This file is indexed.

/usr/bin/bp_biogetseq is in bioperl 1.6.923-1.

This file is owned by root:root, with mode 0o755.

The actual contents of the file can be viewed below.

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
#!/usr/bin/perl 

eval 'exec /usr/bin/perl  -S $0 ${1+"$@"}'
    if 0; # not running under some shell
#
# OBDA Registry compliant sequence retrieval script
#
# Copyright Heikki Lehvaslaiho <heikki-at-bioperl-dot-org>
# You may distribute this program under the same terms as perl itself


use Bio::DB::Registry;
use Bio::SeqIO;
use Getopt::Long;
use strict;
use warnings;

my ($help, $format, $namespace, $dbname) = ('', 'embl', 'acc', 'embl');
GetOptions ("help" => \$help, "format=s" => \$format,
            "namespace=s" => \$namespace, "dbname=s" => \$dbname );
if ($help || !@ARGV) {
  system("perldoc $0");
  exit 0;
}

my $get_function = 'get_Seq_by_'. $namespace;

my $registry = new Bio::DB::Registry();
while (my $id = shift) {
    my $db = $registry->get_database($dbname);
    my $seq = $db->$get_function($id);

    if ($seq) {
        my $out = new Bio::SeqIO('-format' => $format);
        $out->write_seq($seq);
    } else {
        print STDERR "Could not find sequence with identifier [$id]\n";
    }
}

=head1 NAME

bp_biogetseq - sequence retrieval using OBDA registry

=head1 DESCRIPTION

This script retrives sequences from the source defined by users
registry setup.  The current alternatives are from a local indexed
file, sql database or over the web.

=head1 USAGE

  Usage: bp_biogetseq --dbname embl --format embl
                   --namespace acc id [ ids... ]
         * dbname defaults to embl
         * format defaults to embl
         * namespace defaults to 'acc' ['id', 'acc', 'version']
         * unnamed arguments are ids in the given namespace

=cut