Class: Bio::Sequence::Format::Formatter::Fastq

Inherits:
Bio::Sequence::Format::FormatterBase show all
Defined in:
lib/bio/db/fastq/format_fastq.rb

Overview

INTERNAL USE ONLY, YOU SHOULD NOT USE THIS CLASS.

FASTQ format output class for Bio::Sequence.

The default FASTQ format is fastq-sanger.

Direct Known Subclasses

Fastq_illumina, Fastq_solexa

Instance Method Summary collapse

Methods inherited from Bio::Sequence::Format::FormatterBase

output

Constructor Details

#initialize ⇒ Fastq

INTERNAL USE ONLY, YOU SHOULD NOT CALL THIS METHOD.

Creates a new Fasta format generater object from the sequence.

Arguments:

  • sequence: Bio::Sequence object

  • (optional) :repeat_title => (true or false) if true, repeating title in the “+” line; if not true, “+” only (default false)

  • (optional) :width => width: (Fixnum) width to wrap sequence and quality lines; nil to prevent wrapping (default nil)

  • (optional) :title => title: (String) completely replaces title line with the title (default nil)

  • (optional) :default_score => score: (Integer) default score for bases that have no valid quality scores or error probabilities; false or nil means the lowest score, true means the highest score (default nil)



31
 
# File 'lib/bio/db/fastq/format_fastq.rb', line 31

def initialize; end

Dynamic Method Handling

This class handles dynamic methods through the method_missing method in the class Bio::Sequence::Format::FormatterBase

Instance Method Details

#output ⇒ Object

INTERNAL USE ONLY, YOU SHOULD NOT CALL THIS METHOD.

Output the FASTQ format string of the sequence.

Currently, this method is used in Bio::Sequence#output like so,

s = Bio::Sequence.new('atgc')
puts s.output(:fastq_sanger)
Returns

String object



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# File 'lib/bio/db/fastq/format_fastq.rb', line 43

def output
  title = @options[:title]
  width = @options.has_key?(:width) ? @options[:width] : nil
  seq = @sequence.seq.to_s
  entry_id = @sequence.entry_id || 
    "#{@sequence.primary_accession}.#{@sequence.sequence_version}"
  definition = @sequence.definition
  unless title then
    title = definition.to_s
    unless title[0, entry_id.length] == entry_id and
        /\s/ =~ title[entry_id.length, 1].to_s then
      title = "#{entry_id} #{title}"
    end
  end
  title2 = @options[:repeat_title] ? title : ''
  qstr = fastq_quality_string(seq, @options[:default_score])

  "@#{title}\n" +
    if width then
      seq.gsub(Regexp.new(".{1,#{width}}"), "\\0\n")
    else
      seq + "\n"
    end +
    "+#{title2}\n" +
    if width then
      qstr.gsub(Regexp.new(".{1,#{width}}"), "\\0\n")
    else
      qstr + "\n"
    end
end