class Bio::Sequence::Format::Formatter::Fastq_sanger

INTERNAL USE ONLY, YOU SHOULD NOT USE THIS CLASS.

FASTQ format output class for Bio::Sequence.

The default FASTQ format is fastq-sanger.

Public Class Methods

Source

   # File lib/bio/db/fastq/format_fastq.rb
31 def initialize; end

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)

Public Instance Methods

output ()

Source

   # File lib/bio/db/fastq/format_fastq.rb
43 def output
44   title = @options[:title]
45   width = @options.has_key?(:width) ? @options[:width] : nil
46   seq = @sequence.seq.to_s
47   entry_id = @sequence.entry_id || 
48     "#{@sequence.primary_accession}.#{@sequence.sequence_version}"
49   definition = @sequence.definition
50   unless title then
51     title = definition.to_s
52     unless title[0, entry_id.length] == entry_id and
53         /\s/ =~ title[entry_id.length, 1].to_s then
54       title = "#{entry_id} #{title}"
55     end
56   end
57   title2 = @options[:repeat_title] ? title : ''
58   qstr = fastq_quality_string(seq, @options[:default_score])
59 
60   "@#{title}\n" +
61     if width then
62       seq.gsub(Regexp.new(".{1,#{width}}"), "\\0\n")
63     else
64       seq + "\n"
65     end +
66     "+#{title2}\n" +
67     if width then
68       qstr.gsub(Regexp.new(".{1,#{width}}"), "\\0\n")
69     else
70       qstr + "\n"
71     end
72 end

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