Class: FastqFile

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

Overview

Provides simple interface for parsing four-line-per-record fastq format files. Gzipped files are no problem.

Instance Method Summary collapse

Instance Method Details

#each_record {|header, sequence, description, quality_string| ... } ⇒ Object

Analagous to IO#each_line, #each_record is used to go through a fastq file record by record. It will accept gzipped files as well.

Examples:

Parsing a fastq file

FastqFile.open('reads.fq').each_record do |head, seq, desc, qual|
  # do some fun stuff here!
end

Use the same syntax for gzipped files!

FastqFile.open('reads.fq.gz').each_record do |head, seq, desc, qual|
  # do some fun stuff here!
end

Yields:

  • The header, sequence, description and quality string for each record in the fastq file to the block

Yield Parameters:

  • header (String) —

    The header of the fastq record without the leading '@'

  • sequence (Sequence) —

    The sequence of the fastq record

  • description (String) —

    The description line of the fastq record without the leading '+'

  • quality_string (Quality) —

    The quality string of the fastq record



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# File 'lib/parse_fasta/fastq_file.rb', line 46

def each_record
  count = 0
  header = ''
  sequence = ''
  description = ''
  quality = ''

  begin
    f = Zlib::GzipReader.open(self)
  rescue Zlib::GzipFile::Error => e
    f = self
  end      
  
  f.each_line do |line|
    line.chomp!

    case count % 4
    when 0
      header = line.sub(/^@/, '')
    when 1
      sequence = Sequence.new(line)
    when 2
      description = line.sub(/^\+/, '')
    when 3
      quality = Quality.new(line)
      yield(header, sequence, description, quality)
    end
    
    count += 1
  end
  
  f.close if f.instance_of?(Zlib::GzipReader)
  return f
end