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

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.

Methods

output  

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(:ncbi)                   #=> "> \natgc\n"

Returns:String object

[Source]

    # File lib/bio/db/fasta/format_fasta.rb, line 77
77:     def output
78:       width = 70
79:       seq = @sequence.seq
80:       #gi = @sequence.gi_number
81:       dbname = 'lcl'
82:       if @sequence.primary_accession.to_s.empty? then
83:         idstr = @sequence.entry_id
84:       else
85:         idstr = "#{@sequence.primary_accession}.#{@sequence.sequence_version}"
86:       end
87: 
88:       definition = @sequence.definition
89:       header = "#{dbname}|#{idstr} #{definition}"
90: 
91:       ">#{header}\n" + seq.to_s.gsub(Regexp.new(".{1,#{width}}"), "\\0\n")
92:     end

[Validate]