genevalidator 1.5.6 → 1.6.0

checksums.yaml

@@ -1,7 +1,7 @@
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data/.travis.yml

@@ -10,7 +10,6 @@ before_install:
   - ruby -pi -e "gsub(/^PREFIX = \/usr\/local/, 'PREFIX = ~/mafft/')" ~/mafft-7.205-with-extensions/core/Makefile
   - (cd ~/mafft-7.205-with-extensions/core/ && make clean && make && make install)
   - export PATH=$PATH:~/mafft/bin
-  - sudo apt-get install -y libgsl0-dev
 script: bundle exec rake test
 addons:
   code_climate:

data/README.md

@@ -1,11 +1,9 @@
 # GeneValidator - Identify problems with predicted genes 
-
-[![Build Status](https://travis-ci.org/wurmlab/GeneValidator.svg?branch=master)](https://travis-ci.org/wurmlab/GeneValidator)
-[![Gem Version](https://badge.fury.io/rb/GeneValidator.svg)](http://badge.fury.io/rb/GeneValidator)
+[![Build Status](https://travis-ci.org/wurmlab/genevalidator.svg?branch=master)](https://travis-ci.org/wurmlab/genevalidator)
+[![Gem Version](https://badge.fury.io/rb/genevalidator.svg)](http://badge.fury.io/rb/genevalidator)
 [![Dependency Status](https://gemnasium.com/wurmlab/GeneValidator.svg)](https://gemnasium.com/wurmlab/GeneValidator)
 [![Scrutinizer Code Quality](https://scrutinizer-ci.com/g/wurmlab/GeneValidator/badges/quality-score.png?b=master)](https://scrutinizer-ci.com/g/wurmlab/GeneValidator/?branch=master)
 [![Test Coverage](https://codeclimate.com/github/wurmlab/GeneValidator/badges/coverage.svg)](https://codeclimate.com/github/wurmlab/GeneValidator)
-[![total downloads](http://ruby-gem-downloads-badge.herokuapp.com/GeneValidator?type=total&color=brightgreen)](https://rubygems.org/gems/GeneValidator)
 
 ## Introduction
 The goal of GeneValidator is to identify problems with gene predictions and provide useful information based on the similarities to genes in public databases. The results produced will make provide evidence on how sequencing curation may be done and will be useful in improving or trying out new approaches for gene prediction tools. The main target of this tool are biologists who wish to validate the data produced in their labs.
@@ -38,7 +36,6 @@ It is also possible to add your own custom validations to GeneValidator.
 * NCBI BLAST+ (>= 2.2.30+)
 * MAFFT installation (download [here](http://mafft.cbrc.jp/alignment/software/)).
 * Mozilla FireFox - In order to dynamically produce graphs for some of the validation, GeneValidator relies on dependency called 'd3'. Unfortunately, at this moment of time, d3 only works in Firefox (download [here](https://www.mozilla.org/en-GB/firefox/new/)).
-* GSL libraries (GNU Scientific Library) (see link below for installation help)
 
 Please see [here](https://gist.github.com/IsmailM/b783e8a06565197084e6) for more help with installing the prerequisites.
   

data/lib/genevalidator.rb

@@ -11,6 +11,7 @@ require 'genevalidator/validation_gene_merge'
 require 'genevalidator/validation_duplication'
 require 'genevalidator/validation_open_reading_frame'
 require 'genevalidator/validation_alignment'
+require 'genevalidator/pool'
 require 'bio-blastxmlparser'
 require 'open-uri'
 require 'uri'
@@ -37,7 +38,6 @@ module GeneValidator
     # array of indexes for the start offsets of each query in the fasta file
     attr_reader :query_offset_lst
     attr_reader :overall_evaluation
-    attr_reader :multithreading
 
     # global variables
     attr_reader :no_queries
@@ -64,9 +64,7 @@ module GeneValidator
     # db: 'remote', raw_sequences: nil, num_threads: 1 fast: false}
     # +start_idx+: number of the sequence from the file to start with
     # +overall_evaluation+: boolean variable for printing overall evaluation
-    # +multithreading+: boolean variable for enabling multithreading
-    def initialize(opt, start_idx = 1, overall_evaluation = true,
-                   multithreading = false)
+    def initialize(opt, start_idx = 1, overall_evaluation = true)
       # Validate opts
       @opt = GVArgValidation.validate_args(opt)
 
@@ -76,7 +74,6 @@ module GeneValidator
       @idx                    = 0
       @start_idx              = start_idx
 
-      @multithreading         = multithreading
       @overall_evaluation     = overall_evaluation
 
       # start a worker thread
@@ -240,6 +237,8 @@ module GeneValidator
     ##
     #
     def run_validations(iterator)
+      p = Pool.new(@opt[:num_threads]) if @opt[:num_threads] > 1
+
       while @idx + 1 < @query_offset_lst.length
         prediction = get_info_on_each_query_sequence
         @idx += 1
@@ -250,18 +249,18 @@ module GeneValidator
           @idx -= 1
           break
         end
-
+        current_idx = @idx
         # the first validation should be treated separately
-        if @idx == @start_idx || @multithreading == false
-          validate(prediction, hits, idx)
+        if current_idx == @start_idx || @opt[:num_threads] == 1
+          validate(prediction, hits, current_idx)
         else
-          @threads << Thread.new(prediction, hits, @idx) do |prediction, hits, idx|
-            validate(prediction, hits, idx)
+          p.schedule(prediction, hits, current_idx) do |prediction, hits, current_idx|
+            validate(prediction, hits, current_idx)
           end
         end
-
       end
-      @threads.each(&:join) unless @multithreading == false
+    ensure
+      p.shutdown if @opt[:num_threads] > 1
     end
 
     def parse_next_iteration(iterator, prediction)
@@ -297,8 +296,8 @@ module GeneValidator
     # +prediction+: Sequence object
     # +hits+: Array of +Sequence+ objects
     # +idx+: the index number of the query
-    def validate(prediction, hits, idx)
-      query_output = do_validations(prediction, hits, idx)
+    def validate(prediction, hits, current_idx)
+      query_output = do_validations(prediction, hits, current_idx)
       query_output.generate_html
       query_output.print_output_file_yaml
       query_output.print_output_console
@@ -382,7 +381,7 @@ module GeneValidator
     # +idx+: the index number of the query
     # Output:
     # +Output+ object
-    def do_validations(prediction, hits, idx)
+    def do_validations(prediction, hits, current_idx)
       begin
         hits = remove_identical_hits(prediction, hits)
         rescue Exception => error # NoPIdentError
@@ -390,12 +389,12 @@ module GeneValidator
 
       query_output                = Output.new(@mutex, @mutex_yaml, @mutex_html,
                                                @filename, @html_path,
-                                               @yaml_path, idx, @start_idx)
+                                               @yaml_path, current_idx, @start_idx)
       query_output.prediction_len = prediction.length_protein
       query_output.prediction_def = prediction.definition
       query_output.nr_hits        = hits.length
 
-      plot_path                   = File.join(@plot_dir, "#{@filename}_#{@idx}")
+      plot_path                   = File.join(@plot_dir, "#{@filename}_#{current_idx}")
 
       validations = []
       validations.push LengthClusterValidation.new(@type, prediction, hits,

data/lib/genevalidator/pool.rb

@@ -0,0 +1,64 @@
+# From http://burgestrand.se/code/ruby-thread-pool/
+#
+# Copyright © 2012, Kim Burgestrand kim@burgestrand.se
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the “Software”), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED “AS IS”, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+# SOFTWARE.
+
+require 'thread'
+
+class Pool
+  def initialize(size)
+    @size = size
+    @jobs = Queue.new
+    @pool = Array.new(@size) do |i|
+      Thread.new do
+        Thread.current[:id] = i
+        catch(:exit) do
+          loop do
+            job, args = @jobs.pop
+            job.call(*args)
+          end
+        end
+      end
+    end
+  end
+
+  def schedule(*args, &block)
+    @jobs << [block, args]
+  end
+
+  def shutdown
+    @size.times do
+      schedule { throw :exit }
+    end
+    @pool.map(&:join)
+  end
+end
+
+if $0 == __FILE__
+  p = Pool.new(10)
+
+  20.times do |i|
+    p.schedule do
+      sleep rand(4) + 2
+      puts "Job #{i} finished by thread #{Thread.current[:id]}"
+    end
+  end
+  at_exit { p.shutdown }
+end

data/lib/genevalidator/version.rb

@@ -1,3 +1,3 @@
 module GeneValidator
-  VERSION = '1.5.6'
+  VERSION = '1.6.0'
 end

data/test/test_all_validations.rb

@@ -32,7 +32,7 @@ module GeneValidator
     tab_options            = "qseqid sseqid sacc slen qstart qend sstart send length qframe pident evalue"
 
     database               = 'swissprot -remote'
-    threads                = '8'
+    threads                = '1'
 
     # Unwanted Output Files 
     prot_xml_out           = "#{prot_blast_xml_file}.out"
@@ -63,7 +63,7 @@ module GeneValidator
           test: true
         }
 
-        (GeneValidator::Validation.new(opts, 1, false, false)).run
+        (GeneValidator::Validation.new(opts, 1, false)).run
         $stdout.reopen original_stdout
         $stdout.reopen(prot_tab_out, 'w')
 
@@ -81,7 +81,7 @@ module GeneValidator
           test: true
         }
 
-        (GeneValidator::Validation.new(opts1, 1, false, false)).run
+        (GeneValidator::Validation.new(opts1, 1, false)).run
         $stdout.reopen original_stdout
 
         diff = FileUtils.compare_file(prot_xml_out, prot_tab_out)
@@ -115,7 +115,7 @@ module GeneValidator
           test: true
         }
 
-        (GeneValidator::Validation.new(opts, 1, false, false)).run
+        (GeneValidator::Validation.new(opts, 1, false)).run
         $stdout.reopen original_stdout
         $stdout.reopen(mrna_tab_out, 'w')
 
@@ -133,7 +133,7 @@ module GeneValidator
           test: true
         }
 
-        (GeneValidator::Validation.new(opts1, 1, false, false)).run
+        (GeneValidator::Validation.new(opts1, 1, false)).run
         $stdout.reopen original_stdout
 
         diff = FileUtils.compare_file(mrna_xml_out, mrna_tab_out)

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: genevalidator
 version: !ruby/object:Gem::Version
-  version: 1.5.6
+  version: 1.6.0
 platform: ruby
 authors:
 - Monica Dragan
@@ -11,7 +11,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2015-05-22 00:00:00.000000000 Z
+date: 2015-05-28 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bundler
@@ -209,6 +209,7 @@ files:
 - lib/genevalidator/get_raw_sequences.rb
 - lib/genevalidator/hsp.rb
 - lib/genevalidator/output.rb
+- lib/genevalidator/pool.rb
 - lib/genevalidator/sequences.rb
 - lib/genevalidator/tabular_parser.rb
 - lib/genevalidator/validation_alignment.rb