scbi_fastq 0.0.14

data/History.txt

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+=== 0.0.14 2011-05-31
+
+release to rubygems
+
+=== 0.0.1 2010-11-29
+
+* Initial release

data/Manifest.txt

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+History.txt
+Manifest.txt
+PostInstall.txt
+README.rdoc
+Rakefile
+lib/scbi_fastq.rb
+lib/scbi_fastq/fastq_file.rb
+script/console
+script/destroy
+script/generate
+test/test_helper.rb
+test/test_scbi_fastq.rb

data/PostInstall.txt

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+
+For more information on scbi_fastq, see http://scbi_fastq.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_fastq
+
+* http://www.scbi.uma.es/downloads
+
+== DESCRIPTION:
+
+scbi_fastq is a ruby gem to read/write FASTQ files (DNA/RNA sequences) with qualities in a variety of formats (Sanger, Solexa, Ilumina).
+
+
+== FEATURES/PROBLEMS:
+
+* Read FASTQ files in Sanger Solexa and Ilumina, making the appropriate quality values conversions
+* Quality values can be automatically splitted
+* Write FASTQ files in Sanger format
+* Iteration over large files without extra memory usage
+
+
+== SYNOPSIS:
+
+=== Reading a FASTQ with iterator:
+
+  require 'scbi_fastq'
+
+  # open file in sanger mode
+  fqr=FastqFile.new('file1.fastq')
+
+
+  fqr.each do |name,seq_fasta,qual,comments|
+
+    puts name
+    puts seq_fasta
+    puts qual
+    puts comments
+  end
+ 
+  fqr.close
+
+=== Reading a FASTQ one sequence at a time:
+
+  require 'scbi_fastq'
+
+  # open file in sanger mode
+  fqr=FastqFile.new('file1.fastq')
+
+  
+	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
+
+
+=== Writing a FASTQ:
+
+  require 'scbi_fastq'
+
+  # open new file
+  f=FastqFile.new('file.fastq','w')
+
+  # prepare sample data
+  name = 'seq1'
+  seq_fasta= 'acgtacgtacact'
+  seq_qual= [40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40]
+
+  # write sequence to disk  
+  f.write_seq(name,seq_fasta,seq_qual,'comments')
+
+
+  # close file
+  f.close
+
+== REQUIREMENTS:
+
+* This is a standalone gem.
+
+== INSTALL:
+
+* gem install scbi_fastq
+
+== LICENSE:
+
+(The MIT License)
+
+Copyright (c) 2010 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_fastq'
+
+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_fastq' do
+  self.developer 'Dario Guerrero', 'dariogf@scbi.uma.es'
+  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]

data/lib/scbi_fastq/fastq_file.rb

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+
+# add ord method to ruby 1.8
+if !String.instance_methods.include?(:ord)
+   class String 
+      
+     def ord
+       return self[0]
+     end
+     
+   end
+end
+      
+
+
+class FastqFile
+
+  attr_accessor :num_seqs
+
+  #------------------------------------
+  # Initialize instance
+  #------------------------------------
+  def initialize(fasta_file_name, mode='r', fastq_type = :sanger, qual_to_array=true, qual_to_phred=true)
+
+  	
+    if mode.upcase.index('W')
+      @fastq_file = File.open(fasta_file_name,'w')
+    elsif mode.upcase.index('A')
+      if !File.exist?(fasta_file_name)
+      	raise "File #{fasta_file_name} doesn't exists" 
+      end
+    	
+      @fastq_file = File.open(fasta_file_name,'a')
+    else #read only
+      if !File.exist?(fasta_file_name)
+      	raise "File #{fasta_file_name} doesn't exists" 
+      end
+    	
+      if fasta_file_name.is_a?(IO)
+    	  @fastq_file = fasta_file_name
+      else
+        @fastq_file = File.open(fasta_file_name,'r')
+      end
+    end
+    
+    @mode = mode
+    @num_seqs = 0
+    @fastq_type=fastq_type
+    
+    #  S - Sanger        Phred+33,  raw reads typically (0, 40)
+    #  X - Solexa        Solexa+64, raw reads typically (-5, 40)
+    #  I - Illumina 1.3+ Phred+64,  raw reads typically (0, 40)
+    #  J - Illumina 1.5+ Phred+64,  raw reads typically (3, 40)
+    # > >>> def solexa_quality_from_phred(phred_quality) :
+    # > ...     return 10*log(10**(phred_quality/10.0) - 1, 10)
+    # > ...
+    # > >>> solexa_quality_from_phred(90)
+    # > 89.999999995657035
+    # > >>> solexa_quality_from_phred(50)
+    # > 49.99995657033466
+    # > >>> solexa_quality_from_phred(10)
+    # > 9.5424250943932485
+    # > >>> solexa_quality_from_phred(1)
+    # > -5.8682532438011537
+    # > >>> solexa_quality_from_phred(0.1)
+    # > -16.32774717238372
+    # > 
+    # > >>> def phred_quality_from_solexa(solexa_quality) :
+    # > ...     return 10*log(10**(solexa_quality/10.0) + 1, 10)
+    # > ...
+    # > >>> phred_quality_from_solexa(90)
+    # > 90.000000004342922
+    # > >>> phred_quality_from_solexa(10)
+    # > 10.41392685158225
+    # > >>> phred_quality_from_solexa(0)
+    # > 3.0102999566398116
+    # > >>> phred_quality_from_solexa(-20)
+    # > 0.043213737826425784
+    
+    
+    #sanger by default
+    @to_phred = lambda{|q| q - 33}
+    @from_phred = lambda{|q| (q+33).chr}
+    
+    if @fastq_type == :ilumina
+        @to_phred = lambda{|q| q - 64}
+        # @from_phred = lambda{|q| (q+64).chr}
+        
+    elsif @fastq_type == :solexa
+       # 
+       # solexa to phred quals
+       
+       @to_phred = lambda{|q| (10*Math.log(10**(q/10.0)+1,10)).round}
+       # @from_phred = lambda{|q| (10*Math.log(10**(q/10.0)-1,10)).round.chr}
+       
+       #phred to solexa quals
+       
+    end
+    
+    @qual_to_array = qual_to_array
+    
+    @qual_to_phred = qual_to_phred
+    
+  end
+  
+  def close
+      @fastq_file.close
+  end
+ 
+  
+  #------------------------------------
+  # Iterate over all sequences
+  #------------------------------------
+  def each
+        
+    rewind
+
+	  n,f,q,c=next_seq
+	  
+    while (!n.nil?)
+			yield(n,f,q,c)
+			n,f,q,c=next_seq
+    end
+
+  	rewind
+  	
+  end
+
+  # goto first position in file
+  def rewind
+     
+     @num_seqs = 0 ;
+     @fastq_file.pos=0
+    
+  end
+
+  #------------------------------------
+  # Get next sequence
+  #------------------------------------
+  def next_seq
+    #init variables
+    res = read_fastq
+  	return res
+  end
+  
+  # write sequence to file in sanger format
+  def write_seq(seq_name,seq_fasta,seq_qual,comments='')
+	  name = ""
+	  
+		@fastq_file.puts("@#{seq_name} #{comments}")
+		@fastq_file.puts(seq_fasta)
+		@fastq_file.puts("+#{seq_name} #{comments}")
+		
+		if seq_qual.is_a?(Array)
+		  @fastq_file.puts(seq_qual.map{|e| @from_phred.call(e)}.join)
+	  else
+		  @fastq_file.puts(seq_qual.split(/\s+/).map{|e| @from_phred.call(e.to_i)}.join)
+		end
+    
+  end
+
+  
+  # creates fastq otuput in sanger format
+  def self.to_fastq(seq_name,seq_fasta,seq_qual,comments='')
+    
+    res=[]
+    
+	  name = ""
+	  
+		res << ("@#{seq_name} #{comments}")
+		res << (seq_fasta)
+		res << ("+#{seq_name} #{comments}")
+		
+		if seq_qual.is_a?(Array)
+		  res<<(seq_qual.map{|e| (e+33).chr}.join)
+	  else
+		  res<<(seq_qual.split(/\s+/).map{|e| (e.to_i+33).chr}.join)
+		end
+		
+    return res
+  end
+  
+  def with_qual?
+    true
+  end
+  
+  
+  private 
+  
+  #------------------------------------
+  #  Read one sequence in fastq
+  #------------------------------------
+  # @GEM-108-D02
+  # AAAAGCTGG
+  # +
+  # :::::::::
+
+  def read_fastq
+
+    seq_name = nil
+    seq_fasta = nil
+    seq_qual = nil
+    comments = nil
+    
+    reading = :fasta
+    
+    if !@fastq_file.eof
+      
+      begin
+        #read four lines
+        name_line = @fastq_file.readline.chomp
+        seq_fasta = @fastq_file.readline.chomp
+        name2_line = @fastq_file.readline.chomp
+        seq_qual = @fastq_file.readline.chomp
+
+      
+        # parse name
+        if name_line =~ /^@\s*([^\s]+)\s*(.*)$/
+          # remove comments
+          seq_name = $1
+          comments=$2
+        else
+          raise "Invalid sequence name in #{name_line}"
+        end
+      
+        # parse fasta
+        seq_fasta.strip! if !seq_fasta.empty?
+
+        # parse qual_name
+    
+        if !seq_name.nil? && !seq_qual.empty?
+
+           @num_seqs += 1
+       
+           if @qual_to_phred
+             seq_qual=seq_qual.each_char.map{|e| (@to_phred.call(e.ord))}
+
+             if !@qual_to_array
+                 seq_qual=seq_qual.join(' ')
+             end
+           end
+       
+        end
+      rescue EOFError
+        raise "Bad format in FastQ file"
+      end
+    end
+    
+    return [seq_name,seq_fasta,seq_qual,comments]
+  end
+  
+  
+end

data/lib/scbi_fastq.rb

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+$:.unshift(File.dirname(__FILE__)) unless
+  $:.include?(File.dirname(__FILE__)) || $:.include?(File.expand_path(File.dirname(__FILE__)))
+
+require 'scbi_fastq/fastq_file'
+module ScbiFastq
+   VERSION = '0.0.14'
+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.expand_path(File.dirname(__FILE__) + '/../lib/scbi_fastq.rb')}"
+puts "Loading scbi_fastq 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

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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/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_helper.rb

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+require 'stringio'
+require 'test/unit'
+require File.dirname(__FILE__) + '/../lib/scbi_fastq'

data/test/test_scbi_fastq.rb

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+require File.dirname(__FILE__) + '/test_helper.rb'
+
+class TestScbiFastq < Test::Unit::TestCase
+
+  def setup
+   	@test_file='/tmp/sanger.fastq';
+  	
+  	@seq_fasta='ACTG'
+		@seq_qual=[31]
+	  @seq_name='SEQ'
+	  
+  end
+  
+  
+  def fill_file(n,offset=33)
+  	f=FastqFile.new(@test_file,'w')
+  	
+  	n.times do |c|
+  	  i = c+1
+  	  
+  	  name = "#{@seq_name+i.to_s}"
+  	  f.write_seq(name,@seq_fasta*i,(@seq_qual*i*@seq_fasta.length),'comments')
+      # f.puts('@'+name)
+      # f.puts(@seq_fasta*i)
+      # f.puts('+'+name)
+      # f.puts((@seq_qual*i*@seq_fasta.length).map{|e| (e+offset).chr}.join)
+  	end
+  	
+  	f.close
+  end
+
+  def test_each
+
+    	 # make new file and fill with data
+		  fill_file(100) 	
+		
+
+			fqr=FastqFile.new(@test_file)
+
+			i=1
+			
+			fqr.each do |n,s,q|
+
+			  assert_equal(@seq_name+i.to_s,n)
+			  assert_equal(@seq_fasta*i,s)
+			  assert_equal((@seq_qual*i*@seq_fasta.length),q)
+
+				i+=1
+			end
+			 
+		  fqr.close			
+  end
+
+  def test_each_comments
+
+    	 # make new file and fill with data
+		  fill_file(100) 	
+		
+
+			fqr=FastqFile.new(@test_file)
+
+			i=1
+			
+			fqr.each do |n,s,q,c|
+			  
+			  assert_equal(@seq_name+i.to_s,n)
+			  assert_equal(@seq_fasta*i,s)
+			  assert_equal((@seq_qual*i*@seq_fasta.length),q)
+			  assert_equal('comments',c)
+
+				i+=1
+			end
+			 
+		  fqr.close			
+  end
+
+  def test_next_seq_comments
+
+    	 # make new file and fill with data
+		  fill_file(100) 	
+		
+
+			fqr=FastqFile.new(@test_file)
+
+			i=1
+			
+			begin
+			  n,s,q,c = fqr.next_seq
+
+			  if !n.nil?
+			  assert_equal(@seq_name+i.to_s,n)
+			  assert_equal(@seq_fasta*i,s)
+			  assert_equal((@seq_qual*i*@seq_fasta.length),q)
+			  assert_equal('comments',c)
+
+				i+=1
+			  end
+			end until n.nil?
+			 
+		  fqr.close			
+  end
+
+
+  
+  # def test_open_file
+  #   fill_file(100)
+  #   fq=FastqFile.new('test/sanger.fastq')
+  #   
+  #   fq.each do |n,f,q|
+  #      puts n,f,q
+  #      puts fq.num_seqs
+  #   end
+  #   
+  #   fq.close
+  #   
+  # end
+end

metadata

@@ -0,0 +1,80 @@
+--- !ruby/object:Gem::Specification 
+name: scbi_fastq
+version: !ruby/object:Gem::Version 
+  prerelease: 
+  version: 0.0.14
+platform: ruby
+authors: 
+- Dario Guerrero
+autorequire: 
+bindir: bin
+cert_chain: []
+
+date: 2011-05-31 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_fastq is a ruby gem to read/write FASTQ files (DNA/RNA sequences) with qualities in a variety of formats (Sanger, Solexa, Ilumina).
+email: 
+- dariogf@scbi.uma.es
+executables: []
+
+extensions: []
+
+extra_rdoc_files: 
+- History.txt
+- Manifest.txt
+- PostInstall.txt
+files: 
+- History.txt
+- Manifest.txt
+- PostInstall.txt
+- README.rdoc
+- Rakefile
+- lib/scbi_fastq.rb
+- lib/scbi_fastq/fastq_file.rb
+- script/console
+- script/destroy
+- script/generate
+- test/test_helper.rb
+- test/test_scbi_fastq.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_fastq
+rubygems_version: 1.7.2
+signing_key: 
+specification_version: 3
+summary: scbi_fastq is a ruby gem to read/write FASTQ files (DNA/RNA sequences) with qualities in a variety of formats (Sanger, Solexa, Ilumina).
+test_files: 
+- test/test_helper.rb
+- test/test_scbi_fastq.rb