Class Bio::Sequence::Format::Formatter::Fasta
In: lib/bio/db/fasta/format_fasta.rb
Parent: Bio::Sequence::Format::FormatterBase

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

Methods

new   output  

Public Class methods

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)

[Source]

    # File lib/bio/db/fasta/format_fasta.rb, line 26
26:     def initialize; end

Public Instance methods

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

[Source]

    # File lib/bio/db/fasta/format_fasta.rb, line 38
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

[Validate]