bio-kmer_counter 0.0.4 → 0.1.0

data/VERSION

@@ -1 +1 @@
-0.0.4
+0.1.0

data/bin/kmer_counter.rb

@@ -18,8 +18,6 @@ options = {
   :contig_name => false,
   :sequence_length => false,
   :logger => 'stderr',
-  :threads => 1,
-  :processes => 1,
   :progressbar => true,
 }
 
@@ -67,20 +65,6 @@ o = OptionParser.new do |opts|
     options[:sequence_length] = true
   end
   
-  opts.on("-p", "--processes NUM_PROCESSES", "Use this many processes. Currently setting multiple processes means there is no progress bar [default #{options[:processes]}]") do |v|
-    options[:processes] = v.to_i
-    if options[:processes] < 1
-      raise "Unexpected number of processes specified (after converting to integer) - '#{options[:processes]}'"
-    end
-  end
-  
-  opts.on("-t", "--threads NUM_THREADS", "Use this many threads. This currently only makes sense if you are running on JRuby, since the standard MRI ruby 1.9 can't use multiple cores. Maybe use --processes instead? [default #{options[:threads]}]") do |v|
-    options[:threads] = v.to_i
-    if options[:threads] < 1
-      raise "Unexpected number of threads specified (after converting to integer) - '#{options[:threads]}'"
-    end
-  end
-  
   
   # logger options
   opts.on("-q", "--quiet", "Run quietly, set logging to ERROR level [default INFO]") do |q|
@@ -97,8 +81,6 @@ if ARGV.length != 1
   $stderr.puts o
   exit 1
 end
-# multiple processes doesn't work well with ProgressBar
-options[:progressbar] = false if options[:processes] != 1
 
 LOG_NAME = 'bio-kmer_counter'
 Bio::Log::CLI.logger(options[:logger]) #bio-logger defaults to STDERR not STDOUT, I disagree
@@ -120,7 +102,6 @@ process_window = lambda do |window,kmer,sequence_name,contig_name|
   
   window.window_search(options[:kmer],1) do |tetranucleotide|
     str = tetranucleotide.to_s
-    str.upcase!
     next unless str.gsub(/[ATGC]+/,'') == ''
     num_kmers_counted += 1
     counts[str]+=1
@@ -147,9 +128,10 @@ fasta_filename = ARGV[0]
 progress = nil
 progress = ProgressBar.new('kmer_counter', `grep -c '>' '#{fasta_filename}'`.to_i) if options[:progressbar]
 ff = Bio::FlatFile.open(fasta_filename) 
-Parallel.each(ff, :in_processes => options[:processes], :threads => options[:threads]) do |sequence|
-#ff.each do |sequence|
+
+ff.each do |sequence|
   window_counter = 0
+  sequence.seq.upcase!
   sequence.seq.window_search(options[:window_size],options[:window_offset]) do |window|
     process_window.call(window, options[:kmer], "#{sequence.definition}_#{window_counter}",sequence.definition)
     window_counter += 1

data/test/test_bio-kmer_counter.rb

@@ -61,41 +61,6 @@ class TestBioKmerCounter < Test::Unit::TestCase
     end
   end
   
-  should "not give a progressbar with multiple processes" do
-    Tempfile.open('one') do |tempfile|
-      tempfile.puts '>one'
-      tempfile.puts 'ATGCATGCAT' #10 letters long
-      tempfile.close
-      
-      expected = ["ID\tA\tC\n",
-      "one_0\t0.5\t0.5\n",
-      "one_1\t0.5\t0.5\n",
-      "one_leftover_2\t1.0\t0.0\n"]
-
-      # execute command and capture both stdout, and stderr
-      # no extra processes
-      command = "#{script_path} -w 4 -k 1 -m 2 #{tempfile.path}"
-      Open3.popen3(command) do |stdin, stdout, stderr|
-        result = stdout.readlines # convert to string?
-        error  = stderr.readlines
-        
-        assert_not_equal [], error
-        assert_equal expected, result
-      end
-      
-      # execute command and capture both stdout, and stderr
-      # extra processes
-      command = "#{script_path} -p 2 -w 4 -k 1 -m 2 #{tempfile.path}"
-      Open3.popen3(command) do |stdin, stdout, stderr|
-        result = stdout.readlines # convert to string?
-        error  = stderr.readlines
-        
-        assert_equal [], error
-        assert_equal expected, result
-      end
-    end
-  end
-  
   should "print help when no arguments are given" do
     command = "#{script_path}"
     Open3.popen3(command) do |stdin, stdout, stderr|

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: bio-kmer_counter
 version: !ruby/object:Gem::Version
-  version: 0.0.4
+  version: 0.1.0
   prerelease: 
 platform: ruby
 authors:
@@ -9,11 +9,11 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2012-08-09 00:00:00.000000000 Z
+date: 2012-08-29 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bio
-  requirement: &79074710 !ruby/object:Gem::Requirement
+  requirement: &85076110 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -21,10 +21,10 @@ dependencies:
         version: 1.4.2
   type: :runtime
   prerelease: false
-  version_requirements: *79074710
+  version_requirements: *85076110
 - !ruby/object:Gem::Dependency
   name: progressbar
-  requirement: &79238200 !ruby/object:Gem::Requirement
+  requirement: &85075540 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -32,10 +32,10 @@ dependencies:
         version: 0.11.0
   type: :runtime
   prerelease: false
-  version_requirements: *79238200
+  version_requirements: *85075540
 - !ruby/object:Gem::Dependency
   name: parallel
-  requirement: &79249880 !ruby/object:Gem::Requirement
+  requirement: &85075130 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -43,10 +43,10 @@ dependencies:
         version: 0.5.17
   type: :runtime
   prerelease: false
-  version_requirements: *79249880
+  version_requirements: *85075130
 - !ruby/object:Gem::Dependency
   name: bio-logger
-  requirement: &79249150 !ruby/object:Gem::Requirement
+  requirement: &85074690 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -54,10 +54,10 @@ dependencies:
         version: 1.0.1
   type: :runtime
   prerelease: false
-  version_requirements: *79249150
+  version_requirements: *85074690
 - !ruby/object:Gem::Dependency
   name: shoulda
-  requirement: &79246850 !ruby/object:Gem::Requirement
+  requirement: &85074250 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -65,10 +65,10 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *79246850
+  version_requirements: *85074250
 - !ruby/object:Gem::Dependency
   name: rdoc
-  requirement: &79245070 !ruby/object:Gem::Requirement
+  requirement: &85073740 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -76,10 +76,10 @@ dependencies:
         version: '3.12'
   type: :development
   prerelease: false
-  version_requirements: *79245070
+  version_requirements: *85073740
 - !ruby/object:Gem::Dependency
   name: jeweler
-  requirement: &79286630 !ruby/object:Gem::Requirement
+  requirement: &85093940 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -87,10 +87,10 @@ dependencies:
         version: 1.8.3
   type: :development
   prerelease: false
-  version_requirements: *79286630
+  version_requirements: *85093940
 - !ruby/object:Gem::Dependency
   name: bundler
-  requirement: &79285430 !ruby/object:Gem::Requirement
+  requirement: &85093260 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -98,10 +98,10 @@ dependencies:
         version: 1.0.21
   type: :development
   prerelease: false
-  version_requirements: *79285430
+  version_requirements: *85093260
 - !ruby/object:Gem::Dependency
   name: rdoc
-  requirement: &79284460 !ruby/object:Gem::Requirement
+  requirement: &85092790 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -109,7 +109,7 @@ dependencies:
         version: '3.12'
   type: :development
   prerelease: false
-  version_requirements: *79284460
+  version_requirements: *85092790
 description: A biogem for counting small kmers for fingerprinting nucleotide sequences.
   See README for details.
 email: gmail.com after donttrustben
@@ -147,7 +147,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
       version: '0'
       segments:
       - 0
-      hash: -548048899
+      hash: 285575987
 required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
   requirements: