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()
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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::Format#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 def output width = 70 seq = @sequence.seq #gi = @sequence.gi_number dbname = 'lcl' if @sequence.primary_accession.to_s.empty? then idstr = @sequence.entry_id else idstr = "#{@sequence.primary_accession}.#{@sequence.sequence_version}" end definition = @sequence.definition header = "#{dbname}|#{idstr} #{definition}" ">#{header}\n" + seq.to_s.gsub(Regexp.new(".{1,#{width}}"), "\\0\n") end