unipept 0.10.0 → 1.0.0

checksums.yaml

@@ -1,7 +1,7 @@
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data/Gemfile.lock

@@ -110,3 +110,6 @@ DEPENDENCIES
   rake (~> 10.4)
   rubocop (~> 0.32)
   typhoeus (= 0.7.2)
+
+BUNDLED WITH
+   1.10.3

data/Rakefile

@@ -23,7 +23,7 @@ Jeweler::Tasks.new do |gem|
   gem.summary = 'Command line interface to Unipept web services.'
   gem.description = <<-EOS
   Command line interface to the Unipept (http://unipept.ugent.be) web services
-  (pept2lca, taxa2lca, pept2taxa and taxonomy) and some utility commands for
+  (pept2lca, taxa2lca, pept2taxa, pept2prot and taxonomy) and some utility commands for
   handling proteins using the command line.
   EOS
   gem.email = 'unipept@ugent.be'

data/VERSION

@@ -1 +1 @@
-0.10.0
+1.0.0

data/lib/commands/unipept.rb

@@ -93,9 +93,9 @@ module Unipept
     def add_pept2taxa_command
       @root_command.define_command('pept2taxa') do
         usage 'pept2taxa [options]'
-        summary 'Fetch taxa of Uniprot records that match tryptic peptides.'
+        summary 'Fetch taxa of UniProt entries that match tryptic peptides.'
         description <<-EOS
-        For each tryptic peptide the unipept pept2taxa command retrieves from Unipept the set of taxa from all Uniprot records whose protein sequence contains an exact matches to the tryptic peptide. The command expects a list of tryptic peptides that are passed
+        For each tryptic peptide the unipept pept2taxa command retrieves from Unipept the set of taxa from all UniProt entries whose protein sequence contains an exact matches to the tryptic peptide. The command expects a list of tryptic peptides that are passed
 
         - as separate command line arguments
 
@@ -117,9 +117,9 @@ module Unipept
     def add_pept2lca_command
       @root_command.define_command('pept2lca') do
         usage 'pept2lca [options]'
-        summary 'Fetch taxonomic lowest common ancestor of Uniprot records that match tryptic peptides.'
+        summary 'Fetch taxonomic lowest common ancestor of UniProt entries that match tryptic peptides.'
         description <<-EOS
-        For each tryptic peptide the unipept pept2lca command retrieves from Unipept the lowest common ancestor of the set of taxa from all Uniprot records whose protein sequence contains an exact matches to the tryptic peptide. The lowest common ancestor is based on the topology of the Unipept Taxonomy -- a cleaned up version of the NCBI Taxonomy -- and is itself a record from the NCBI Taxonomy. The command expects a list of tryptic peptides that are passed
+        For each tryptic peptide the unipept pept2lca command retrieves from Unipept the lowest common ancestor of the set of taxa from all UniProt entries whose protein sequence contains an exact matches to the tryptic peptide. The lowest common ancestor is based on the topology of the Unipept Taxonomy -- a cleaned up version of the NCBI Taxonomy -- and is itself a record from the NCBI Taxonomy. The command expects a list of tryptic peptides that are passed
 
          - as separate command line arguments
 
@@ -164,9 +164,9 @@ module Unipept
     def add_pept2prot_command
       @root_command.define_command('pept2prot') do
         usage 'pept2prot [options]'
-        summary 'Fetch Uniprot records that match tryptic peptides.'
+        summary 'Fetch UniProt entries that match tryptic peptides.'
         description <<-EOS
-        For each tryptic peptide the unipept pept2prot command retrieves from Unipept all Uniprot records whose protein sequence contains an exact matches to the tryptic peptide. The command expects a list of tryptic peptides that are passed
+        For each tryptic peptide the unipept pept2prot command retrieves from Unipept all UniProt entries whose protein sequence contains an exact matches to the tryptic peptide. The command expects a list of tryptic peptides that are passed
 
         - as separate command line arguments
 
@@ -178,7 +178,7 @@ module Unipept
         EOS
 
         flag :e, :equate, 'equate isoleucine (I) and leucine (L) when matching peptides'
-        flag :a, :all, 'report all information fields of Uniprot records available in Unipept. Note that this may have a performance penalty.'
+        flag :a, :all, 'report all information fields of UniProt entries available in Unipept. Note that this may have a performance penalty.'
         option :s, :select, 'select the information fields to return. Selected fields are passed as a comma separated list of field names. Multiple -s (or --select) options may be used.', argument: :required, multiple: true
 
         runner Commands::Pept2prot

data/lib/commands/uniprot.rb

@@ -8,16 +8,16 @@ module Unipept::Commands
     valid_formats = Set.new %w(fasta txt xml rdf gff sequence)
     @root_command = Cri::Command.define do
       name 'uniprot'
-      summary 'Command line interface to Uniprot web services.'
+      summary 'Command line interface to UniProt web services.'
       usage 'uniprot [options]'
       description <<-EOS
-      The uniprot command is a command line wrapper around the Uniprot web services. The command expects a list of Uniprot Accession Numbers that are passed
+      The uniprot command fetches UniProt entries from the UniProt web services. The command expects a list of UniProt Accession Numbers that are passed
 
       - as separate command line arguments
 
       - to standard input
 
-      The command will give priority to the first way Uniprot Accession Numbers are passed, in the order as listed above. The standard input should have one Uniprot Accession Number per line.
+      The command will give priority to the first way UniProt Accession Numbers are passed, in the order as listed above. The standard input should have one UniProt Accession Number per line.
 
       The uniprot command yields just the protein sequences as a default, but can return several formats.
       EOS
@@ -48,14 +48,14 @@ module Unipept::Commands
       @root_command.run(args)
     end
 
-    # Fetches a Uniprot record from the uniprot website with the given accession
+    # Fetches a UniProt entry from the UniProt website with the given accession
     # number in the requested format.
     #
     # @param [String] accession The accession number of the record to fetch
     #
     # @param [String] format The format of of the record. If the format is 'sequence', the sequence will be returned in as a single line
     #
-    # @return [String] The requested Uniprot record in the requested format
+    # @return [String] The requested UniProt entry in the requested format
     def self.get_uniprot_entry(accession, format)
       if format == 'sequence'
         get_uniprot_entry(accession, 'fasta').lines.map(&:chomp)[1..-1].join('')

data/test/commands/unipept/test_api_runner.rb

@@ -14,7 +14,7 @@ module Unipept
       assert_equal(%w(a b c), runner.arguments)
       assert(!runner.configuration.nil?)
       assert_equal('http://test_host/api/v1/test.json', runner.url)
-      assert(/Unipept CLI - unipept [0-9]\.[0-9]\.[0-9]/.match runner.user_agent)
+      assert(/Unipept CLI - unipept [0-9]*\.[0-9]*\.[0-9]*/.match runner.user_agent)
     end
 
     def test_config_host

data/unipept.gemspec

@@ -2,16 +2,17 @@
 # DO NOT EDIT THIS FILE DIRECTLY
 # Instead, edit Jeweler::Tasks in Rakefile, and run 'rake gemspec'
 # -*- encoding: utf-8 -*-
-# stub: unipept 0.10.0 ruby lib
+# stub: unipept 1.0.0 ruby lib
 
 Gem::Specification.new do |s|
   s.name = "unipept"
-  s.version = "0.10.0"
+  s.version = "1.0.0"
 
   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 = "2015-07-01"
-  s.description = "  Command line interface to the Unipept (http://unipept.ugent.be) web services\n  (pept2lca, taxa2lca, pept2taxa and taxonomy) and some utility commands for\n  handling proteins using the command line.\n"
+  s.date = "2015-07-14"
+  s.description = "  Command line interface to the Unipept (http://unipept.ugent.be) web services\n  (pept2lca, taxa2lca, pept2taxa, pept2prot and taxonomy) and some utility commands for\n  handling proteins using the command line.\n"
   s.email = "unipept@ugent.be"
   s.executables = ["unipept", "prot2pept", "peptfilter", "uniprot"]
   s.extra_rdoc_files = [
@@ -75,9 +76,8 @@ Gem::Specification.new do |s|
   ]
   s.homepage = "https://github.com/unipept/unipept-cli/"
   s.licenses = ["MIT"]
-  s.require_paths = ["lib"]
   s.required_ruby_version = Gem::Requirement.new(">= 1.9.3")
-  s.rubygems_version = "2.1.11"
+  s.rubygems_version = "2.4.8"
   s.summary = "Command line interface to Unipept web services."
 
   if s.respond_to? :specification_version then

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: unipept
 version: !ruby/object:Gem::Version
-  version: 0.10.0
+  version: 1.0.0
 platform: ruby
 authors:
 - Toon Willems
@@ -10,7 +10,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2015-07-01 00:00:00.000000000 Z
+date: 2015-07-14 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: cri
@@ -112,7 +112,7 @@ dependencies:
         version: '0'
 description: |2
     Command line interface to the Unipept (http://unipept.ugent.be) web services
-    (pept2lca, taxa2lca, pept2taxa and taxonomy) and some utility commands for
+    (pept2lca, taxa2lca, pept2taxa, pept2prot and taxonomy) and some utility commands for
     handling proteins using the command line.
 email: unipept@ugent.be
 executables:
@@ -198,7 +198,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.1.11
+rubygems_version: 2.4.8
 signing_key: 
 specification_version: 4
 summary: Command line interface to Unipept web services.