3 # Copyright (C) 2007-2009 Martin A. Hansen.
5 # This program is free software; you can redistribute it and/or
6 # modify it under the terms of the GNU General Public License
7 # as published by the Free Software Foundation; either version 2
8 # of the License, or (at your option) any later version.
10 # This program is distributed in the hope that it will be useful,
11 # but WITHOUT ANY WARRANTY; without even the implied warranty of
12 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
13 # GNU General Public License for more details.
15 # You should have received a copy of the GNU General Public License
16 # along with this program; if not, write to the Free Software
17 # Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
19 # http://www.gnu.org/copyleft/gpl.html
22 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DESCRIPTION <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
24 # Sort records in the stream.
26 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
31 use Maasha::Biopieces;
34 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
37 my ( $options, $in, $out, @keys, $key, @sort_cmd, $sort_str, $sort_sub, @records, $record, $i, $ok );
39 $options = Maasha::Biopieces::parse_options(
41 { long => 'keys', short => 'k', type => 'list', mandatory => 'yes', default => undef, allowed => undef, disallowed => undef },
42 { long => 'reverse', short => 'r', type => 'flag', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
46 $in = Maasha::Biopieces::read_stream( $options->{ "stream_in" } );
47 $out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } );
49 foreach $key ( @{ $options->{ "keys" } } )
51 if ( $key =~ s/n$// ) {
52 push @sort_cmd, qq(\$a->{ "$key" } <=> \$b->{ "$key" });
54 push @sort_cmd, qq(\$a->{ "$key" } cmp \$b->{ "$key" });
58 $sort_str = join " or ", @sort_cmd;
59 $sort_sub = eval "sub { $sort_str }"; # NB security issue!
61 while ( $record = Maasha::Biopieces::get_record( $in ) )
64 foreach $key ( @{ $options->{ "keys" } } )
66 if ( not exists $record->{ $key } )
73 push @records, $record if $ok;
76 @records = sort $sort_sub @records;
78 if ( $options->{ "reverse" } )
80 for ( $i = scalar @records - 1; $i >= 0; $i-- ) {
81 Maasha::Biopieces::put_record( $records[ $i ], $out );
86 for ( $i = 0; $i < scalar @records; $i++ ) {
87 Maasha::Biopieces::put_record( $records[ $i ], $out );
91 Maasha::Biopieces::close_stream( $in );
92 Maasha::Biopieces::close_stream( $out );
95 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
100 Maasha::Biopieces::status_set();
106 Maasha::Biopieces::status_log();
110 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<