#!/usr/bin/env ruby # Copyright (C) 2007-2010 Martin A. Hansen. # This program is free software; you can redistribute it and/or # modify it under the terms of the GNU General Public License # as published by the Free Software Foundation; either version 2 # of the License, or (at your option) any later version. # This program is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # GNU General Public License for more details. # You should have received a copy of the GNU General Public License # along with this program; if not, write to the Free Software # Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. # http://www.gnu.org/copyleft/gpl.html # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< # This program is part of the Biopieces framework (www.biopieces.org). # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DESCRIPTION <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< # Join sequences in the stream. # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< require 'maasha/biopieces' require 'maasha/fasta' require 'maasha/seq' casts = [] bp = Biopieces.new options = bp.parse(ARGV, casts) seq = Seq.new(nil, "") bp.each_record do |record| if record.has_key? :SEQ unless seq.seq_name seq.seq_name = record[:SEQ_NAME] end seq.seq << record[:SEQ] end bp.puts record end if seq.seq != "" new_record = seq.to_bp new_record[:REC_TYPE] = "JOIN" bp.puts new_record end # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< __END__