unipept 0.3.2 → 0.3.3

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 600ed2755ace1b8b8b617e9e0065ee94ba7ca54a
-  data.tar.gz: 2a243e1447775619c9647e8686392dda876d9531
+  metadata.gz: 50644c602dbd81f19cb9fe9227c961b7f201c558
+  data.tar.gz: f3d2c2640f96499686872f522f0862381268cda4
 SHA512:
-  metadata.gz: 05527d12256c915151a261e29ab6be21bce9f787ed004b9607e4b63f76bc4b8d1d0224933e32702915bd90ac663779f8b626f44d36d69759d1ca8a70885b3dea
-  data.tar.gz: cb2590b866380a7658827e615598bbe640004bfe5d19cc72160cc8081da37f57c8dafde1bf181ecf475f0ac69c66db4aad13011d33336688225282818d06db86
+  metadata.gz: a093829d561541fb505d676c386aa7503baf38c8295c8c002c012b24f4131324c1ade7261c0cdadb660a02cbe85ce332c3bffa11f138859bd20dd58cee35895c
+  data.tar.gz: 6824cac10d9ef6eb5621795ca0a0ab5e06cfb653c3470294fe918b45ea81d52ed054f7784077d2b359c74a70299b5ea7601460213f8448d6d67a505eabbffd22

data/VERSION

@@ -1 +1 @@
-0.3.2
+0.3.3

data/bin/peptfilter

@@ -1,10 +1,8 @@
 #!/usr/bin/env ruby
 require 'cri'
 
-trap "INT" do
-  $interupted = true
-end
 Signal.trap("PIPE", "EXIT")
+Signal.trap("INT", "EXIT")
 root_cmd = Cri::Command.new_basic_root.modify do
   name 'peptfilter'
   flag :i, :unique, "only output unique peptides"
@@ -18,7 +16,6 @@ root_cmd = Cri::Command.new_basic_root.modify do
     lacks = opts.fetch(:lacks, "").chars.to_a
     contains = opts.fetch(:contains, "").chars.to_a
     $stdin.each_line do |pept|
-      break if $interupted
       pept = pept.chomp
       length_ok = pept.length >= minlen && pept.length <= maxlen
       lacks_ok = (pept.chars.to_a & lacks).size == 0

data/bin/prot2pept

@@ -1,17 +1,14 @@
 #!/usr/bin/env ruby
 require 'cri'
 
-trap "INT" do
-  $interupted = true
-end
 Signal.trap("PIPE", "EXIT")
+Signal.trap("INT", "EXIT")
 root_cmd = Cri::Command.new_basic_root.modify do
   name 'prot2pept'
   required :p, :pattern, "cleavage pattern to split input protein (default: ([KR])([^P]))"
   run do |opts, args, cmd|
     pattern = opts.fetch(:pattern, "([KR])([^P])")
     $stdin.each_line do |prot|
-      break if $interupted
       puts prot.gsub(/#{pattern}/,"\\1\n\\2").gsub(/#{pattern}/, "\\1\n\\2").split("\n").reject(&:empty?)
     end
   end

data/bin/unipept

@@ -8,13 +8,8 @@ require 'fileutils'
 
 require_relative '../lib/unipept'
 
-$interupted = false
-
-trap "INT" do
-  puts "Interupted, exiting..."
-  $interupted = true
-end
-
+Signal.trap("PIPE", "EXIT")
+Signal.trap("INT", "EXIT")
 class ApiRunner < Cri::CommandRunner
 
   def initialize(args, opts, cmd)
@@ -79,11 +74,6 @@ class ApiRunner < Cri::CommandRunner
     num_req = 0
 
     peptide_iterator(peptides) do |sub_division, i|
-      if $interupted
-        $stdin.close
-        exit 1
-      end
-
       request = Typhoeus::Request.new(
         @url,
         method: :post,

data/bin/uniprot

@@ -1,5 +1,7 @@
 #!/usr/bin/env ruby
 require 'faraday'
+Signal.trap("PIPE", "EXIT")
+Signal.trap("INT", "EXIT")
 ARGV.each do |arg|
   resp = Faraday.get("http://www.uniprot.org/uniprot/#{arg}.fasta")
   if resp.success?

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: unipept
 version: !ruby/object:Gem::Version
-  version: 0.3.2
+  version: 0.3.3
 platform: ruby
 authors:
 - Toon Willems
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-05-07 00:00:00.000000000 Z
+date: 2014-05-09 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: shoulda