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 73
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

[Validate]