3 # Copyright (C) 2007-2013 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 # Substitute values to keys in the stream.
26 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
31 use Maasha::Biopieces;
34 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
37 my ( $options, $in, $out, $record, $search, $replace, $keys, $key );
39 $options = Maasha::Biopieces::parse_options(
41 { long => 'search', short => 's', type => 'string', mandatory => 'yes', default => undef, allowed => undef, disallowed => undef },
42 { long => 'replace', short => 'r', type => 'string', mandatory => 'yes', default => undef, allowed => undef, disallowed => undef },
43 { long => 'global', short => 'g', type => 'flag', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
44 { long => 'ignore_case', short => 'i', type => 'flag', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
45 { long => 'keys', short => 'k', type => 'list', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
49 $in = Maasha::Biopieces::read_stream( $options->{ "stream_in" } );
50 $out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } );
52 $search = $options->{ "search" };
53 $replace = $options->{ "replace" };
55 while ( $record = Maasha::Biopieces::get_record( $in ) )
57 $keys = $options->{ "keys" } || [ keys %{ $record } ];
59 foreach $key (@{ $keys })
61 if ( $options->{ 'global' } and $options->{ 'ignore_case' } ) {
62 $record->{ $key } =~ s/$search/$replace/gi;
63 } elsif ( $options->{ 'global' } ) {
64 $record->{ $key } =~ s/$search/$replace/g;
65 } elsif ( $options->{ 'ignore_case' } ) {
66 $record->{ $key } =~ s/$search/$replace/i;
68 $record->{ $key } =~ s/$search/$replace/;
72 Maasha::Biopieces::put_record( $record, $out );
75 Maasha::Biopieces::close_stream( $in );
76 Maasha::Biopieces::close_stream( $out );
79 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
84 Maasha::Biopieces::status_set();
90 Maasha::Biopieces::status_log();
94 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<