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#
# = bio/db/fasta/format_fasta.rb - Fasta format generater
#
# Copyright:: Copyright (C) 2006-2008
# Toshiaki Katayama <k@bioruby.org>,
# Naohisa Goto <ng@bioruby.org>,
# Jan Aerts <jan.aerts@bbsrc.ac.uk>
# License:: The Ruby License
#
module Bio::Sequence::Format::Formatter
# INTERNAL USE ONLY, YOU SHOULD NOT USE THIS CLASS.
# Simple Fasta format output class for Bio::Sequence.
class Fasta < Bio::Sequence::Format::FormatterBase
# INTERNAL USE ONLY, YOU SHOULD NOT CALL THIS METHOD.
#
# Creates a new Fasta format generater object from the sequence.
#
# ---
# *Arguments*:
# * _sequence_: Bio::Sequence object
# * (optional) :header => _header_: String (default nil)
# * (optional) :width => _width_: Fixnum (default 70)
def initialize; end if false # dummy for RDoc
# 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(:fasta) #=> "> \natgc\n"
# ---
# *Returns*:: String object
def output
header = @options[:header]
width = @options.has_key?(:width) ? @options[:width] : 70
seq = @sequence.seq
entry_id = @sequence.entry_id ||
"#{@sequence.primary_accession}.#{@sequence.sequence_version}"
definition = @sequence.definition
header ||= "#{entry_id} #{definition}"
">#{header}\n" +
if width
seq.to_s.gsub(Regexp.new(".{1,#{width}}"), "\\0\n")
else
seq.to_s + "\n"
end
end
end #class Fasta
# 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.
class Fasta_ncbi < Bio::Sequence::Format::FormatterBase
# 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
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
end #class Ncbi
end #module Bio::Sequence::Format::Formatter
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