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

new()

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 30
30:     def initialize; end

Public Instance methods

output()

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 42
42:     def output
43:       header = @options[:header]
44:       width = @options.has_key?(:width) ? @options[:width] : 70
45:       seq = @sequence.seq
46:       entry_id = @sequence.entry_id || 
47:         "#{@sequence.primary_accession}.#{@sequence.sequence_version}"
48:       definition = @sequence.definition
49:       header ||= "#{entry_id} #{definition}"
50: 
51:       ">#{header}\n" +
52:         if width
53:           seq.to_s.gsub(Regexp.new(".{1,#{width}}"), "\\0\n")
54:         else
55:           seq.to_s + "\n"
56:         end
57:     end

[Validate]