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 # Scan sequences in the stream for restriction enzyme cleavage sites.
26 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
32 use Maasha::RestrictEnz;
33 use Maasha::Biopieces;
37 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
40 my ( $options, $in, $out, $record, $re_data, $re, $matches, $match, %re_hash, $res_enz, $new_record );
42 $options = Maasha::Biopieces::parse_options(
44 { long => 'res_enz', short => 'r', type => 'list', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
45 { long => 'res_enz_in', short => 'R', type => 'file!', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
46 { long => 'res_enz_only', short => 'o', type => 'flag', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
47 { long => 'no_matches', short => 'M', type => 'flag', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
51 $in = Maasha::Biopieces::read_stream( $options->{ "stream_in" } );
52 $out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } );
54 $re_data = Maasha::RestrictEnz::parse_re_data();
56 if ( $options->{ 'res_enz_in' } ) {
57 $res_enz = Maasha::Patscan::read_patterns( $options->{ "res_enz_in" } );
60 push @{ $res_enz }, @{ $options->{ 'res_enz' } } if defined $options->{ 'res_enz' };
62 map { $re_hash{ $_ } = 1 } @{ $res_enz };
64 while ( $record = Maasha::Biopieces::get_record( $in ) )
66 if ( $record->{ 'SEQ' } )
68 foreach $re ( @{ $re_data } )
70 next if not exists $re_hash{ $re->{ 'name' } };
72 $matches = Maasha::RestrictEnz::re_scan( $record->{ 'SEQ' }, $re );
74 %{ $new_record } = %{ $record } if not $options->{ 'res_enz_only' };
75 $new_record->{ 'RE' } = $re->{ 'name' };
76 $new_record->{ 'RE_COUNT' } = scalar @{ $matches };
77 $new_record->{ 'RE_MATCHES' } = join( ";", @{ $matches } ) if not $options->{ 'no_matches' };
79 Maasha::Biopieces::put_record( $new_record, $out );
83 # Maasha::Biopieces::put_record( $record, $out );
86 Maasha::Biopieces::close_stream( $in );
87 Maasha::Biopieces::close_stream( $out );
90 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
95 Maasha::Biopieces::status_set();
101 Maasha::Biopieces::status_log();
105 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<