unipept 1.0.1 → 1.1.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 1709761b341ebd499d5e631b2f3bd5538533408f
-  data.tar.gz: 35551d52792f8af5cbbf5174a9073f64ba4310c5
+  metadata.gz: e4a1d5d01af5e00b706fe387a78a1a661d11a0ed
+  data.tar.gz: 22064ff35a1789a2cbc48fca2c4f4ec967c3d3a0
 SHA512:
-  metadata.gz: b3e93b0fc0997a12418e8d4e0e024766ab464992fbbad7920ec490e83786fae26b462ae43f959047c51976264d0ca61576cffbd55d1d0e58b8dfdc6502070650
-  data.tar.gz: bf92c339ab872bd4cc9faf526b08ffed8eb800554b6d7b7141f6332247bb0df3312b02ec0e7ee5c69c45db818831164d429c7609ce4b9e7414c87bfb9769f26e
+  metadata.gz: e880e9f0737b91efae32a9724cb20ded630af7ad6bc3853af3b3993ebafea024d957f66d9fb14315f2670ade638dc7d708cafb92e54d540906ad1539a529c334
+  data.tar.gz: f7cd476ef08424f6a840033a33a025c70ce6eebeda8e71ea454c89246696678cb5049460bdc32904b54b72a447778d5b4aae01f134ac375153560bc5e9b1e684

data/VERSION

@@ -1 +1 @@
-1.0.1
+1.1.0

data/lib/commands/prot2pept.rb

@@ -46,7 +46,7 @@ module Unipept::Commands
     end
 
     def self.split(protein, pattern)
-      protein.gsub(/#{pattern}/, "\\1\n\\2").gsub(/#{pattern}/, "\\1\n\\2").split("\n").reject(&:empty?)
+      protein.gsub(/\*/, "\n").gsub(/#{pattern}/, "\\1\n\\2").gsub(/#{pattern}/, "\\1\n\\2").split("\n").reject(&:empty?)
     end
 
     # Invokes the uniprot command-line tool with the given arguments.

data/test/commands/test_prot2pept.rb

@@ -8,6 +8,11 @@ module Unipept
       end
       assert_equal("AALTER\nAALTERPAALTER", out.chomp)
 
+      out, _err = capture_io_with_input('AALTERAAL*TERPAALTER') do
+        Commands::Prot2pept.run(%w())
+      end
+      assert_equal("AALTER\nAAL\nTERPAALTER", out.chomp)
+
       out, _err = capture_io_with_input('KRKPR') do
         Commands::Prot2pept.run(%w())
       end

data/test/commands/unipept/test_pept2prot.rb

@@ -32,7 +32,7 @@ module Unipept
       end
       lines = out.each_line
       assert_equal('', err)
-      assert(lines.next.start_with? 'peptide,uniprot_id,taxon_id')
+      assert(lines.next.start_with? 'peptide,uniprot_id,protein_name,taxon_id')
       assert(lines.next.start_with? 'ENFVYIAK,')
     end
 
@@ -42,7 +42,7 @@ module Unipept
       end
       lines = out.each_line
       assert_equal('', err)
-      assert(lines.next.start_with? 'fasta_header,peptide,uniprot_id,taxon_id')
+      assert(lines.next.start_with? 'fasta_header,peptide,uniprot_id,protein_name,taxon_id')
       assert(lines.count { |line| line.start_with? '>test,EGGAGSSTGQR,' } >= 1)
       assert(lines.count { |line| line.start_with? '>test,ENFVYIAK,' } >= 1)
       assert(lines.count { |line| line.start_with? '>tost,EGGAGSSTGQR,' } >= 1)

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 1.0.1 ruby lib
+# stub: unipept 1.1.0 ruby lib
 
 Gem::Specification.new do |s|
   s.name = "unipept"
-  s.version = "1.0.1"
+  s.version = "1.1.0"
 
   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 = "2015-07-31"
+  s.date = "2015-09-16"
   s.description = "  Command line interface to the Unipept (http://unipept.ugent.be) web services\n  (pept2lca, taxa2lca, pept2taxa, pept2prot and taxonomy) and some utility\n  commands for handling proteins using the command line.\n"
   s.email = "unipept@ugent.be"
   s.executables = ["unipept", "prot2pept", "peptfilter", "uniprot"]

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: unipept
 version: !ruby/object:Gem::Version
-  version: 1.0.1
+  version: 1.1.0
 platform: ruby
 authors:
 - Toon Willems
@@ -10,7 +10,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2015-07-31 00:00:00.000000000 Z
+date: 2015-09-16 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: cri