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 EMBL files and output a file index.
26 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
32 use Maasha::Biopieces;
37 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
40 my ( $options, $in, $out, $record, $file, $data_in, $entry, $id, $offset );
42 $options = Maasha::Biopieces::parse_options(
44 { long => 'data_in', short => 'i', type => 'files!', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
48 $in = Maasha::Biopieces::read_stream( $options->{ "stream_in" } );
49 $out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } );
51 while ( $record = Maasha::Biopieces::get_record( $in ) ) {
52 Maasha::Biopieces::put_record( $record, $out );
55 foreach $file ( @{ $options->{ 'data_in' } } )
57 Maasha::Common::error( qq(File "$file" is gzipped) ) if Maasha::Filesys::is_gzipped( $file );
59 $data_in = Maasha::Filesys::file_read_open( $file );
63 while ( $entry = Maasha::EMBL::get_embl_entry( $data_in ) )
65 if ( $entry =~ /^ID ([^;]+)/ )
70 FILE => "$ENV{ 'PWD' }/$file",
76 Maasha::Biopieces::put_record( $record, $out );
78 $offset += length $entry;
82 Maasha::Common::error( "Bad EMBL entry" );
89 Maasha::Biopieces::close_stream( $in );
90 Maasha::Biopieces::close_stream( $out );
93 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
98 Maasha::Biopieces::status_set();
104 Maasha::Biopieces::status_log();
108 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<