Class: Bio::Sequence::Format::Formatter::Fasta

Inherits:
Bio::Sequence::Format::FormatterBase show all
Defined in:
lib/bio/db/fasta/format_fasta.rb

Overview

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

Instance Method Summary collapse

Methods inherited from Bio::Sequence::Format::FormatterBase

output

Constructor Details

#initialize ⇒ Fasta

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)



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# File 'lib/bio/db/fasta/format_fasta.rb', line 30

def initialize; end

Dynamic Method Handling

This class handles dynamic methods through the method_missing method in the class Bio::Sequence::Format::FormatterBase

Instance Method Details

#output ⇒ Object

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



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# File 'lib/bio/db/fasta/format_fasta.rb', line 42

def output
  header = @options[:header]
  width = @options.has_key?(:width) ? @options[:width] : 70
  seq = @sequence.seq
  entry_id = @sequence.entry_id || 
    "#{@sequence.primary_accession}.#{@sequence.sequence_version}"
  definition = @sequence.definition
  header ||= "#{entry_id} #{definition}"

  ">#{header}\n" +
    if width
      seq.to_s.gsub(Regexp.new(".{1,#{width}}"), "\\0\n")
    else
      seq.to_s + "\n"
    end
end