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.
INTERNAL USE ONLY, YOU SHOULD NOT CALL THIS METHOD.
Creates a new Fasta format generater object from the sequence.
Arguments:
# File lib/bio/db/fasta/format_fasta.rb, line 26 26: def initialize; 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 |
# 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