/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
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