Class: FastqFile

Inherits:
Object
  • Object
show all
Defined in:
lib/scbi_fastq/fastq_file.rb

Instance Attribute Summary collapse

Class Method Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(fasta_file_name, mode = 'r', fastq_type = :sanger, qual_to_array = true, qual_to_phred = true) ⇒ FastqFile

Initialize instance



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# File 'lib/scbi_fastq/fastq_file.rb', line 24

def initialize(fasta_file_name, mode='r', fastq_type = :sanger, qual_to_array=true, qual_to_phred=true)

   
  if mode.upcase.index('W.GZ')
    @fastq_file = Zlib::GzipWriter.open(fasta_file_name)
  elsif 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
      if ScbiZcatFile.gz_file?(fasta_file_name)
        #@fastq_file = Zlib::GzipReader.open(fasta_file_name)
        #@fastq_file = MultiGzReader.new(fasta_file_name)
        @fastq_file = ScbiZcatFile.new(fasta_file_name)
        # puts "GZIP file detected"
      else
        @fastq_file = File.open(fasta_file_name,'r')
        # puts "NORMAL file detected"
      end
      
    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

Instance Attribute Details

#num_seqs ⇒ Object

Returns the value of attribute num_seqs.



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# File 'lib/scbi_fastq/fastq_file.rb', line 19

def num_seqs
  @num_seqs
end

Class Method Details

.to_fastq(seq_name, seq_fasta, seq_qual, comments = '') ⇒ Object

creates fastq otuput in sanger format



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# File 'lib/scbi_fastq/fastq_file.rb', line 176

def self.to_fastq(seq_name,seq_fasta,seq_qual,comments='')

  res=[]

  name = ""

  res << ("@#{seq_name} #{comments}")
  res << (seq_fasta)
  res << ("+")
  #res << ("+#{seq_name} #{comments}")

  if !seq_qual.empty?
    # if @qual_to_phred
      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
    # else
    #   res << seq_qual
    # end
  else # no qual provided, use a default value
    q='D'*seq_fasta.length;
    res << q
  end

  return res
end

Instance Method Details

#close ⇒ Object 



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# File 'lib/scbi_fastq/fastq_file.rb', line 118

def close
  @fastq_file.close
end

#each ⇒ Object

Iterate over all sequences



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# File 'lib/scbi_fastq/fastq_file.rb', line 126

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

#next_seq ⇒ Object

Get next sequence



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# File 'lib/scbi_fastq/fastq_file.rb', line 151

def next_seq
  #init variables
  res = read_fastq
  return res
end

#rewind ⇒ Object

goto first position in file



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# File 'lib/scbi_fastq/fastq_file.rb', line 142

def rewind
  @num_seqs = 0 ;
  # @fastq_file.pos=0
  @fastq_file.rewind
end

#with_qual? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/scbi_fastq/fastq_file.rb', line 205

def with_qual?
  true
end

#write_seq(seq_name, seq_fasta, seq_qual, comments = '') ⇒ Object

write sequence to file in sanger format



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# File 'lib/scbi_fastq/fastq_file.rb', line 158

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("+")
  #@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