BioDSL 1.0.1 → 1.0.2

data/Rakefile

@@ -1,17 +1,18 @@
 require 'bundler'
+require 'English'
 require 'rake/testtask'
 require 'pp'
 
 Bundler::GemHelper.install_tasks
 
-task :default => 'test'
- 
+task default: 'test'
+
 Rake::TestTask.new do |t|
-  t.description = "Run test suite"
+  t.description = 'Run test suite'
   t.test_files  = Dir['test/**/*'].select { |f| f.match(/\.rb$/) }
   t.warning     = true
 end
- 
+
 desc 'Run test suite with simplecov'
 task :simplecov do
   ENV['SIMPLECOV'] = 'true'
@@ -23,7 +24,7 @@ task :doc do
   run_docgen
 end
 
-task :build => :boilerplate
+task build: :boilerplate
 
 desc 'Add or update license boilerplate in source files'
 task :boilerplate do
@@ -31,9 +32,9 @@ task :boilerplate do
 end
 
 def run_docgen
-  $stderr.puts "Building docs"
+  $stderr.puts 'Building docs'
   `yardoc lib/`
-  $stderr.puts "Docs done"
+  $stderr.puts 'Docs done'
 end
 
 def run_boilerplate
@@ -61,7 +62,7 @@ def run_boilerplate
 #                                                                              #
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
 #                                                                              #
-# This software is part of BioDSL (www.github.com/maasha/BioDSL).              #
+# This software is part of BioDSL (http://maasha.github.io/BioDSL).            #
 #                                                                              #
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
 END
@@ -69,26 +70,27 @@ END
   files = Rake::FileList.new('bin/**/*', 'lib/**/*.rb', 'test/**/*.rb')
 
   files.each do |file|
-    body = ""
+    body = ''
 
     File.open(file) do |ios|
       body = ios.read
     end
 
-    if body.match(/Copyright \(C\) 2007-(\d{4}) Martin Asser Hansen/) and $1.to_i != Time.now.year
+    if body.match(/Copyright \(C\) 2007-(\d{4}) Martin Asser Hansen/) &&
+       Regexp.last_match[1].to_i != Time.now.year
       STDERR.puts "Updating boilerplate: #{file}"
 
-      body.sub!(/Copyright \(C\) 2007-(\d{4}) Martin Asser Hansen/, "Copyright (C) 2007-#{Time.now.year} Martin Asser Hansen")
+      body.sub!(/Copyright \(C\) 2007-(\d{4}) Martin Asser Hansen/,
+                "Copyright (C) 2007-#{Time.now.year} Martin Asser Hansen")
 
       File.open(file, 'w') do |ios|
         ios.puts body
       end
     end
 
-    unless body.match('Copyright')
-      STDERR.puts "Warning: missing boilerplate in #{file}"
-      STDERR.puts body.split($/).first(10).join($/)
-      exit
-    end
+    next if body.match('Copyright')
+    STDERR.puts "Warning: missing boilerplate in #{file}"
+    STDERR.puts body.split($RS).first(10).join($RS)
+    exit
   end
 end

data/lib/BioDSL.rb

@@ -21,7 +21,7 @@
 #                                                                              #
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
 #                                                                              #
-# This software is part of BioDSL (www.github.com/maasha/BioDSL).              #
+# This software is part of BioDSL (http://maasha.github.io/BioDSL).            #
 #                                                                              #
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
 

data/lib/BioDSL/cary.rb

@@ -1,34 +1,37 @@
-# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
-#                                                                                #
-# Copyright (C) 2007-2015 Martin Asser Hansen (mail@maasha.dk).                  #
-#                                                                                #
-# This program is free software; you can redistribute it and/or                  #
-# modify it under the terms of the GNU General Public License                    #
-# as published by the Free Software Foundation; either version 2                 #
-# of the License, or (at your option) any later version.                         #
-#                                                                                #
-# This program is distributed in the hope that it will be useful,                #
-# but WITHOUT ANY WARRANTY; without even the implied warranty of                 #
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the                  #
-# GNU General Public License for more details.                                   #
-#                                                                                #
-# You should have received a copy of the GNU General Public License              #
-# along with this program; if not, write to the Free Software                    #
-# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. #
-#                                                                                #
-# http://www.gnu.org/copyleft/gpl.html                                           #
-#                                                                                #
-# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
-#                                                                                #
-# This software is part of BioDSL (www.BioDSL.org).                        #
-#                                                                                #
-# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
-
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
+#                                                                              #
+# Copyright (C) 2007-2015 Martin Asser Hansen (mail@maasha.dk).                #
+#                                                                              #
+# This program is free software; you can redistribute it and/or                #
+# modify it under the terms of the GNU General Public License                  #
+# as published by the Free Software Foundation; either version 2               #
+# of the License, or (at your option) any later version.                       #
+#                                                                              #
+# This program is distributed in the hope that it will be useful,              #
+# but WITHOUT ANY WARRANTY; without even the implied warranty of               #
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the                #
+# GNU General Public License for more details.                                 #
+#                                                                              #
+# You should have received a copy of the GNU General Public License            #
+# along with this program; if not, write to the Free Software                  #
+# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301,    #
+# USA.                                                                         #
+#                                                                              #
+# http://www.gnu.org/copyleft/gpl.html                                         #
+#                                                                              #
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
+#                                                                              #
+# This software is part of BioDSL (http://maasha.github.io/BioDSL).            #
+#                                                                              #
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
+
+# Namespace for BioDSL.
 module BioDSL
   # Error class for all exceptions to do with CAry.
   class CAryError < StandardError; end
 
-  # Class to manipulate a Ruby byte array which is fit for inline C manipulation.
+  # Class to manipulate a Ruby byte array which is fit for inline C
+  # manipulation.
   class CAry
     require 'inline'
 
@@ -37,8 +40,8 @@ module BioDSL
     # Class method to store to a given file a given ary.
     def self.store(file, ary)
       File.open(file, 'w') do |ios|
-        ios.write([ary.count].pack("I"))
-        ios.write([ary.size].pack("I"))
+        ios.write([ary.count].pack('I'))
+        ios.write([ary.size].pack('I'))
         ios.write(ary.ary)
       end
 
@@ -52,20 +55,20 @@ module BioDSL
       ary   = nil
 
       File.open(file) do |ios|
-        count = ios.read(4).unpack("I").first
-        size  = ios.read(4).unpack("I").first
+        count = ios.read(4).unpack('I').first
+        size  = ios.read(4).unpack('I').first
         ary   = ios.read
       end
 
       CAry.new(count, size, ary)
     end
 
-    # Method to initialize a new CAry object which is either empty
-    # or created from a given byte string. Count is the number of
-    # elements in the ary, and size is the byte size of a element.
+    # Method to initialize a new CAry object which is either empty or created
+    # from a given byte string. Count is the number of elements in the ary, and
+    # size is the byte size of a element.
     def initialize(count, size, ary = nil)
-      raise CAryError, "count must be positive - not #{count}" if count <= 0
-      raise CAryError, "size must be positive - not #{size}"   if size  <= 0
+      fail CAryError, "count must be positive - not #{count}" if count <= 0
+      fail CAryError, "size must be positive - not #{size}"   if size <= 0
 
       @count = count
       @size  = size
@@ -95,34 +98,58 @@ module BioDSL
     end
 
     # Method to do bitwise AND operation between two CArys.
-    def &(cary)
-      raise BioDSL::CAryError, "Bad object type: #{cary.class}" unless cary.is_a? CAry
-      raise BioDSL::CAryError, "Counts mismatch: #{self.count} != #{cary.count}" if self.count != cary.count
-      raise BioDSL::CAryError, "Sizes mismatch: #{self.size} != #{cary.size}"    if self.size != cary.size
+    def &(other)
+      unless other.is_a? CAry
+        fail BioDSL::CAryError, "Bad object type: #{other.class}"
+      end
 
-      bitwise_and_C(@ary, cary.ary, @count * @size)
+      if @count != other.count
+        fail BioDSL::CAryError, "Counts mismatch: #{@count} != #{other.count}"
+      end
+
+      if @size != other.size
+        fail BioDSL::CAryError, "Sizes mismatch: #{@size} != #{other.size}"
+      end
+
+      bitwise_and_C(@ary, other.ary, @count * @size)
 
       self
     end
 
     # Method to do bitwise OR operation between two CArys.
-    def |(cary)
-      raise BioDSL::CAryError, "Bad object type: #{cary.class}" unless cary.is_a? CAry
-      raise BioDSL::CAryError, "Counts mismatch: #{self.count} != #{cary.count}" if self.count != cary.count
-      raise BioDSL::CAryError, "Sizes mismatch: #{self.size} != #{cary.size}"    if self.size != cary.size
+    def |(other)
+      unless other.is_a? CAry
+        fail BioDSL::CAryError, "Bad object type: #{other.class}"
+      end
 
-      bitwise_or_C(@ary, cary.ary, @count * @size)
+      if @count != other.count
+        fail BioDSL::CAryError, "Counts mismatch: #{@count} != #{other.count}"
+      end
+
+      if @size != other.size
+        fail BioDSL::CAryError, "Sizes mismatch: #{@size} != #{other.size}"
+      end
+
+      bitwise_or_C(@ary, other.ary, @count * @size)
 
       self
     end
 
     # Method to do bitwise XOR operation between two CArys.
-    def ^(cary)
-      raise BioDSL::CAryError, "Bad object type: #{cary.class}" unless cary.is_a? CAry
-      raise BioDSL::CAryError, "Counts mismatch: #{self.count} != #{cary.count}" if self.count != cary.count
-      raise BioDSL::CAryError, "Sizes mismatch: #{self.size} != #{cary.size}"    if self.size != cary.size
+    def ^(other)
+      unless other.is_a? CAry
+        fail BioDSL::CAryError, "Bad object type: #{other.class}"
+      end
+
+      if @count != other.count
+        fail BioDSL::CAryError, "Counts mismatch: #{@count} != #{other.count}"
+      end
+
+      if @size != other.size
+        fail BioDSL::CAryError, "Sizes mismatch: #{@size} != #{other.size}"
+      end
 
-      bitwise_xor_C(@ary, cary.ary, @count * @size)
+      bitwise_xor_C(@ary, other.ary, @count * @size)
 
       self
     end
@@ -138,8 +165,6 @@ module BioDSL
       @ary.unpack('B*').first
     end
 
-    private
-
     inline do |builder|
       # Method that given a byte array and its size in bytes
       # sets all bytes to 0.

data/lib/BioDSL/command.rb

@@ -20,7 +20,7 @@
 #                                                                              #
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
 #                                                                              #
-# This software is part of BioDSL (www.github.com/maasha/BioDSL).              #
+# This software is part of BioDSL (http://maasha.github.io/BioDSL).            #
 #                                                                              #
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
 module BioDSL
@@ -80,7 +80,7 @@ module BioDSL
     # @return [BioDSL::Status] returns self.
     def calc_time_elapsed
       delta = @status[:time_stop] - @status[:time_start]
-      @status[:time_elapsed] = (Time.mktime(0) + delta).strftime("%H:%M:%S")
+      @status[:time_elapsed] = (Time.mktime(0) + delta).strftime('%H:%M:%S')
 
       self
     end

data/lib/BioDSL/commands.rb

@@ -16,7 +16,7 @@
 #                                                                              #
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
 #                                                                              #
-# This software is part of BioDSL (www.github.com/maasha/BioDSL).              #
+# This software is part of BioDSL (http://maasha.github.io/BioDSL).            #
 #                                                                              #
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
 

data/lib/BioDSL/commands/add_key.rb

@@ -21,7 +21,7 @@
 #                                                                              #
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
 #                                                                              #
-# This software is part of the BioDSL framework (www.BioDSL.org).        #
+# This software is part of the BioDSL (www.BioDSL.org).                        #
 #                                                                              #
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
 

data/lib/BioDSL/commands/align_seq_mothur.rb

@@ -21,7 +21,7 @@
 #                                                                              #
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
 #                                                                              #
-# This software is part of the BioDSL framework (www.BioDSL.org).        #
+# This software is part of the BioDSL (www.BioDSL.org).                        #
 #                                                                              #
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
 
@@ -145,7 +145,7 @@ module BioDSL
       entry    = BioDSL::Seq.new(seq_name: seq_name, seq: record[:SEQ])
 
       @status[:sequences_in] += 1
-      @status[:residues_in]  += entry.length
+      @status[:residues_in] += entry.length
 
       ios.puts entry.to_fasta
     end
@@ -158,9 +158,9 @@ module BioDSL
       BioDSL::Fasta.open(tmp_out) do |ios|
         ios.each do |entry|
           output << entry.to_bp
-          @status[:records_out]   += 1
+          @status[:records_out] += 1
           @status[:sequences_out] += 1
-          @status[:residues_out]  += entry.length
+          @status[:residues_out] += entry.length
         end
       end
     end

data/lib/BioDSL/commands/analyze_residue_distribution.rb

@@ -21,7 +21,7 @@
 #                                                                              #
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
 #                                                                              #
-# This software is part of the BioDSL framework (www.BioDSL.org).        #
+# This software is part of the BioDSL (www.BioDSL.org).                        #
 #                                                                              #
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
 
@@ -166,15 +166,15 @@ module BioDSL
     #
     # @param seq [String] - Sequence to analyze.
     def analyze_residues(seq)
-      @status[:sequences_in]  += 1
+      @status[:sequences_in] += 1
       @status[:sequences_out] += 1
-      @status[:residues_in]   += seq.length
-      @status[:residues_out]  += seq.length
+      @status[:residues_in] += seq.length
+      @status[:residues_out] += seq.length
 
       seq.upcase.chars.each_with_index do |char, i|
         c = char.to_sym
         @counts[i][c] += 1
-        @total[i]     += 1
+        @total[i] += 1
         @residues.add(c)
       end
     end

data/lib/BioDSL/commands/assemble_pairs.rb

@@ -21,7 +21,7 @@
 #                                                                              #
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
 #                                                                              #
-# This software is part of the BioDSL framework (www.BioDSL.org).        #
+# This software is part of the BioDSL (www.BioDSL.org).                        #
 #                                                                              #
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
 
@@ -160,7 +160,7 @@ module BioDSL
     # Set default options.
     def defaults
       @options[:mismatch_percent] ||= 20
-      @options[:overlap_min]      ||= 1
+      @options[:overlap_min] ||= 1
     end
 
     # Output a record to the stream if a stram is provided.
@@ -182,7 +182,7 @@ module BioDSL
       entry1, entry2 = records2entries(record1, record2)
 
       if overlap_possible?(entry1, entry2, @options[:overlap_min]) &&
-         assembled = assemble_entries(entry1, entry2)
+         (assembled = assemble_entries(entry1, entry2))
         output_assembled(assembled, output)
       elsif @options[:merge_unassembled]
         output_merged(entry1, entry2, output)
@@ -211,7 +211,7 @@ module BioDSL
       end
 
       @status[:sequences_in] += 2
-      @status[:residues_in]  += entry1.length + entry2.length
+      @status[:residues_in] += entry1.length + entry2.length
 
       [entry1, entry2]
     end
@@ -252,10 +252,10 @@ module BioDSL
     def output_assembled(assembled, output)
       output << assembled2record(assembled)
 
-      @status[:assembled]     += 1
-      @status[:records_out]   += 1
+      @status[:assembled] += 1
+      @status[:records_out] += 1
       @status[:sequences_out] += 1
-      @status[:residues_out]  += assembled.length
+      @status[:residues_out] += assembled.length
     end
 
     # Convert a sequence entry to a BioPiece record with hamming distance and
@@ -289,10 +289,10 @@ module BioDSL
 
       output << entry2record(entry1)
 
-      @status[:unassembled]   += 1
+      @status[:unassembled] += 1
       @status[:sequences_out] += 1
-      @status[:residues_out]  += entry1.length
-      @status[:records_out]   += 1
+      @status[:residues_out] += entry1.length
+      @status[:records_out] += 1
     end
 
     # Output unassembled entries to the stream.
@@ -304,10 +304,10 @@ module BioDSL
       output << entry2record(entry1)
       output << entry2record(entry2)
 
-      @status[:unassembled]   += 2
+      @status[:unassembled] += 2
       @status[:sequences_out] += 2
-      @status[:residues_out]  += entry1.length + entry2.length
-      @status[:records_out]   += 2
+      @status[:residues_out] += entry1.length + entry2.length
+      @status[:records_out] += 2
     end
 
     # Converts a sequence entry to a BioPeice record.