equal false, result.transmembrane_type_1?
+    assert_equal false, result.transmembrane_type_2?
+  end
+end

data/test/test_tm_hmm_wrapper.rb

@@ -3,58 +3,6 @@ require 'helper'
 
 class TmHmmWrapperTest < Test::Unit::TestCase
   include Bio::Transmembrane
-  
-  def test_parser
-    result = Bio::TMHMM::TmHmmResult.create_from_short_line('PFA0635c	len=555	ExpAA=0.00	First60=0.00	PredHel=0	Topology=o')
-    assert result
-    assert_equal false, result.has_domain?
-    
-    # test a single TMD
-    result = Bio::TMHMM::TmHmmResult.create_from_short_line('PFA0685c	len=324	ExpAA=20.36	First60=0.00	PredHel=1	Topology=o281-303i')
-    assert result
-    assert_equal 1, result.transmembrane_domains.length
-    assert_equal 281, result.transmembrane_domains[0].start
-    assert_equal 303, result.transmembrane_domains[0].stop
-    assert_equal Bio::Transmembrane::OrientedTransmembraneDomain::OUTSIDE_IN,
-      result.transmembrane_domains[0].orientation
-    assert result.transmembrane_type_1?
-    assert_equal false, result.transmembrane_type_2?
-    
-    # test 2 TMD
-    result = Bio::TMHMM::TmHmmResult.create_from_short_line('PFA0680c	len=209	ExpAA=43.03	First60=0.02	PredHel=2	Topology=i137-159o164-183i')
-    assert result
-    assert_equal 2, result.transmembrane_domains.length
-    assert_equal 137, result.transmembrane_domains[0].start
-    assert_equal 159, result.transmembrane_domains[0].stop
-    assert_equal Bio::Transmembrane::OrientedTransmembraneDomain::INSIDE_OUT,
-      result.transmembrane_domains[0].orientation
-    assert_equal 164, result.transmembrane_domains[1].start
-    assert_equal 183, result.transmembrane_domains[1].stop
-    assert_equal Bio::Transmembrane::OrientedTransmembraneDomain::OUTSIDE_IN,
-      result.transmembrane_domains[1].orientation
-    assert_equal false, result.transmembrane_type_1?
-    assert_equal false, result.transmembrane_type_2?
-    
-    # test 3 TMD
-    result = Bio::TMHMM::TmHmmResult.create_from_short_line('PFA0705c	len=282	ExpAA=90.97	First60=22.20	PredHel=4	Topology=i22-44o185-207i212-234o259-281i')
-    assert result
-    assert_equal 4, result.transmembrane_domains.length
-    assert_equal 22, result.transmembrane_domains[0].start
-    assert_equal 44, result.transmembrane_domains[0].stop
-    assert_equal Bio::Transmembrane::OrientedTransmembraneDomain::INSIDE_OUT,
-      result.transmembrane_domains[0].orientation
-    assert_equal 185, result.transmembrane_domains[1].start
-    assert_equal 207, result.transmembrane_domains[1].stop
-    assert_equal Bio::Transmembrane::OrientedTransmembraneDomain::OUTSIDE_IN,
-      result.transmembrane_domains[1].orientation
-    assert_equal 259, result.transmembrane_domains[3].start
-    assert_equal 281, result.transmembrane_domains[3].stop
-    assert_equal Bio::Transmembrane::OrientedTransmembraneDomain::OUTSIDE_IN,
-      result.transmembrane_domains[3].orientation
-    assert_equal false, result.transmembrane_type_1?
-    assert_equal false, result.transmembrane_type_2?
-  end
-  
   def test_wrapper
     prog = Bio::TMHMM::TmHmmWrapper.new
     seq = Bio::FlatFile.auto(File.join(File.dirname(__FILE__),'data','falciparum1.fa')).next_entry

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: bio-tm_hmm
 version: !ruby/object:Gem::Version
-  version: 0.2.1
+  version: 0.2.2
   prerelease: 
 platform: ruby
 authors:
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2012-05-03 00:00:00.000000000 Z
+date: 2012-12-01 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: shoulda
@@ -98,13 +98,13 @@ executables:
 extensions: []
 extra_rdoc_files:
 - LICENSE.txt
-- README.rdoc
+- README.md
 files:
 - .document
 - .travis.yml
 - Gemfile
 - LICENSE.txt
-- README.rdoc
+- README.md
 - Rakefile
 - VERSION
 - bin/bio-tm_hmm
@@ -114,6 +114,7 @@ files:
 - lib/bio/transmembrane.rb
 - test/data/falciparum1.fa
 - test/helper.rb
+- test/test_tm_hmm_parser.rb
 - test/test_tm_hmm_wrapper.rb
 - test/test_transmembrane.rb
 homepage: http://github.com/wwood/bioruby-tm_hmm
@@ -131,7 +132,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
       version: '0'
       segments:
       - 0
-      hash: 1004564205
+      hash: 24340783
 required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
   requirements:
@@ -140,7 +141,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 1.8.21
+rubygems_version: 1.8.24
 signing_key: 
 specification_version: 3
 summary: A bioruby plugin for interaction with the transmembrane predictor TMHMM

data/README.rdoc

@@ -1,56 +0,0 @@
-= 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
-
-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
-
-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
- 
-* [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) 2012 Ben J Woodcroft. See LICENSE.txt for further details.
-