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 median values in the stream for given keys.
26 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
31 use Maasha::Biopieces;
35 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
38 my ( $options, $in, $out, $record, $new_record, $key, %median_hash, $median, $fh );
40 $options = Maasha::Biopieces::parse_options(
42 { long => 'no_stream', short => 'x', type => 'flag', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
43 { long => 'data_out', short => 'o', type => 'file', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
44 { long => 'keys', short => 'k', type => 'list', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
45 { long => 'list', short => 'l', type => 'string', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
49 Maasha::Common::error( qq(both --keys and --list specified) ) if $options->{ "keys" } and $options->{ "list" };
50 Maasha::Common::error( qq(no --keys or --list specified) ) if not $options->{ "keys" } and not $options->{ "list" };
52 $in = Maasha::Biopieces::read_stream( $options->{ "stream_in" } );
53 $out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } );
55 while ( $record = Maasha::Biopieces::get_record( $in ) )
57 foreach $key ( @{ $options->{ "keys" } } ) {
58 push @{ $median_hash{ $key } }, $record->{ $key } if defined $record->{ $key };
61 if ( $options->{ 'list' } and $record->{ $options->{ 'list' } } ) {
62 $record->{ $options->{ 'list' } . "_MEDIAN" } = sprintf( "%.2f", Maasha::Calc::median( [ split ";", $record->{ $options->{ 'list' } } ] ) );
65 Maasha::Biopieces::put_record( $record, $out ) if not $options->{ "no_stream" };
68 Maasha::Biopieces::close_stream( $in );
69 Maasha::Biopieces::close_stream( $out );
71 $fh = Maasha::Biopieces::write_stream( $options->{ "data_out" } );
73 foreach $key ( @{ $options->{ "keys" } } )
75 if ( $median_hash{ $key } ) {
76 $median = Maasha::Calc::median( $median_hash{ $key } );
81 $new_record->{ $key . "_MEDIAN" } = $median;
84 if ( $options->{ "keys" } and $new_record )
86 $new_record->{ 'REC_TYPE' } = "MEDIAN";
88 Maasha::Biopieces::put_record( $new_record, $fh );
94 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
99 Maasha::Biopieces::status_set();
105 Maasha::Biopieces::status_log();
109 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<