unipept 0.6.1 → 0.6.2

checksums.yaml

@@ -1,7 +1,7 @@
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-  data.tar.gz: df8d0bb303b89dc56780cbf41f27c74c3573bdd6
+  metadata.gz: 567da9af48d82125a8bb3d330d25ee0f51429833
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data/Gemfile

@@ -3,6 +3,9 @@ source "http://rubygems.org"
 # Example:
 #   gem "activesupport", ">= 2.3.5"
 
+gem "cri", "~> 2.7"
+gem "typhoeus", "~> 0.6"
+
 # Add dependencies to develop your gem here.
 # Include everything needed to run rake, tests, features, etc.
 group :development do

data/Gemfile.lock

@@ -1,31 +1,37 @@
 GEM
   remote: http://rubygems.org/
   specs:
-    activesupport (4.1.1)
-      i18n (~> 0.6, >= 0.6.9)
+    activesupport (4.2.1)
+      i18n (~> 0.7)
       json (~> 1.7, >= 1.7.7)
       minitest (~> 5.1)
-      thread_safe (~> 0.1)
+      thread_safe (~> 0.3, >= 0.3.4)
       tzinfo (~> 1.1)
-    addressable (2.3.6)
+    addressable (2.3.8)
     builder (3.2.2)
+    colored (1.2)
+    cri (2.7.0)
+      colored (~> 1.2)
     descendants_tracker (0.0.4)
       thread_safe (~> 0.3, >= 0.3.1)
     docile (1.1.5)
-    faraday (0.9.0)
+    ethon (0.7.3)
+      ffi (>= 1.3.0)
+    faraday (0.9.1)
       multipart-post (>= 1.2, < 3)
-    git (1.2.7)
-    github_api (0.11.3)
+    ffi (1.9.8)
+    git (1.2.9.1)
+    github_api (0.12.3)
       addressable (~> 2.3)
-      descendants_tracker (~> 0.0.1)
+      descendants_tracker (~> 0.0.4)
       faraday (~> 0.8, < 0.10)
-      hashie (>= 1.2)
+      hashie (>= 3.3)
       multi_json (>= 1.7.5, < 2.0)
-      nokogiri (~> 1.6.0)
+      nokogiri (~> 1.6.3)
       oauth2
-    hashie (3.0.0)
-    highline (1.6.21)
-    i18n (0.6.9)
+    hashie (3.4.1)
+    highline (1.7.2)
+    i18n (0.7.0)
     jeweler (2.0.1)
       builder
       bundler (>= 1.0)
@@ -35,38 +41,40 @@ GEM
       nokogiri (>= 1.5.10)
       rake
       rdoc
-    json (1.8.1)
-    jwt (1.0.0)
-    mini_portile (0.6.0)
-    minitest (5.3.5)
-    multi_json (1.10.1)
+    json (1.8.2)
+    jwt (1.4.1)
+    mini_portile (0.6.2)
+    minitest (5.6.1)
+    multi_json (1.11.0)
     multi_xml (0.5.5)
     multipart-post (2.0.0)
-    nokogiri (1.6.2.1)
-      mini_portile (= 0.6.0)
-    oauth2 (0.9.4)
+    nokogiri (1.6.6.2)
+      mini_portile (~> 0.6.0)
+    oauth2 (1.0.0)
       faraday (>= 0.8, < 0.10)
       jwt (~> 1.0)
       multi_json (~> 1.3)
       multi_xml (~> 0.5)
       rack (~> 1.2)
-    rack (1.5.2)
-    rake (10.3.2)
+    rack (1.6.0)
+    rake (10.4.2)
     rdoc (3.12.2)
       json (~> 1.4)
     shoulda (3.5.0)
       shoulda-context (~> 1.0, >= 1.0.1)
       shoulda-matchers (>= 1.4.1, < 3.0)
     shoulda-context (1.2.1)
-    shoulda-matchers (2.6.1)
+    shoulda-matchers (2.8.0)
       activesupport (>= 3.0.0)
-    simplecov (0.8.2)
+    simplecov (0.10.0)
       docile (~> 1.1.0)
-      multi_json
-      simplecov-html (~> 0.8.0)
-    simplecov-html (0.8.0)
-    thread_safe (0.3.4)
-    tzinfo (1.2.1)
+      json (~> 1.8)
+      simplecov-html (~> 0.10.0)
+    simplecov-html (0.10.0)
+    thread_safe (0.3.5)
+    typhoeus (0.7.1)
+      ethon (>= 0.7.1)
+    tzinfo (1.2.2)
       thread_safe (~> 0.1)
 
 PLATFORMS
@@ -74,7 +82,9 @@ PLATFORMS
 
 DEPENDENCIES
   bundler (~> 1.0)
+  cri (~> 2.7)
   jeweler (~> 2.0)
   rdoc (~> 3.12)
   shoulda (~> 3.5)
   simplecov (~> 0.8)
+  typhoeus (~> 0.6)

data/Rakefile

@@ -23,9 +23,6 @@ Jeweler::Tasks.new do |gem|
   gem.email = "unipept@ugent.be"
   gem.authors = ["Toon Willems", "Bart Mesuere", "Tom Naessens"]
   gem.required_ruby_version = '>= 1.9.3'
-  # dependencies defined in Gemfile
-  gem.add_dependency 'typhoeus', '~> 0.6'
-  gem.add_dependency 'cri', '~> 2.6'
 end
 Jeweler::RubygemsDotOrgTasks.new
 

data/VERSION

@@ -1 +1 @@
-0.6.1
+0.6.2

data/bin/uniprot

@@ -5,26 +5,35 @@ require 'cri'
 Signal.trap("PIPE", "EXIT")
 Signal.trap("INT", "EXIT")
 
-def get_uniprot_entry(arg, fasta = false)
-  resp = Typhoeus.get("http://www.uniprot.org/uniprot/#{arg}.fasta")
-  if resp.success?
-    if fasta
-      puts resp.response_body
-    else
+valid_formats = Set.new ["fasta", "txt", "xml", "rdf", "gff"]
+
+def get_uniprot_entry(arg, format)
+  if format.nil? || format.empty?
+    resp = Typhoeus.get("http://www.uniprot.org/uniprot/#{arg}.fasta")
+    if resp.success?
       puts resp.response_body.lines.map(&:chomp)[1..-1].join("")
     end
+  else
+    # other format has been specified, just download and output
+    resp = Typhoeus.get("http://www.uniprot.org/uniprot/#{arg}.#{format}")
+    if resp.success?
+      puts resp.response_body
+    end
   end
 end
 
 root_cmd = Cri::Command.new_basic_root.modify do
   name 'uniprot'
   description 'Download protein sequence from uniprot.org'
-  required :f, :format, "specify output format (available: fasta, plain)"
+  required :f, :format, "specify output format (available: " + valid_formats.to_a.join(", ") + ")"
   run do |opts, args, cmd|
-    fasta = opts[:format] == 'fasta'
+    if !opts[:format].nil? and !valid_formats.include? opts[:format]
+      $stderr.puts opts[:format] + " is not a valid output format. Available formats are: " + valid_formats.to_a.join(", ")
+      exit 1
+    end
     iterator = args.empty? ? $stdin.each_line : args
     iterator.each do |pept|
-      get_uniprot_entry(pept.chomp, fasta)
+      get_uniprot_entry(pept.chomp, opts[:format])
     end
   end
 end

data/unipept.gemspec

@@ -2,16 +2,16 @@
 # DO NOT EDIT THIS FILE DIRECTLY
 # Instead, edit Jeweler::Tasks in Rakefile, and run 'rake gemspec'
 # -*- encoding: utf-8 -*-
-# stub: unipept 0.6.1 ruby lib
+# stub: unipept 0.6.2 ruby lib
 
 Gem::Specification.new do |s|
   s.name = "unipept"
-  s.version = "0.6.1"
+  s.version = "0.6.2"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.require_paths = ["lib"]
   s.authors = ["Toon Willems", "Bart Mesuere", "Tom Naessens"]
-  s.date = "2015-04-22"
+  s.date = "2015-04-30"
   s.description = "Command line interface to Unipept web services."
   s.email = "unipept@ugent.be"
   s.executables = ["unipept", "prot2pept", "peptfilter", "uniprot"]
@@ -57,30 +57,30 @@ Gem::Specification.new do |s|
     s.specification_version = 4
 
     if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
+      s.add_runtime_dependency(%q<cri>, ["~> 2.7"])
+      s.add_runtime_dependency(%q<typhoeus>, ["~> 0.6"])
       s.add_development_dependency(%q<shoulda>, ["~> 3.5"])
       s.add_development_dependency(%q<rdoc>, ["~> 3.12"])
       s.add_development_dependency(%q<bundler>, ["~> 1.0"])
       s.add_development_dependency(%q<jeweler>, ["~> 2.0"])
       s.add_development_dependency(%q<simplecov>, ["~> 0.8"])
-      s.add_runtime_dependency(%q<typhoeus>, ["~> 0.6"])
-      s.add_runtime_dependency(%q<cri>, ["~> 2.6"])
     else
+      s.add_dependency(%q<cri>, ["~> 2.7"])
+      s.add_dependency(%q<typhoeus>, ["~> 0.6"])
       s.add_dependency(%q<shoulda>, ["~> 3.5"])
       s.add_dependency(%q<rdoc>, ["~> 3.12"])
       s.add_dependency(%q<bundler>, ["~> 1.0"])
       s.add_dependency(%q<jeweler>, ["~> 2.0"])
       s.add_dependency(%q<simplecov>, ["~> 0.8"])
-      s.add_dependency(%q<typhoeus>, ["~> 0.6"])
-      s.add_dependency(%q<cri>, ["~> 2.6"])
     end
   else
+    s.add_dependency(%q<cri>, ["~> 2.7"])
+    s.add_dependency(%q<typhoeus>, ["~> 0.6"])
     s.add_dependency(%q<shoulda>, ["~> 3.5"])
     s.add_dependency(%q<rdoc>, ["~> 3.12"])
     s.add_dependency(%q<bundler>, ["~> 1.0"])
     s.add_dependency(%q<jeweler>, ["~> 2.0"])
     s.add_dependency(%q<simplecov>, ["~> 0.8"])
-    s.add_dependency(%q<typhoeus>, ["~> 0.6"])
-    s.add_dependency(%q<cri>, ["~> 2.6"])
   end
 end
 

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: unipept
 version: !ruby/object:Gem::Version
-  version: 0.6.1
+  version: 0.6.2
 platform: ruby
 authors:
 - Toon Willems
@@ -10,106 +10,106 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2015-04-22 00:00:00.000000000 Z
+date: 2015-04-30 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
-  name: shoulda
+  name: cri
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '3.5'
-  type: :development
+        version: '2.7'
+  type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '3.5'
+        version: '2.7'
 - !ruby/object:Gem::Dependency
-  name: rdoc
+  name: typhoeus
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '3.12'
-  type: :development
+        version: '0.6'
+  type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '3.12'
+        version: '0.6'
 - !ruby/object:Gem::Dependency
-  name: bundler
+  name: shoulda
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '1.0'
+        version: '3.5'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '1.0'
+        version: '3.5'
 - !ruby/object:Gem::Dependency
-  name: jeweler
+  name: rdoc
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '2.0'
+        version: '3.12'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '2.0'
+        version: '3.12'
 - !ruby/object:Gem::Dependency
-  name: simplecov
+  name: bundler
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '0.8'
+        version: '1.0'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '0.8'
+        version: '1.0'
 - !ruby/object:Gem::Dependency
-  name: typhoeus
+  name: jeweler
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '0.6'
-  type: :runtime
+        version: '2.0'
+  type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '0.6'
+        version: '2.0'
 - !ruby/object:Gem::Dependency
-  name: cri
+  name: simplecov
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '2.6'
-  type: :runtime
+        version: '0.8'
+  type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '2.6'
+        version: '0.8'
 description: Command line interface to Unipept web services.
 email: unipept@ugent.be
 executables: