bio-plasmoap 0.0.2 → 0.1.0

checksums.yaml

@@ -0,0 +1,7 @@
+---
+SHA1:
+  metadata.gz: 6ec59ad4901505b49516d6333cc3790fb5492ca2
+  data.tar.gz: 6b2a7d96cc21a428f28384c06ca524b1d6bad86b
+SHA512:
+  metadata.gz: f1b98cfff30d0eb08642e8a6d35ee778621c895518f8a8370ddf375b4d4c32619140da0375c64d79ee950c658bdf33aa9332499dd22b03b04d4d1c565b631496
+  data.tar.gz: 07ae6c71ee91af90661eeeebc5197b3b3f95028f3b665e80fcd165bf5e39f31a9e93c7e7bfeab57c7faf967fdb6ce3e195e189a91d7a1ea60f74e7373e73506d

data/Gemfile

@@ -2,13 +2,12 @@ source "http://rubygems.org"
 
 gem 'bio', '>=1.4.1'
 gem 'bio-signalp', '>=0.2.0'
+gem 'test-unit', '>=3.1.8'
 
 # 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", ">= 1.4.1"
+  gem "bundler", ">= 1.0.0"
+  gem "jeweler", ">= 1.6.4"
 end

data/README.rdoc

@@ -1,19 +1,20 @@
 = bio-plasmoap
 
-Description goes here.
+PlasmoAP is a program for predicting apicoplast targetting sequences
+in Plasmodium falciparum (the most fatal causative agent of malaria).
+This biogem implements the PlasmoAP algorithm, designed from the PlasmoAP journal article:
 
-== Contributing to bio-plasmoap
- 
-* 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.
+    Dissecting apicoplast targeting in the malaria parasite Plasmodium falciparum.
+    Foth BJ, Ralph SA, Tonkin CJ, Struck NS, Fraunholz M, Roos DS, Cowman AF, McFadden GI.
+    Science. 2003 Jan 31;299(5607):705-8.
+    PMID: 12560551
+
+PlasmoAP requires the bio-signalp BioRuby plugin to be installed and therefore SignalP itself. See http://github.com/wwood/bioruby-signalp for more details.
+
+Specifically, it requires version 3 of SignalP.
 
 == Copyright
 
-Copyright (c) 2012 Ben J Woodcroft. See LICENSE.txt for
+Copyright (c) 2012-2016 Ben J Woodcroft. See LICENSE.txt for
 further details.
 

data/Rakefile

@@ -32,17 +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
-  test.rcov_opts << '--exclude "gems/*"'
-end
-
 task :default => :test
 
-require 'rake/rdoctask'
+require 'rdoc/task'
 Rake::RDocTask.new do |rdoc|
   version = File.exist?('VERSION') ? File.read('VERSION') : ""
 
@@ -51,3 +43,4 @@ Rake::RDocTask.new do |rdoc|
   rdoc.rdoc_files.include('README*')
   rdoc.rdoc_files.include('lib/**/*.rb')
 end
+

data/VERSION

@@ -1 +1 @@
-0.0.2
+0.1.0

data/bin/plasmoap.rb

@@ -2,28 +2,47 @@
 
 require 'rubygems'
 require 'bio'
+require 'optparse'
+
+$:.unshift File.join(File.dirname(__FILE__),'..','lib')
 require 'bio-plasmoap'
 
-if $0 == __FILE__
-  runner = Bio::PlasmoAP.new
-  
-  # print out a list of proteins with yes/no answers
-  puts [
-    'Name',
-    'PlasmoAP Score',
-    'Apicoplast Targeted',
-    'Points'
-  ].join("\t")
-  
-  Bio::FlatFile.auto(ARGF).each do |seq|
-    result = runner.calculate_score(seq.seq)
-    to_print = [seq.definition, result.to_s]
-    if result.apicoplast_targeted?
-      to_print.push 1
-    else
-      to_print.push 0
-    end
-    to_print.push result.points
-    puts to_print.join("\t")
+SCRIPT_NAME = File.basename(__FILE__); LOG_NAME = SCRIPT_NAME.gsub('.rb','')
+
+o = OptionParser.new do |opts|
+  opts.banner = "
+    Usage: #{SCRIPT_NAME} <fasta_file>
+
+    Predict whether protein(s) are targeted to the apicoplast
+    using the PlasmoAP algorithm described here:
+
+    Dissecting apicoplast targeting in the malaria parasite Plasmodium falciparum.
+    Foth BJ, Ralph SA, Tonkin CJ, Struck NS, Fraunholz M, Roos DS, Cowman AF, McFadden GI.
+    Science. 2003 Jan 31;299(5607):705-8.
+    PMID: 12560551
+
+    It uses SignalP version 3 (not 4!), which it expects to be on the PATH.
+\n"
+end; o.parse!
+
+# print out a list of proteins with yes/no answers
+puts [
+  'Name',
+  'PlasmoAP Score',
+  'Apicoplast Targeted',
+  'Points'
+].join("\t")
+
+runner = Bio::PlasmoAP.new
+
+Bio::FlatFile.auto(ARGF).each do |seq|
+  result = runner.calculate_score(seq.seq)
+  to_print = [seq.definition, result.to_s]
+  if result.apicoplast_targeted?
+    to_print.push 1
+  else
+    to_print.push 0
   end
+  to_print.push result.points
+  puts to_print.join("\t")
 end

data/bio-plasmoap.gemspec

@@ -2,17 +2,19 @@
 # DO NOT EDIT THIS FILE DIRECTLY
 # Instead, edit Jeweler::Tasks in Rakefile, and run 'rake gemspec'
 # -*- encoding: utf-8 -*-
+# stub: bio-plasmoap 0.1.0 ruby lib
 
 Gem::Specification.new do |s|
-  s.name = %q{bio-plasmoap}
-  s.version = "0.0.2"
+  s.name = "bio-plasmoap"
+  s.version = "0.1.0"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
-  s.authors = [%q{Ben J Woodcroft}]
-  s.date = %q{2012-01-06}
-  s.description = %q{The PlasmoAP algorithm (Foth and Ralph et. al. 2003) predicts apicoplast transit peptides in Plasmodium falciparum. This is an implementation of that algorithm.}
-  s.email = %q{gmail.com after donttrustben}
-  s.executables = [%q{plasmoap.rb}]
+  s.require_paths = ["lib"]
+  s.authors = ["Ben J Woodcroft"]
+  s.date = "2016-04-14"
+  s.description = "The PlasmoAP algorithm (Foth and Ralph et. al. 2003) predicts apicoplast transit peptides in Plasmodium falciparum. This is an implementation of that algorithm."
+  s.email = "gmail.com after donttrustben"
+  s.executables = ["plasmoap.rb"]
   s.extra_rdoc_files = [
     "LICENSE.txt",
     "README.rdoc"
@@ -31,40 +33,36 @@ Gem::Specification.new do |s|
     "test/helper.rb",
     "test/test_bio-plasmoap.rb"
   ]
-  s.homepage = %q{http://github.com/wwood/bioruby-plasmoap}
-  s.licenses = [%q{MIT}]
-  s.require_paths = [%q{lib}]
-  s.rubygems_version = %q{1.8.6}
-  s.summary = %q{Implementation of the PlasmoAP algorithm}
+  s.homepage = "http://github.com/wwood/bioruby-plasmoap"
+  s.licenses = ["MIT"]
+  s.rubygems_version = "2.4.5.1"
+  s.summary = "Implementation of the PlasmoAP algorithm"
 
   if s.respond_to? :specification_version then
-    s.specification_version = 3
+    s.specification_version = 4
 
     if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
       s.add_runtime_dependency(%q<bio>, [">= 1.4.1"])
       s.add_runtime_dependency(%q<bio-signalp>, [">= 0.2.0"])
+      s.add_runtime_dependency(%q<test-unit>, [">= 3.1.8"])
       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>, [">= 1.4.1"])
+      s.add_development_dependency(%q<bundler>, [">= 1.0.0"])
+      s.add_development_dependency(%q<jeweler>, [">= 1.6.4"])
     else
       s.add_dependency(%q<bio>, [">= 1.4.1"])
       s.add_dependency(%q<bio-signalp>, [">= 0.2.0"])
+      s.add_dependency(%q<test-unit>, [">= 3.1.8"])
       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>, [">= 1.4.1"])
+      s.add_dependency(%q<bundler>, [">= 1.0.0"])
+      s.add_dependency(%q<jeweler>, [">= 1.6.4"])
     end
   else
     s.add_dependency(%q<bio>, [">= 1.4.1"])
     s.add_dependency(%q<bio-signalp>, [">= 0.2.0"])
+    s.add_dependency(%q<test-unit>, [">= 3.1.8"])
     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>, [">= 1.4.1"])
+    s.add_dependency(%q<bundler>, [">= 1.0.0"])
+    s.add_dependency(%q<jeweler>, [">= 1.6.4"])
   end
 end
 

data/lib/bio/appl/plasmoap.rb

@@ -1,4 +1,5 @@
 #!/usr/bin/ruby
+# coding: utf-8
 
 require 'bio'
 require 'bio-signalp'
@@ -23,6 +24,10 @@ module Bio
       if has_signal_sequence.nil?
         # to_s means the sequence can be amino acid string or proper Bio::Sequence::AA object
         signalp = Bio::SignalP::Wrapper.new.calculate(sequence.to_s)
+        unless signalp.kind_of?(Bio::SignalP::Version3::Result)
+          raise "PlasmoAP uses signalp version 3, but different version (#{signalp.class}) was found"
+        end
+        
         has_signal_sequence = signalp.classical_signal_sequence?
         
         signalp_cleaved_sequence = signalp.cleave(sequence)

metadata

@@ -1,93 +1,99 @@
 --- !ruby/object:Gem::Specification
 name: bio-plasmoap
 version: !ruby/object:Gem::Version
-  version: 0.0.2
-  prerelease: 
+  version: 0.1.0
 platform: ruby
 authors:
 - Ben J Woodcroft
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2012-01-06 00:00:00.000000000Z
+date: 2016-04-14 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bio
-  requirement: &80036180 !ruby/object:Gem::Requirement
-    none: false
+  requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ! '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: 1.4.1
   type: :runtime
   prerelease: false
-  version_requirements: *80036180
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 1.4.1
 - !ruby/object:Gem::Dependency
   name: bio-signalp
-  requirement: &80034850 !ruby/object:Gem::Requirement
-    none: false
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 0.2.0
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ! '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: 0.2.0
+- !ruby/object:Gem::Dependency
+  name: test-unit
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 3.1.8
   type: :runtime
   prerelease: false
-  version_requirements: *80034850
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 3.1.8
 - !ruby/object:Gem::Dependency
   name: shoulda
-  requirement: &79901560 !ruby/object:Gem::Requirement
-    none: false
+  requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ! '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *79901560
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
 - !ruby/object:Gem::Dependency
   name: bundler
-  requirement: &79900380 !ruby/object:Gem::Requirement
-    none: false
+  requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - ">="
       - !ruby/object:Gem::Version
         version: 1.0.0
   type: :development
   prerelease: false
-  version_requirements: *79900380
-- !ruby/object:Gem::Dependency
-  name: jeweler
-  requirement: &79899470 !ruby/object:Gem::Requirement
-    none: false
+  version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - ">="
       - !ruby/object:Gem::Version
-        version: 1.6.4
-  type: :development
-  prerelease: false
-  version_requirements: *79899470
+        version: 1.0.0
 - !ruby/object:Gem::Dependency
-  name: rcov
-  requirement: &79898480 !ruby/object:Gem::Requirement
-    none: false
+  name: jeweler
+  requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ! '>='
+    - - ">="
       - !ruby/object:Gem::Version
-        version: '0'
+        version: 1.6.4
   type: :development
   prerelease: false
-  version_requirements: *79898480
-- !ruby/object:Gem::Dependency
-  name: bio
-  requirement: &79897650 !ruby/object:Gem::Requirement
-    none: false
+  version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ! '>='
+    - - ">="
       - !ruby/object:Gem::Version
-        version: 1.4.1
-  type: :development
-  prerelease: false
-  version_requirements: *79897650
+        version: 1.6.4
 description: The PlasmoAP algorithm (Foth and Ralph et. al. 2003) predicts apicoplast
   transit peptides in Plasmodium falciparum. This is an implementation of that algorithm.
 email: gmail.com after donttrustben
@@ -98,7 +104,7 @@ extra_rdoc_files:
 - LICENSE.txt
 - README.rdoc
 files:
-- .document
+- ".document"
 - Gemfile
 - LICENSE.txt
 - README.rdoc
@@ -113,29 +119,25 @@ files:
 homepage: http://github.com/wwood/bioruby-plasmoap
 licenses:
 - MIT
+metadata: {}
 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: -875790545
 required_rubygems_version: !ruby/object:Gem::Requirement
-  none: false
   requirements:
-  - - ! '>='
+  - - ">="
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 1.8.6
+rubygems_version: 2.4.5.1
 signing_key: 
-specification_version: 3
+specification_version: 4
 summary: Implementation of the PlasmoAP algorithm
 test_files: []