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 # Read EMBL entries from one or more files.
26 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
31 use Maasha::Biopieces;
36 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
39 my ( $options, $in, $out, %options2, $file, $data_in, $num, $entry, $record );
41 $options = Maasha::Biopieces::parse_options(
43 { long => 'data_in', short => 'i', type => 'files!', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
44 { long => 'num', short => 'n', type => 'uint', mandatory => 'no', default => undef, allowed => undef, disallowed => '0' },
45 { long => 'keys', short => 'k', type => 'list', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
46 { long => 'feats', short => 'f', type => 'list', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
47 { long => 'quals', short => 'q', type => 'list', 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 map { $options2{ "keys" }{ $_ } = 1 } @{ $options->{ "keys" } };
55 map { $options2{ "feats" }{ $_ } = 1 } @{ $options->{ "feats" } };
56 map { $options2{ "quals" }{ $_ } = 1 } @{ $options->{ "quals" } };
58 while ( $record = Maasha::Biopieces::get_record( $in ) ) {
59 Maasha::Biopieces::put_record( $record, $out );
62 if ( $options->{ 'data_in' } )
64 $data_in = Maasha::Filesys::files_read_open( $options->{ 'data_in' } );
68 while ( $entry = Maasha::EMBL::get_embl_entry( $data_in ) )
70 $record = Maasha::EMBL::parse_embl_entry( $entry, \%options2 );
72 my ( $feat, $feat2, $qual, $qual_val, $record_copy );
74 $record_copy = dclone $record;
76 delete $record_copy->{ "FT" };
78 Maasha::Biopieces::put_record( $record_copy, $out );
80 delete $record_copy->{ "SEQ" };
82 foreach $feat ( keys %{ $record->{ "FT" } } )
84 $record_copy->{ "FEAT_TYPE" } = $feat;
86 foreach $feat2 ( @{ $record->{ "FT" }->{ $feat } } )
88 foreach $qual ( keys %{ $feat2 } )
90 $qual_val = join "; ", @{ $feat2->{ $qual } };
95 $record_copy->{ $qual } = $qual_val;
98 Maasha::Biopieces::put_record( $record_copy, $out );
102 last if $options->{ "num" } and $num == $options->{ "num" };
110 Maasha::Biopieces::close_stream( $in );
111 Maasha::Biopieces::close_stream( $out );
114 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
119 Maasha::Biopieces::status_set();
125 Maasha::Biopieces::status_log();
129 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<