#!/usr/bin/env perl # Copyright (C) 2007-2009 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 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DESCRIPTION <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< # Align sequences in the stream. # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< use warnings; use strict; use Maasha::Biopieces; use Maasha::AlignTwoSeq; use Data::Dumper; # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< my ( $options, $in, $out, $count, $record, @records, $space, $matches ); $options = Maasha::Biopieces::parse_options(); $in = Maasha::Biopieces::read_stream( $options->{ "stream_in" } ); $out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } ); $count = 0; while ( $record = Maasha::Biopieces::get_record( $in ) ) { if ( defined $record->{ "SEQ" } and $count < 2 ) { push @records, $record; $count++; if ( $count == 2 ) { $matches = Maasha::AlignTwoSeq::align_two_seq( { 'Q_SEQ' => \$records[ 0 ]->{ 'SEQ' } , 'S_SEQ' => \$records[ 1 ]->{ 'SEQ' } }, [] ); Maasha::AlignTwoSeq::shift_case( $matches, \$records[ 0 ]->{ 'SEQ' } ,\$records[ 1 ]->{ 'SEQ' } ); Maasha::AlignTwoSeq::insert_indels( $matches, \$records[ 0 ]->{ 'SEQ' } ,\$records[ 1 ]->{ 'SEQ' } ); map { Maasha::Biopieces::put_record( $_, $out ) } @records; } } else { Maasha::Biopieces::put_record( $record, $out ); } } Maasha::Biopieces::close_stream( $in ); Maasha::Biopieces::close_stream( $out ); # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< BEGIN { Maasha::Biopieces::status_set(); } END { Maasha::Biopieces::status_log(); } # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< __END__