class Bio::Sequence::Format::Formatter::Fasta

INTERNAL USE ONLY, YOU SHOULD NOT USE THIS CLASS. Simple Fasta format output class for Bio::Sequence.

Public Class Methods

Source

   # File lib/bio/db/fasta/format_fasta.rb
26 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) :header => header: String (default nil)
(optional) :width => width: Fixnum (default 70)

Public Instance Methods

output ()

Source

   # File lib/bio/db/fasta/format_fasta.rb
38 def output
39   header = @options[:header]
40   width = @options.has_key?(:width) ? @options[:width] : 70
41   seq = @sequence.seq
42   entry_id = @sequence.entry_id || 
43     "#{@sequence.primary_accession}.#{@sequence.sequence_version}"
44   definition = @sequence.definition
45   header ||= "#{entry_id} #{definition}"
46 
47   ">#{header}\n" +
48     if width
49       seq.to_s.gsub(Regexp.new(".{1,#{width}}"), "\\0\n")
50     else
51       seq.to_s + "\n"
52     end
53 end

INTERNAL USE ONLY, YOU SHOULD NOT CALL THIS METHOD.

Output the FASTA format string of the sequence.

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

s = Bio::Sequence.new('atgc')
puts s.output(:fasta)                   #=> "> \natgc\n"

Returns: String object