unipept 0.5.6 → 0.5.7

checksums.yaml

@@ -1,7 +1,7 @@
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-  data.tar.gz: 804ec2db29552953e0769ee1ef6df9e005828b8c
+  metadata.gz: dc51bfb9426c0e63f031b38e701e8629d2752ca5
+  data.tar.gz: 3d09c51e3487bab60beab0bf14382b00d8a517eb
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data/Gemfile.lock

@@ -1,20 +1,20 @@
 GEM
   remote: http://rubygems.org/
   specs:
-    activesupport (4.0.3)
-      i18n (~> 0.6, >= 0.6.4)
-      minitest (~> 4.2)
-      multi_json (~> 1.3)
+    activesupport (4.1.1)
+      i18n (~> 0.6, >= 0.6.9)
+      json (~> 1.7, >= 1.7.7)
+      minitest (~> 5.1)
       thread_safe (~> 0.1)
-      tzinfo (~> 0.3.37)
-    addressable (2.3.5)
-    atomic (1.1.15)
+      tzinfo (~> 1.1)
+    addressable (2.3.6)
     builder (3.2.2)
-    descendants_tracker (0.0.3)
-    docile (1.1.3)
+    descendants_tracker (0.0.4)
+      thread_safe (~> 0.3, >= 0.3.1)
+    docile (1.1.5)
     faraday (0.9.0)
       multipart-post (>= 1.2, < 3)
-    git (1.2.6)
+    git (1.2.7)
     github_api (0.11.3)
       addressable (~> 2.3)
       descendants_tracker (~> 0.0.1)
@@ -23,7 +23,7 @@ GEM
       multi_json (>= 1.7.5, < 2.0)
       nokogiri (~> 1.6.0)
       oauth2
-    hashie (2.0.5)
+    hashie (3.0.0)
     highline (1.6.21)
     i18n (0.6.9)
     jeweler (2.0.1)
@@ -36,39 +36,38 @@ GEM
       rake
       rdoc
     json (1.8.1)
-    jwt (0.1.11)
-      multi_json (>= 1.5)
-    mini_portile (0.5.2)
-    minitest (4.7.5)
-    multi_json (1.9.0)
+    jwt (1.0.0)
+    mini_portile (0.6.0)
+    minitest (5.3.5)
+    multi_json (1.10.1)
     multi_xml (0.5.5)
     multipart-post (2.0.0)
-    nokogiri (1.6.1)
-      mini_portile (~> 0.5.0)
-    oauth2 (0.9.3)
+    nokogiri (1.6.2.1)
+      mini_portile (= 0.6.0)
+    oauth2 (0.9.4)
       faraday (>= 0.8, < 0.10)
-      jwt (~> 0.1.8)
+      jwt (~> 1.0)
       multi_json (~> 1.3)
       multi_xml (~> 0.5)
       rack (~> 1.2)
     rack (1.5.2)
-    rake (10.1.1)
+    rake (10.3.2)
     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 (1.1.6)
-    shoulda-matchers (2.5.0)
+    shoulda-context (1.2.1)
+    shoulda-matchers (2.6.1)
       activesupport (>= 3.0.0)
     simplecov (0.8.2)
       docile (~> 1.1.0)
       multi_json
       simplecov-html (~> 0.8.0)
     simplecov-html (0.8.0)
-    thread_safe (0.2.0)
-      atomic (>= 1.1.7, < 2)
-    tzinfo (0.3.39)
+    thread_safe (0.3.4)
+    tzinfo (1.2.1)
+      thread_safe (~> 0.1)
 
 PLATFORMS
   ruby

data/VERSION

@@ -1 +1 @@
-0.5.6
+0.5.7

data/bin/prot2pept

@@ -9,7 +9,7 @@ root_cmd = Cri::Command.new_basic_root.modify do
   run do |opts, args, cmd|
     pattern = opts.fetch(:pattern, "([KR])([^P])")
     # decide if we have FASTA input
-    fasta_header = gets
+    fasta_header = $stdin.gets
     if fasta_header.start_with? '>'
       # fasta input, need to join lines
       while !$stdin.eof?

data/bin/unipept

@@ -66,7 +66,7 @@ root_cmd = Cri::Command.new_basic_root.modify do
   option :f, :format, "output format (available: #{Unipept::Formatter.available.join "," }) (default: #{Unipept::Formatter.default})", :argument => :required
 
   # Configuration options
-  option nil, "config-host", "Override host setting", argument: :required
+  option nil, "host", "Override host setting", argument: :required
 
   run do |opts, args, cmd|
     if opts[:version]

data/bin/uniprot

@@ -16,14 +16,18 @@ def get_uniprot_entry(arg, fasta = false)
   end
 end
 
-fasta = ARGV.delete "--fasta"
-
-if ARGV.empty?
-  STDIN.each_line do |pept|
-    get_uniprot_entry(pept.chomp, fasta)
-  end
-else
-  ARGV.each do |pept|
-    get_uniprot_entry(pept, fasta)
+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)"
+  run do |opts, args, cmd|
+    fasta = opts[:format] == 'fasta'
+    iterator = args.empty? ? $stdin.each_line : args
+    iterator.each do |pept|
+      get_uniprot_entry(pept.chomp, fasta)
+    end
   end
 end
+
+# run_this runs this command without subcommands! Absolutely needed here
+root_cmd.run_this(ARGV)

data/lib/unipept/api_runner.rb

@@ -13,8 +13,8 @@ module Unipept
 
     def set_configuration
       # find host in opts first
-      if options[:'config-host']
-        host = options[:'config-host']
+      if options[:host]
+        host = options[:host]
       else
         host = @configuration['host']
       end
@@ -86,8 +86,8 @@ module Unipept
       peptides = input_iterator
 
       filter_list = options[:select] ? options[:select] : []
-      filter_list = filter_list.map {|f| glob_to_regex(f) }
-      output = STDOUT.tty? ? STDOUT : STDERR
+      # Parse filter list: convert to regex and split on commas
+      filter_list = filter_list.map { |f| f.include?(",") ? f.split(",") : f }.flatten.map { |f| glob_to_regex(f) }
 
       batch_order = Unipept::BatchOrder.new
 
@@ -214,9 +214,9 @@ module Unipept
 
     private
 
-    def glob_to_regex(glob_string)
-      # only implement * -> . for now
-      Regexp.new glob_string.gsub("*", ".*")
+    def glob_to_regex(string)
+      /^#{string.gsub('*','.*')}$/
     end
+
   end
 end

data/unipept.gemspec

@@ -2,11 +2,11 @@
 # DO NOT EDIT THIS FILE DIRECTLY
 # Instead, edit Jeweler::Tasks in Rakefile, and run 'rake gemspec'
 # -*- encoding: utf-8 -*-
-# stub: unipept 0.5.6 ruby lib
+# stub: unipept 0.5.7 ruby lib
 
 Gem::Specification.new do |s|
   s.name = "unipept"
-  s.version = "0.5.6"
+  s.version = "0.5.7"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.require_paths = ["lib"]

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: unipept
 version: !ruby/object:Gem::Version
-  version: 0.5.6
+  version: 0.5.7
 platform: ruby
 authors:
 - Toon Willems