unipept 0.2.3 → 0.2.4

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 916121b8faa447c8d47611a59241c2635976579f
-  data.tar.gz: 578e9800d943b98e90d6abd2dbb0eccd59ab5c62
+  metadata.gz: 24fa491dfa6ce5dbfbe53ff9bd7ee63159ff0b8f
+  data.tar.gz: d353c545fdd8db4bb33d873046f4dbf7d2a5fdab
 SHA512:
-  metadata.gz: c30aee8e009a16872f8bc8e436cd78766a7e88a372fab19e78e4fdf90d12711a87fa49c847da6c0dd14d9e8575e14a97f7b23ec76302ff514b6da8a6e0e13c0e
-  data.tar.gz: 9671cef3e615013e4988e886f21feabff0d69c5ff2e47f5379d39fdc475b3c37c324b8053766cd1b8389347d71ba36aaecb9ac34eb1e324d3dd522dc48fd0048
+  metadata.gz: 309a643a2f2f0b98c305e269aae484aa1c9c3dfed0c665a69ab2475dbf9a23b2c0519dae6b6fe5c25ab1e21dbc44fcd65d123c0a231c087242a178eed6f7c693
+  data.tar.gz: 43d0c9c573c2cab2facc26730873401dc07d5c1876b5927e9c226a6356a24189b652a5229292286719f1cae09dbba47f639be5caf72b97067bbd8e8285e00c4f

data/VERSION

@@ -1 +1 @@
-0.2.3
+0.2.4

data/bin/peptfilter

@@ -16,8 +16,8 @@ root_cmd = Cri::Command.new_basic_root.modify do
     filtered = $stdin.readlines.select do |pept|
       pept = pept.chomp
       length_ok = pept.length >= minlen && pept.length <= maxlen
-      lacks_ok = (pept.chars & lacks).size == 0
-      contains_ok = (pept.chars & contains).size == contains.size
+      lacks_ok = (pept.chars.to_a & lacks).size == 0
+      contains_ok = (pept.chars.to_a & contains).size == contains.size
 
       length_ok && lacks_ok && contains_ok
     end

data/bin/unipept

@@ -73,7 +73,7 @@ class ApiRunner < Cri::CommandRunner
     printed_header = false
     result = []
 
-    peptides.each_slice(self.batch_size) do |sub_division|
+    peptide_iterator(peptides) do |sub_division|
       begin
         sub_result = JSON[Faraday.post(@url, url_options(sub_division)).body]
       rescue
@@ -105,18 +105,17 @@ class ApiRunner < Cri::CommandRunner
   end
 
   def write_to_output(string)
-      if options[:output]
-        File.open(options[:output], 'a') do |f|
-          f.write string
-        end
+    if options[:output]
+      File.open(options[:output], 'a') do |f|
+        f.write string
+      end
+    else
+      if STDOUT.tty?
+        progress.log string
       else
-        if STDOUT.tty?
-          progress.log string
-        else
-          puts string
-        end
+        puts string
       end
-
+    end
   end
 
 
@@ -128,6 +127,10 @@ class ApiRunner < Cri::CommandRunner
     end
   end
 
+  def peptide_iterator(peptides, &block)
+    peptides.each_slice(batch_size, &block)
+  end
+
   private
 
   def glob_to_regex(glob_string)
@@ -146,8 +149,12 @@ class Taxa2lca < ApiRunner
     {:taxon_ids => sub_part, :full_lineage => options[:lineage]}
   end
 
+  def peptide_iterator(peptides, &block)
+    block.call(peptides)
+  end
+
   def batch_size
-    100_000_000_000
+    raise "NOT NEEDED FOR TAXA2LCA"
   end
 
 end

data/bin/uniprot

@@ -3,6 +3,6 @@ require 'faraday'
 ARGV.each do |arg|
   resp = Faraday.get("http://www.uniprot.org/uniprot/#{arg}.fasta")
   if resp.success?
-    puts resp.body.lines[1..-1].map(&:chomp).join("")
+    puts resp.body.lines.map(&:chomp)[1..-1].join("")
   end
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: unipept
 version: !ruby/object:Gem::Version
-  version: 0.2.3
+  version: 0.2.4
 platform: ruby
 authors:
 - Toon Willems
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-04-24 00:00:00.000000000 Z
+date: 2014-04-25 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: shoulda