INTERNAL USE ONLY, YOU SHOULD NOT USE THIS CLASS.
FASTQ format output class for Bio::Sequence.
The default FASTQ format is fastq-sanger.
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)
# File lib/bio/db/fastq/format_fastq.rb, line 31 def initialize; 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 |
# 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
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