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 # Find the mean values in the stream for given keys.
26 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
30 use Maasha::Biopieces;
33 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
36 my ( $run_time_beg, $run_time_end, $options, $in, $out, $record, $key, %sum_hash, %count_hash, $mean, $fh );
38 $options = Maasha::Biopieces::parse_options(
40 { long => 'no_stream', short => 'x', type => 'flag', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
41 { long => 'data_out', short => 'o', type => 'file', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
42 { long => 'keys', short => 'k', type => 'list', mandatory => 'yes', 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 while ( $record = Maasha::Biopieces::get_record( $in ) )
51 foreach $key ( @{ $options->{ "keys" } } )
53 if ( $record->{ $key } )
55 $sum_hash{ $key } += $record->{ $key };
56 $count_hash{ $key }++;
60 Maasha::Biopieces::put_record( $record, $out ) if not $options->{ "no_stream" };
63 $fh = Maasha::Biopieces::write_stream( $options->{ "data_out" } );
65 foreach $key ( @{ $options->{ "keys" } } )
67 if ( exists $count_hash{ $key } ) {
68 $mean = sprintf( "%.2f", ( $sum_hash{ $key } / $count_hash{ $key } ) );
73 Maasha::Biopieces::put_record( { $key . "_MEAN" => $mean } , $fh );
79 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
84 $run_time_beg = Maasha::Biopieces::run_time();
86 Maasha::Biopieces::log_biopiece();
92 Maasha::Biopieces::close_stream( $in );
93 Maasha::Biopieces::close_stream( $out );
95 $run_time_end = Maasha::Biopieces::run_time();
97 Maasha::Biopieces::run_time_print( $run_time_beg, $run_time_end, $options );
101 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<