unipept 0.2.6 → 0.2.7

checksums.yaml

@@ -1,7 +1,7 @@
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data/VERSION

@@ -1 +1 @@
-0.2.6
+0.2.7

data/bin/peptfilter

@@ -13,18 +13,15 @@ root_cmd = Cri::Command.new_basic_root.modify do
     maxlen = opts.fetch(:maxlen, "50").to_i
     lacks = opts.fetch(:lacks, "").chars.to_a
     contains = opts.fetch(:contains, "").chars.to_a
-    filtered = $stdin.readlines.select do |pept|
+    $stdin.each_line do |pept|
       pept = pept.chomp
       length_ok = pept.length >= minlen && pept.length <= maxlen
       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
-    if opts[:unique]
-      puts filtered.uniq
-    else
-      puts filtered
+      if length_ok && lacks_ok && contains_ok
+        puts pept
+      end
     end
   end
 end

data/bin/prot2pept

@@ -6,8 +6,7 @@ root_cmd = Cri::Command.new_basic_root.modify do
   required :p, :pattern, "cleavage pattern to split input protein (default: ([KR])([^P]))"
   run do |opts, args, cmd|
     pattern = opts.fetch(:pattern, "([KR])([^P])")
-    puts $stdin.readlines.map { |prot| prot.gsub(/#{pattern}/,"\\1\n\\2").gsub(/#{pattern}/, "\\1\n\\2") }.
-      map {|s| s.split("\n")}.flatten.reject(&:empty?)
+    $stdin.each_line { |prot| puts prot.gsub(/#{pattern}/,"\\1\n\\2").gsub(/#{pattern}/, "\\1\n\\2").split("\n").reject(&:empty?) }
   end
 end
 

data/bin/unipept

@@ -2,7 +2,6 @@
 
 require 'cri'
 require 'faraday'
-require 'ruby-progressbar'
 require 'yaml'
 require 'json'
 require 'fileutils'
@@ -12,8 +11,6 @@ require_relative '../lib/unipept'
 
 class ApiRunner < Cri::CommandRunner
 
-  attr_accessor :progress
-
   def initialize(args, opts, cmd)
     super
     host = Unipept::Configuration.new['host']
@@ -33,14 +30,12 @@ class ApiRunner < Cri::CommandRunner
     {'pept2taxa' => 'single', 'pept2lca' => 'lca'}
   end
 
-  def read_input
+  def input_iterator
     if options[:input]
-      peptides = File.readlines(options[:input])
+       File.readlines(options[:input]).each
     else
-      peptides = STDIN.readlines
+      STDIN.each_line
     end
-
-    peptides
   end
 
   def batch_size
@@ -63,12 +58,11 @@ class ApiRunner < Cri::CommandRunner
 
   def run
     formatter = Unipept::Formatter.new_for_format(options[:format])
-    peptides = read_input
+    peptides = input_iterator
 
     filter_list = options[:select] ? options[:select] : []
     filter_list = filter_list.map {|f| glob_to_regex(f) }
     output = STDOUT.tty? ? STDOUT : STDERR
-    self.progress = ProgressBar.create(total: peptides.size, output: output)
 
     printed_header = false
     result = []
@@ -93,7 +87,6 @@ class ApiRunner < Cri::CommandRunner
       end
 
       write_to_output formatter.format(sub_result)
-      progress.progress += sub_division.size
     end
 
     begin
@@ -110,11 +103,7 @@ class ApiRunner < Cri::CommandRunner
         f.write string
       end
     else
-      if STDOUT.tty?
-        progress.log string
-      else
-        puts string
-      end
+      puts string
     end
   end
 
@@ -150,7 +139,7 @@ class Taxa2lca < ApiRunner
   end
 
   def peptide_iterator(peptides, &block)
-    block.call(peptides)
+    block.call(peptides.to_a)
   end
 
   def batch_size

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: unipept
 version: !ruby/object:Gem::Version
-  version: 0.2.6
+  version: 0.2.7
 platform: ruby
 authors:
 - Toon Willems
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-04-28 00:00:00.000000000 Z
+date: 2014-04-29 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: shoulda