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 65

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[1..-1]
    when 1
      sequence = Sequence.new(line)
    when 2
      description = line[1..-1]
    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

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

Note:

If the fastQ file has spaces in the sequence, they will be retained. If this is a problem, use #each_record instead.

Fast version of #each_record

Examples:

Parsing a fastq file

FastqFile.open('reads.fq').each_record_fast 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_fast 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 (String) —

    The sequence of the fastq record

  • description (String) —

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

  • quality_string (String) —

    The quality string of the fastq record



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# File 'lib/parse_fasta/fastq_file.rb', line 124

def each_record_fast
  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[1..-1]
    when 1
      sequence = line
    when 2
      description = line[1..-1]
    when 3
      quality = line
      yield(header, sequence, description, quality)
    end

    count += 1
  end

  f.close if f.instance_of?(Zlib::GzipReader)
  return f
end

#to_hash ⇒ Hash

Returns the records in the fastq file as a hash map with the headers as keys pointing to a hash map like so { "seq1" => { head: "seq1", seq: "ACTG", desc: "", qual: "II3*"} }

Examples:

Read a fastQ into a hash table.

seqs = FastqFile.open('reads.fq.gz').to_hash

Returns:

  • (Hash) —

    A hash with headers as keys, and a hash map as the value with keys :head, :seq, :desc, :qual, for header, sequence, description, and quality.



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# File 'lib/parse_fasta/fastq_file.rb', line 35

def to_hash
  hash = {}
  self.each_record do |head, seq, desc, qual|
    hash[head] = { head: head, seq: seq, desc: desc, qual: qual }
  end

  hash
end