unipept 0.3.1 → 0.3.2

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
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-  data.tar.gz: e3a91a2e7ca3b2b076c19e0d7291bb90c69dfd04
+  metadata.gz: 600ed2755ace1b8b8b617e9e0065ee94ba7ca54a
+  data.tar.gz: 2a243e1447775619c9647e8686392dda876d9531
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+  data.tar.gz: cb2590b866380a7658827e615598bbe640004bfe5d19cc72160cc8081da37f57c8dafde1bf181ecf475f0ac69c66db4aad13011d33336688225282818d06db86

data/VERSION

@@ -1 +1 @@
-0.3.1
+0.3.2

data/bin/unipept

@@ -78,7 +78,7 @@ class ApiRunner < Cri::CommandRunner
     hydra = Typhoeus::Hydra.new(max_concurrency: 20)
     num_req = 0
 
-    peptide_iterator(peptides).with_index do |sub_division, i|
+    peptide_iterator(peptides) do |sub_division, i|
       if $interupted
         $stdin.close
         exit 1
@@ -159,7 +159,7 @@ class ApiRunner < Cri::CommandRunner
   end
 
   def peptide_iterator(peptides, &block)
-    peptides.each_slice(batch_size, &block)
+    peptides.each_slice(batch_size).with_index(&block)
   end
 
   private
@@ -181,7 +181,7 @@ class Taxa2lca < ApiRunner
   end
 
   def peptide_iterator(peptides, &block)
-    block.call(peptides.to_a)
+    block.call(peptides.to_a, 0)
   end
 
   def batch_size
@@ -197,7 +197,7 @@ class Pept2prot < ApiRunner
   end
 
   def url_options(sub_part)
-    {:sequences => sub_part, :equate_il => options[:equate]}
+    {:sequences => sub_part, :equate_il => options[:equate], :extra => options[:all]}
   end
 
   def download_xml(result)
@@ -294,6 +294,7 @@ root_cmd.define_command('pept2prot') do
   flag :e, :equate, "equate I and L"
   option :s, :select, "select the attributes", :argument => :required, :multiple => true
   option :x, :xml, "download uniprot record in specified directory", :argument => :required
+  flag :a, :all, "include all information. WARNING: will take much longer!"
 
   runner Pept2prot
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: unipept
 version: !ruby/object:Gem::Version
-  version: 0.3.1
+  version: 0.3.2
 platform: ruby
 authors:
 - Toon Willems
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-05-06 00:00:00.000000000 Z
+date: 2014-05-07 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: shoulda