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 # Plot a length distribution histogram.
26 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
31 use Maasha::Biopieces;
36 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
39 my ( $options, $in, $out, $default, $terminals, $record, %data_hash, $max, @data_list, $i, $result, $fh );
41 $default = "Length Distribution";
42 $terminals = "dumb,x11,aqua,post,svg";
44 $options = Maasha::Biopieces::parse_options(
46 { long => 'no_stream', short => 'x', type => 'flag', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
47 { long => 'data_out', short => 'o', type => 'file', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
48 { long => 'key', short => 'k', type => 'string', mandatory => 'yes', default => undef, allowed => undef, disallowed => undef },
49 { long => 'terminal', short => 't', type => 'string', mandatory => 'no', default => 'dumb', allowed => $terminals, disallowed => undef },
50 { long => 'title', short => 'T', type => 'string', mandatory => 'no', default => $default, allowed => undef, disallowed => undef },
51 { long => 'xlabel', short => 'X', type => 'string', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
52 { long => 'ylabel', short => 'Y', type => 'string', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
53 { long => 'logscale_y', short => 'L', type => 'flag', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
57 $in = Maasha::Biopieces::read_stream( $options->{ "stream_in" } );
58 $out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } );
60 while ( $record = Maasha::Biopieces::get_record( $in ) )
62 $data_hash{ $record->{ $options->{ "key" } } }++ if defined $record->{ $options->{ "key" } };
64 Maasha::Biopieces::put_record( $record, $out ) if not $options->{ "no_stream" };
67 $max = Maasha::Calc::list_max( [ keys %data_hash ] );
69 for ( $i = 0; $i < $max; $i++ ) {
70 push @data_list, [ $i, $data_hash{ $i } || 0 ];
73 $result = Maasha::Plot::histogram_lendist( \@data_list, $options );
75 $fh = Maasha::Biopieces::write_stream( $options->{ "data_out" } );
77 print $fh "$_\n" foreach @{ $result };
81 Maasha::Biopieces::close_stream( $in );
82 Maasha::Biopieces::close_stream( $out );
85 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
90 Maasha::Biopieces::status_set();
96 Maasha::Biopieces::status_log();
100 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<