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.
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 |
# 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