class Bio::Sequence::Format::Formatter::Fasta_ncbi

INTERNAL USE ONLY, YOU SHOULD NOT USE THIS CLASS. NCBI-Style Fasta format output class for Bio::Sequence. (like “ncbi” format in EMBOSS)

Note that this class is under construction.

Public Instance Methods

output ()

Source

   # File lib/bio/db/fasta/format_fasta.rb
73 def output
74   width = 70
75   seq = @sequence.seq
76   #gi = @sequence.gi_number
77   dbname = 'lcl'
78   if @sequence.primary_accession.to_s.empty? then
79     idstr = @sequence.entry_id
80   else
81     idstr = "#{@sequence.primary_accession}.#{@sequence.sequence_version}"
82   end
83 
84   definition = @sequence.definition
85   header = "#{dbname}|#{idstr} #{definition}"
86 
87   ">#{header}\n" + seq.to_s.gsub(Regexp.new(".{1,#{width}}"), "\\0\n")
88 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(:ncbi)                   #=> "> \natgc\n"

Returns: String object