BioDSL 1.0.1 → 1.0.2

data/lib/BioDSL/commands/unique_values.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/usearch_global.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).                        #
 #                                                                              #
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
 
@@ -162,7 +162,7 @@ module BioDSL
         ios.each(:uc) do |record|
           record[:RECORD_TYPE] = 'usearch'
           output << record
-          @status[:hits_out]    += 1
+          @status[:hits_out] += 1
           @status[:records_out] += 1
         end
       end

data/lib/BioDSL/commands/usearch_local.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).                        #
 #                                                                              #
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
 
@@ -162,7 +162,7 @@ module BioDSL
         ios.each(:uc) do |record|
           record[:RECORD_TYPE] = 'usearch'
           output << record
-          @status[:hits_out]    += 1
+          @status[:hits_out] += 1
           @status[:records_out] += 1
         end
       end

data/lib/BioDSL/commands/write_fasta.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).                        #
 #                                                                              #
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
 
@@ -137,18 +137,16 @@ module BioDSL
 
         if (entry = record2entry(record))
           $stdout.puts entry.to_fasta(wrap)
-          @status[:sequences_in]  += 1
+          @status[:sequences_in] += 1
           @status[:sequences_out] += 1
-          @status[:residues_in]   += entry.length
-          @status[:residues_out]  += entry.length
+          @status[:residues_in] += entry.length
+          @status[:residues_out] += entry.length
         end
 
         write_output(output, record)
       end
     end
 
-    # rubocop: disable Metrics/AbcSize
-
     # Write all sequence entries to a specified file.
     #
     # @param input  [Enumerator]          The input stream.
@@ -160,10 +158,10 @@ module BioDSL
 
           if (entry = record2entry(record))
             ios.puts entry.to_fasta(@options[:wrap])
-            @status[:sequences_in]  += 1
+            @status[:sequences_in] += 1
             @status[:sequences_out] += 1
-            @status[:residues_in]   += entry.length
-            @status[:residues_out]  += entry.length
+            @status[:residues_in] += entry.length
+            @status[:residues_out] += entry.length
           end
 
           write_output(output, record)

data/lib/BioDSL/commands/write_fastq.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).                        #
 #                                                                              #
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
 
@@ -91,7 +91,7 @@ module BioDSL
     #
     # @return [WriteFastq] Class instance.
     def initialize(options)
-      @options            = options
+      @options = options
       check_options
       @options[:output] ||= $stdout
       @compress           = choose_compression
@@ -139,7 +139,7 @@ module BioDSL
 
         if record[:SEQ]
           @status[:sequences_in] += 1
-          @status[:residues_in]  += record[:SEQ].length
+          @status[:residues_in] += record[:SEQ].length
 
           write_fastq(record, ios) if record[:SEQ_NAME] && record[:SCORES]
         end
@@ -162,7 +162,7 @@ module BioDSL
 
       ios.puts entry.to_fastq
       @status[:sequences_out] += 1
-      @status[:residues_out]  += entry.length
+      @status[:residues_out] += entry.length
     end
 
     # Choose compression to use which can either be gzip or bzip2 or no

data/lib/BioDSL/commands/write_table.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).                        #
 #                                                                              #
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
 
@@ -185,7 +185,7 @@ module BioDSL
     #
     # @return [WriteTable] Class instance.
     def initialize(options)
-      @options               = options
+      @options = options
       check_options
       @options[:delimiter] ||= "\t"
       @compress              = choose_compression
@@ -402,7 +402,7 @@ module BioDSL
     def align_columns(table)
       @rows.first.each_with_index do |cell, i|
         next unless cell.is_a?(Fixnum) ||
-                    cell.is_a?(Float)  ||
+                    cell.is_a?(Float) ||
                     cell.delete(',') =~ /^[0-9]+$/
 
         table.align_column(i, :right)

data/lib/BioDSL/commands/write_tree.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).                        #
 #                                                                              #
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
 
@@ -79,7 +79,6 @@ module BioDSL
       @cmd = compile_command
     end
 
-    # rubocop: disable Metrics/AbcSize
     # rubocop: disable MethodLength
 
     # Return command lambda for write_tree.
@@ -146,7 +145,7 @@ module BioDSL
       entry.seq_name ||= i
 
       @status[:sequences_in] += 1
-      @status[:residues_in]  += entry.length
+      @status[:residues_in] += entry.length
 
       stdin.puts entry.to_fasta
     end

data/lib/BioDSL/config.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).                        #
 #                                                                              #
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
 
@@ -36,7 +36,7 @@ module BioDSL
     HISTORY_FILE             = File.join(ENV['HOME'], '.BioDSL_history')
     LOG_FILE                 = File.join(ENV['HOME'], '.BioDSL_log')
     RC_FILE                  = File.join(ENV['HOME'], '.BioDSLrc')
-    STATUS_PROGRESS_INTERVAL = 0.1   # update progress every n second.
+    STATUS_PROGRESS_INTERVAL = 0.1 # update progress every n second.
 
     options = options_load_rc({}, :pipeline)
 

data/lib/BioDSL/csv.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).            #
 #                                                                              #
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
 
@@ -283,15 +283,13 @@ module BioDSL
       fields.each do |field|
         field = field.to_num
 
-        if field.is_a? Fixnum
-          types << :to_i
-        elsif field.is_a? Float
-          types << :to_f
-        elsif field.is_a? String
-          types << :to_s
-        else
-          types << nil
-        end
+        types << if field.is_a? Fixnum
+                   :to_i
+                 elsif field.is_a? Float
+                   :to_f
+                 elsif field.is_a? String
+                   :to_s
+                 end
       end
 
       @types = types

data/lib/BioDSL/debug.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/fasta.rb

@@ -1,45 +1,48 @@
-# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
-#                                                                                #
-# 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 FASTA.
   class FastaError < StandardError; end
 
+  # Class for reading and writing FASTA files.
   class Fasta
     def self.open(*args)
       ios = IO.open(*args)
 
       if block_given?
         begin
-          yield self.new(ios)
+          yield new(ios)
         ensure
           ios.close
         end
       else
-        return self.new(ios)
+        return new(ios)
       end
     end
 
@@ -60,13 +63,13 @@ module BioDSL
     def initialize(io)
       @io        = io
       @seq_name  = nil
-      @seq       = ""
+      @seq       = ''
       @got_first = nil
       @got_last  = nil
     end
 
     def each
-      while entry = next_entry
+      while (entry = next_entry)
         yield entry
       end
     end
@@ -84,24 +87,33 @@ module BioDSL
         next if line.empty?
 
         if line[0] == '>'
-          if not @got_first and not @seq.empty?
-            raise FastaError, "Bad FASTA format -> content before Fasta header: #{@seq}" unless @seq.empty?
+          if !@got_first && !@seq.empty?
+            unless @seq.empty?
+              fail FastaError, 'Bad FASTA format -> content before Fasta ' \
+                               "header: #{@seq}"
+            end
           end
 
           @got_first = true
 
           if @seq_name
             entry     = Seq.new(seq_name: @seq_name, seq: @seq)
-            @seq_name = line[1 .. -1]
-            @seq      = ""
+            @seq_name = line[1..-1]
+            @seq      = ''
 
-            raise FastaError, "Bad FASTA format -> truncated Fasta header: no content after '>'" if @seq_name.empty?
+            if @seq_name.empty?
+              fail FastaError, 'Bad FASTA format -> truncated Fasta header: ' \
+                               'no content after \'>\''
+            end
 
             return entry
           else
-            @seq_name = line[1 .. -1]
+            @seq_name = line[1..-1]
 
-            raise FastaError, "Bad FASTA format -> truncated Fasta header: no content after '>'" if @seq_name.empty?
+            if @seq_name.empty?
+              fail FastaError, 'Bad FASTA format -> truncated Fasta header: ' \
+                               ' no content after \'>\''
+            end
           end
         else
           @seq << line
@@ -115,16 +127,18 @@ module BioDSL
         return entry
       end
 
-      if not @got_last and not @seq.empty?
-        raise FastaError, "Bad FASTA format -> content witout Fasta header: #{@seq}"
+      if !@got_last && !@seq.empty?
+        fail FastaError, 'Bad FASTA format -> content witout Fasta header: ' +
+          @seq
       end
 
       nil
     end
 
+    # Class for FASTA IO
     class IO < Filesys
       def each
-        while not @io.eof?
+        until @io.eof?
           yield @io.gets
         end
       end

data/lib/BioDSL/fastq.rb

@@ -1,29 +1,31 @@
-# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
-#                                                                                #
-# 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 FASTQ.
   class FastqError < StandardError; end
@@ -35,21 +37,21 @@ module BioDSL
 
       if block_given?
         begin
-          yield self.new(ios)
+          yield new(ios)
         ensure
           ios.close
         end
       else
-        return self.new(ios)
+        return new(ios)
       end
     end
 
     def initialize(io)
-      @io        = io
+      @io = io
     end
 
     def each
-      while entry = next_entry
+      while (entry = next_entry)
         yield entry
       end
     end
@@ -58,17 +60,18 @@ module BioDSL
     # as a Seq object. If no entry is found or eof then nil is returned.
     def next_entry
       return nil if @io.eof?
-      seq_name = @io.gets[1 .. -2]
+      seq_name = @io.gets[1..-2]
       seq      = @io.gets.chomp
       @io.gets
-      qual     = @io.gets.chomp
+      qual = @io.gets.chomp
 
       Seq.new(seq_name: seq_name, seq: seq, qual: qual)
     end
 
+    # Class for FASTQ IO.
     class IO < Filesys
       def each
-        while not @io.eof?
+        until @io.eof?
           yield @io.gets
         end
       end