scbi_fasta 0.1.8

data/History.txt

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+=== 0.1.8 2011-06-13
+
+first rubygems published
+
+=== 0.1.3 2010-09-03
+
+* 1 minor fix, 3 enhancements:
+  * remove comments  from sequence names
+  * FastaQualFile can be used without qual file
+  * added FastaFile
+  * added tests
+  
+=== 0.0.2 2010-05-14
+
+* 1 improvement:
+  * speed improvement in FastaQualFile
+
+=== 0.0.1 2010-05-14
+
+* 1 major enhancement:
+  * Initial release of FastaQualFile
+  

data/Manifest.txt

@@ -0,0 +1,16 @@
+History.txt
+Manifest.txt
+PostInstall.txt
+README.rdoc
+Rakefile
+lib/scbi_fasta.rb
+lib/scbi_fasta/fasta_qual_file.rb
+lib/scbi_fasta/fasta_file.rb
+script/console
+script/destroy
+script/generate
+test/test_helper.rb
+test/test_fasta_file.rb
+test/test_fasta_qual_file.rb
+
+

data/PostInstall.txt

@@ -0,0 +1,7 @@
+
+For more information on scbi_fasta, see http://scbi_fasta.rubyforge.org
+
+NOTE: Change this information in PostInstall.txt 
+You can also delete it if you don't want it.
+
+

data/README.rdoc

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+= scbi_fasta
+
+* http://www.scbi.uma.es/downloads
+
+== DESCRIPTION:
+
+scbi_fasta is a ruby gem to read FASTA+QUAL files (DNA/RNA sequences).
+
+
+== FEATURES/PROBLEMS:
+
+* Read FASTA files with associated QUAL files
+* Quality values can be automatically splitted
+* Iteration over large files without extra memory usage
+
+
+== SYNOPSIS:
+
+=== Reading a FASTA+QUAL with iterator:
+
+  require 'scbi_fasta'
+
+  # open file in sanger mode
+  fqr=FastaQualFile.new('file1.fasta','file1.fasta.qual')
+
+
+  fqr.each do |name,seq_fasta,qual,comments|
+
+    puts name
+    puts seq_fasta
+    puts qual
+    puts comments
+  end
+ 
+  fqr.close
+
+=== Reading a FASTA one sequence at a time:
+
+  require 'scbi_fasta'
+
+  # open file 
+  fqr=FastaQualFile.new('file1.fasta','file1.fasta.qual')
+
+  
+	begin
+	
+    # read one sequence
+    name,seq_fasta,qual,comments=fqr.next_seq
+
+    # name will be nil if there are not more sequences available
+	  if !name.nil?
+      puts name
+      puts seq_fasta
+      puts qual
+      puts comments
+    end
+	end until name.nil?
+
+  fqr.close
+
+
+== REQUIREMENTS:
+
+* This is a standalone gem.
+
+== INSTALL:
+
+* gem install scbi_fasta
+
+== LICENSE:
+
+(The MIT License)
+
+Copyright (c) 2010 Almudena Bocinos, Dario Guerrero
+
+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.

data/Rakefile

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+require 'rubygems'
+gem 'hoe', '>= 2.1.0'
+require 'hoe'
+require 'fileutils'
+require './lib/scbi_fasta'
+
+Hoe.plugin :newgem
+# Hoe.plugin :website
+# Hoe.plugin :cucumberfeatures
+
+# Generate all the Rake tasks
+# Run 'rake -T' to see list of generated tasks (from gem root directory)
+$hoe = Hoe.spec 'scbi_fasta' do
+  self.developer 'Almudena Bocinos', 'alkoke@gmail.com'
+  self.post_install_message = 'PostInstall.txt' # TODO remove if post-install message not required
+  self.rubyforge_name       = self.name # TODO this is default value
+  # self.extra_deps         = [['activesupport','>= 2.0.2']]
+
+end
+
+require 'newgem/tasks'
+Dir['tasks/**/*.rake'].each { |t| load t }
+
+# TODO - want other tests/tasks run by default? Add them to the list
+# remove_task :default
+task :default => [:spec, :features, :redocs]

data/lib/scbi_fasta.rb

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+$:.unshift(File.dirname(__FILE__)) unless
+  $:.include?(File.dirname(__FILE__)) || $:.include?(File.expand_path(File.dirname(__FILE__)))
+
+$: << File.join(File.dirname(__FILE__),File.basename(__FILE__,File.extname(__FILE__)))
+
+require 'fasta_qual_file'
+require 'fasta_file'
+
+
+module ScbiFasta
+   VERSION = '0.1.8'
+end

data/lib/scbi_fasta/fasta_file.rb

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+########################################################
+# Author: Almudena Bocinos Rioboo                      
+# Use: Deprecated. The class FastaReader has been substituted by FastaQualReader  
+# Reads a fasta file and fires events to process it
+# 
+########################################################
+
+class FastaFile
+    
+	attr  :num_seqs
+
+
+    # Initialize instance
+    def initialize(file_name)
+      if File.exist?(file_name)
+		    @num_seqs = 0
+
+		    @file_name = file_name
+		    @file = File.open(file_name)
+		  else
+		  		raise "File #{file_name} doesn't exists" 
+      	
+      end
+      
+    end
+    
+
+    # Scans a file, firing events to process content
+    def each
+      
+      #init variables
+      seq_name = '';
+      seq_fasta = '';
+      seq_found = false;
+    
+      
+      # for each line of the file
+      @file.each do |line|
+        
+        line.chomp!;
+        # if line is name
+        if line =~ /^>/
+          
+          #process previous sequence
+          if seq_found
+			      @num_seqs=@num_seqs+1
+            yield(seq_name,seq_fasta);
+          end
+          
+          #get only name
+
+		     #get only name
+	        line.gsub!(/^>\s*/,'');
+        
+	        line =~ /(^[^\s]+)/
+
+	        # remove comments
+	        seq_name = $1
+
+          seq_fasta='';
+          seq_found = true;
+          
+        else
+
+		      line.strip! if !line.empty?
+	
+          #add line to fasta of seq
+          seq_fasta+=line;
+
+		      seq_fasta.strip! if !seq_fasta.empty?
+		  
+        end
+          
+      end
+    
+      # when found EOF, process last sequence
+      if seq_found
+			@num_seqs=@num_seqs+1
+        yield(seq_name,seq_fasta);
+      end
+    end
+    
+    
+    def close
+    	@file.close
+    end
+    
+    def with_qual?
+      false
+    end
+    
+end

data/lib/scbi_fasta/fasta_qual_file.rb

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+
+########################################################
+# Author: Almudena Bocinos Rioboo                      
+# 
+# Reads a fasta file and qual file, and then fires events to process it
+# 
+#
+# 
+########################################################
+
+class DifferentNamesException < RuntimeError 
+end
+
+class DifferentSizesException < RuntimeError
+end
+
+class FastaQualFile
+
+attr_accessor :num_seqs, :end_fasta
+
+  #------------------------------------
+  # Initialize instance
+  #------------------------------------
+  def initialize(fasta_file_name,qual_file_name='',qual_to_array=false)
+
+  	
+  	if !File.exist?(fasta_file_name)
+    	raise "File #{fasta_file_name} doesn't exists" 
+  	end
+  	
+  	@with_qual = true
+  	
+  	if qual_file_name.nil? or qual_file_name.empty? or !File.exist?(qual_file_name)
+  		@with_qual = false
+      #raise "File #{qual_file_name} doesn't exists" 
+  	end
+  
+  		
+      @num_seqs = 0 ;      
+      
+      @seq_name = '';      
+      @file_fasta = File.open(fasta_file_name) ;
+      @end_fasta=false;
+      
+      if @with_qual  		
+      
+        @qual_to_array = qual_to_array
+
+	      @seq_qual_name='';
+	      @file_qual = File.open(qual_file_name) ;
+	      @end_qual=false;
+      end
+      
+  end
+  
+  def close
+      @file_fasta.close
+      
+      @file_qual.close if @with_qual
+  end
+ 
+  
+  #------------------------------------
+  # Scans all sequences
+  #------------------------------------
+  def each
+        
+    rewind
+
+	  n,f,q=next_seq
+    while (!n.nil?)
+	  
+					if @with_qual
+						yield(n,f,q)
+					else
+					  yield(n,f)
+					end
+					
+  				n,f,q=next_seq
+    end
+
+  	rewind
+  	
+  end
+
+
+  def rewind
+     
+     @num_seqs = 0 ;      
+     
+     @seq_name = '';      
+     @file_fasta.pos=0
+     @end_fasta=false;
+
+     if @with_qual
+				 @seq_qual_name='';
+				 @file_qual.pos=0
+				 @end_qual=false;   
+     end
+    
+  end
+
+  #------------------------------------
+  # Scans a file, firing events to process content
+  #------------------------------------
+  def next_seq
+    
+    #init variables
+    res = nil
+    
+	  # envia on_process_sequence
+    if ((!@end_fasta) && (!@with_qual or !@end_qual))
+
+	      name_f,fasta=read_fasta 
+  	    
+        if @with_qual
+					  
+					  name_q,qual=read_qual 
+					  
+            if (name_f!=name_q)
+							 raise DifferentNamesException.new, "Sequence(<#{name_f}>) and qual(<#{name_q}>) names differs. Sequence will be ignored."
+             else
+							@num_seqs=@num_seqs+1
+				
+							#storage a string of qualities in an array of qualities
+				 	    # a_qual = qual.strip.split(/\s/).map{|e| e.to_i}
+							# if ((!a_qual.nil?) && (!a_qual.empty?) && (fasta.size==a_qual.size))						
+
+							if fasta.length == qual.count(' ') + 1
+								if @qual_to_array
+									a_qual = qual.strip.split(/\s/).map{|e| e.to_i}
+									res =[name_f,fasta,a_qual]
+								else
+									res =[name_f,fasta,qual]
+								end
+						
+							else #if (!a_qual.empty?)
+								 raise DifferentSizesException.new,  "Sequence(<#{name_f}>) and qual(<#{name_q}>) sizes differs (#{fasta.length},#{qual.count(' ')} ). Sequence will be ignored."
+							end 
+						 
+            end
+				 
+        else # without qual				 
+				 		res =[name_f,fasta]
+        end
+    end
+  	
+  	return res
+  end
+  
+  def with_qual?
+    @with_qual
+  end
+
+  
+  private 
+  
+  #------------------------------------
+  #  Read one sequence fasta
+  #------------------------------------
+  
+  def read_fasta
+    seq_fasta='';
+    res = nil
+    
+    # mientras hay lineas en el fichero
+    while (!@file_fasta.eof)        
+      # $LOG.debug "Total fasta #{@seq_fasta} Line fast #{@line_fasta} "
+
+      # lee una linea
+      line_fasta = @file_fasta.readline; line_fasta.chomp!
+      # si llega a fin de ficheor, poner eof
+      @end_fasta=@file_fasta.eof
+
+      # si la linea es una nueva secuencia
+      if ((line_fasta =~ /^>/)) 
+        
+        # puede ocurrir que antes ya se hubiese leido una secuencia, entonces devolverla
+        if !@seq_name.empty?
+          # ya había leido una
+          #puts "leida #{@seq_name} + #{@seq_fasta}"
+          res = [@seq_name,seq_fasta]
+        end
+
+
+        #get only name
+        line_fasta.gsub!(/^>\s*/,'');
+        
+        line_fasta =~ /(^[^\s]+)/
+        # remove comments
+        
+        @seq_name = $1
+        
+        seq_fasta='';
+        
+        # si hay algo que devolver, romper bucle
+        if res
+          break
+        end
+        
+      else # no es una linea de nombre, añadir al fasta
+	      line_fasta.strip! if !line_fasta.empty?
+        #add line to fasta of seq
+        seq_fasta+=line_fasta;
+        seq_fasta.strip! if !seq_fasta.empty?
+      end 
+       
+        
+    end
+    
+    
+    #si no hay más secuencias hay que devolver la última, CASO EOF
+    if res.nil? and !@seq_name.empty?
+      res= [@seq_name,seq_fasta]
+    end
+    
+    return res
+  end
+  
+  #----
+ 
+  #------------------------------------
+  # Read one sequence qual
+  #------------------------------------
+  def read_qual
+    seq_qual='';
+    res = nil
+    
+    # mientras hay lineas en el fichero
+    while (!@file_qual.eof)        
+      # $LOG.debug "Total fasta #{@seq_qual} Line fast #{@line_qual} "
+
+      # lee una linea
+      line_qual = @file_qual.readline; line_qual.chomp!
+      # si llega a fin de ficheor, poner eof
+      @end_qual=@file_qual.eof
+
+      # si la linea es una nueva secuencia
+      if ((line_qual =~ /^>/)) 
+        
+        # puede ocurrir que antes ya se hubiese leido una secuencia, entonces devolverla
+        if !@seq_qual_name.empty?
+          # ya había leido una
+          #puts "leida #{@seq_name} + #{@seq_qual}"
+
+          seq_qual.gsub!(/\s\s+/,' ')	
+          res = [@seq_qual_name,seq_qual]
+        end
+
+        
+        #get only name
+                #get only name
+        line_qual.gsub!(/^>\s*/,'');
+        
+        line_qual =~ /(^[^\s]+)/
+        # remove comments
+
+        @seq_qual_name = $1
+        seq_qual='';
+        
+        # si hay algo que devolver, romper bucle
+        if res
+          break
+        end
+        
+      else # no es una linea de nombre, añadir al fasta
+	      line_qual.strip! if !line_qual.empty?
+        #add line to qual of seq
+        seq_qual=seq_qual+' '+line_qual
+        seq_qual.strip! if !seq_qual.empty?
+      end 
+      
+    end
+    
+    
+    #si no hay más secuencias hay que devolver la última, CASO EOF
+    if res.nil? and !@seq_qual_name.empty?
+      seq_qual.gsub!(/\s\s+/,' ')	
+      res= [@seq_qual_name,seq_qual]
+    end
+    
+    return res
+  end  
+  
+  
+
+  
+end

data/script/console

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+#!/usr/bin/env ruby
+# File: script/console
+irb = RUBY_PLATFORM =~ /(:?mswin|mingw)/ ? 'irb.bat' : 'irb'
+
+libs =  " -r irb/completion"
+# Perhaps use a console_lib to store any extra methods I may want available in the cosole
+# libs << " -r #{File.dirname(__FILE__) + '/../lib/console_lib/console_logger.rb'}"
+libs <<  " -r #{File.dirname(__FILE__) + '/../lib/scbi_fasta.rb'}"
+puts "Loading scbi_fasta gem"
+exec "#{irb} #{libs} --simple-prompt"

data/script/destroy

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+#!/usr/bin/env ruby
+APP_ROOT = File.expand_path(File.join(File.dirname(__FILE__), '..'))
+
+begin
+  require 'rubigen'
+rescue LoadError
+  require 'rubygems'
+  require 'rubigen'
+end
+require 'rubigen/scripts/destroy'
+
+ARGV.shift if ['--help', '-h'].include?(ARGV[0])
+RubiGen::Base.use_component_sources! [:rubygems, :newgem, :newgem_theme, :test_unit]
+RubiGen::Scripts::Destroy.new.run(ARGV)

data/script/generate

@@ -0,0 +1,14 @@
+#!/usr/bin/env ruby
+APP_ROOT = File.expand_path(File.join(File.dirname(__FILE__), '..'))
+
+begin
+  require 'rubigen'
+rescue LoadError
+  require 'rubygems'
+  require 'rubigen'
+end
+require 'rubigen/scripts/generate'
+
+ARGV.shift if ['--help', '-h'].include?(ARGV[0])
+RubiGen::Base.use_component_sources! [:rubygems, :newgem, :newgem_theme, :test_unit]
+RubiGen::Scripts::Generate.new.run(ARGV)

data/test/test_fasta_file.rb

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+require File.dirname(__FILE__) + '/test_helper.rb'
+
+class TestFastaFile < Test::Unit::TestCase
+
+  def setup
+    @test_file='/tmp/fbinfile';
+
+    @seq_fasta='ACTG'
+    @seq_qual=[25]
+    @seq_name='SEQ'
+
+  end
+
+
+  def fill_file(n)
+    f=File.new(@test_file+'.fasta','w')
+    q=File.new(@test_file+'.qual','w')
+
+    n.times do |c|
+      i = c+1
+      name = ">#{@seq_name+i.to_s} comments"
+
+      f.puts(name)
+      f.puts(@seq_fasta*i)
+
+      q.puts(name)
+      q.puts((@seq_qual*i*@seq_fasta.length).join(' '))
+
+
+    end
+
+    f.close
+    q.close
+  end
+
+  def test_each
+
+    # make new file and fill with data
+    fill_file(100)
+
+    fqr=FastaFile.new(@test_file+'.fasta')
+
+    i=1
+
+
+    fqr.each do |n,s|
+
+      #puts n,s.length,q.split(' ').length
+      assert(@seq_name+i.to_s==n)
+      assert(@seq_fasta*i==s)
+
+      i+=1
+    end
+
+    fqr.close
+
+  rescue Exception => e
+    puts "failed in #{n} , #{s}"
+    puts "expected #{@seq_name+i.to_s} , #{@seq_fasta*i==s}"
+
+    puts e.message, e.backtrace
+
+  end
+
+end

data/test/test_fasta_qual_file.rb

@@ -0,0 +1,161 @@
+require File.dirname(__FILE__) + '/test_helper.rb'
+
+class TestFastaQualFile < Test::Unit::TestCase
+
+
+  def setup
+    @test_file='/tmp/fbinfile';
+
+    @seq_fasta='ACTG'
+    @seq_qual=[25]
+    @seq_name='SEQ'
+
+  end
+
+
+  def fill_file(n)
+    f=File.new(@test_file+'.fasta','w')
+    q=File.new(@test_file+'.qual','w')
+
+    n.times do |c|
+      i = c+1
+      name = ">#{@seq_name+i.to_s} comments"
+
+      f.puts(name)
+      f.puts(@seq_fasta*i)
+
+      q.puts(name)
+      q.puts((@seq_qual*i*@seq_fasta.length).join(' '))
+
+
+    end
+
+    f.close
+    q.close
+  end
+
+  def test_next_seq
+
+    # make new file and fill with data
+    fill_file(100)
+
+
+    fqr=FastaQualFile.new(@test_file+'.fasta',@test_file+'.qual')
+    n,s,q = ['']*3
+    i=0
+
+    100.times do |c|
+      i = c+1
+      n,s,q = fqr.next_seq
+
+      #puts n,s.length,q.split(' ').length
+      assert(@seq_name+i.to_s==n)
+      assert(@seq_fasta*i==s)
+      assert((@seq_qual*i*@seq_fasta.length).join(' ')==q)
+
+    end
+
+    fqr.close
+
+  rescue Exception => e
+    puts "failed in #{n} , #{s}, #{q}"
+    puts "expected #{@seq_name+i.to_s} , #{@seq_fasta*i==s}, #{(@seq_qual*i*@seq_fasta.length).join(' ')}"
+    puts e.message, e.backtrace
+
+  end
+
+  def test_each
+
+    # make new file and fill with data
+    fill_file(100)
+
+
+    fqr=FastaQualFile.new(@test_file+'.fasta',@test_file+'.qual')
+
+    i=1
+
+    fqr.each do |n,s,q|
+
+      #puts n,s.length,q.split(' ').length
+      assert(@seq_name+i.to_s==n)
+      assert(@seq_fasta*i==s)
+      assert((@seq_qual*i*@seq_fasta.length).join(' ')==q)
+
+      i+=1
+    end
+
+    fqr.close
+
+  rescue Exception => e
+    puts "failed in #{n} , #{s}, #{q}"
+    puts "expected #{@seq_name+i.to_s} , #{@seq_fasta*i==s}, #{(@seq_qual*i*@seq_fasta.length).join(' ')}"
+    puts e.message, e.backtrace
+
+  end
+
+  def test_next_seq_only_fasta
+
+    # make new file and fill with data
+    fill_file(100)
+
+
+    fqr=FastaQualFile.new(@test_file+'.fasta')
+    n,s = ['']*2
+    i=0
+
+    100.times do |c|
+      i = c+1
+      n,s,q = fqr.next_seq
+
+      #puts n,s.length,q.split(' ').length
+      assert(@seq_name+i.to_s==n)
+      assert(@seq_fasta*i==s)
+      assert(q.nil?)
+
+    end
+
+    fqr.close
+
+  rescue Exception => e
+    puts "failed in #{n} , #{s}"
+    puts "expected #{@seq_name+i.to_s} , #{@seq_fasta*i==s}"
+    puts e.message, e.backtrace
+
+  end
+
+
+  def test_each_only_fasta
+
+    count=100
+    # make new file and fill with data
+    fill_file(count)
+
+
+    fqr=FastaQualFile.new(@test_file+'.fasta')
+
+    i=1
+
+    fqr.each do |n,s,q|
+
+      #puts n,s.length,q.split(' ').length
+      assert(@seq_name+i.to_s==n)
+      assert(@seq_fasta*i==s)
+
+      assert(q.nil?)
+
+      i+=1
+    end
+
+    assert(i==count+1)
+
+    fqr.close
+
+  rescue Exception => e
+    puts "failed in #{n} , #{s}"
+    puts "expected #{@seq_name+i.to_s} , #{@seq_fasta*i==s}"
+    puts e.message, e.backtrace
+
+  end
+
+
+end

data/test/test_helper.rb

@@ -0,0 +1,4 @@
+require 'stringio'
+require 'test/unit'
+require File.dirname(__FILE__) + '/../lib/scbi_fasta'
+

metadata

@@ -0,0 +1,83 @@
+--- !ruby/object:Gem::Specification 
+name: scbi_fasta
+version: !ruby/object:Gem::Version 
+  prerelease: 
+  version: 0.1.8
+platform: ruby
+authors: 
+- Almudena Bocinos
+autorequire: 
+bindir: bin
+cert_chain: []
+
+date: 2011-06-13 00:00:00 Z
+dependencies: 
+- !ruby/object:Gem::Dependency 
+  name: hoe
+  prerelease: false
+  requirement: &id001 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        version: 2.8.0
+  type: :development
+  version_requirements: *id001
+description: scbi_fasta is a ruby gem to read FASTA+QUAL files (DNA/RNA sequences).
+email: 
+- alkoke@gmail.com
+executables: []
+
+extensions: []
+
+extra_rdoc_files: 
+- History.txt
+- Manifest.txt
+- PostInstall.txt
+files: 
+- History.txt
+- Manifest.txt
+- PostInstall.txt
+- README.rdoc
+- Rakefile
+- lib/scbi_fasta.rb
+- lib/scbi_fasta/fasta_qual_file.rb
+- lib/scbi_fasta/fasta_file.rb
+- script/console
+- script/destroy
+- script/generate
+- test/test_helper.rb
+- test/test_fasta_file.rb
+- test/test_fasta_qual_file.rb
+homepage: http://www.scbi.uma.es/downloads
+licenses: []
+
+post_install_message: PostInstall.txt
+rdoc_options: 
+- --main
+- README.rdoc
+require_paths: 
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement 
+  none: false
+  requirements: 
+  - - ">="
+    - !ruby/object:Gem::Version 
+      version: "0"
+required_rubygems_version: !ruby/object:Gem::Requirement 
+  none: false
+  requirements: 
+  - - ">="
+    - !ruby/object:Gem::Version 
+      version: "0"
+requirements: []
+
+rubyforge_project: scbi_fasta
+rubygems_version: 1.7.2
+signing_key: 
+specification_version: 3
+summary: scbi_fasta is a ruby gem to read FASTA+QUAL files (DNA/RNA sequences).
+test_files: 
+- test/test_fasta_file.rb
+- test/test_fasta_qual_file.rb
+- test/test_helper.rb