/usr/bin/bp_einfo is in bioperl 1.6.901-3.
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 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 | #!/usr/bin/perl
eval 'exec /usr/bin/perl -S $0 ${1+"$@"}'
if 0; # not running under some shell
# $Id: einfo.PLS 15088 2008-12-04 02:49:09Z bosborne $
use strict;
use warnings;
=head1 NAME
einfo.pl - query einfo to find all available databases or information about a
specific database (field information or links to other NCBI
databases)
=head1 SYNOPSIS
einfo [-d database] [-f Field Code] [-l Link Name] [-o outfile]
=head1 DESCRIPTION
Command line options:
-e/--email
Valid email (required by NCBI policy)
-d/--db/--database
NCBI database to query
(default = none, which shows available databases)
-f/--field
print out information about a specific field code
(default = none)
-l/--link
print out information about a specific link name
(default = none)
-o/--out
outfile
(default = STDOUT)
-h/--help
show this documentation
As per NCBI's policy regarding eutils access, a valid email is required. This
is not enforced here (if one is provided you will get a standard warning), but
don't be surprised if this doesn't work after June 1, 2010 unless one is
supplied.
If -d is not specified, field and link arguments are ignored and all available
databases are printed instead.
If either link names or field codes (or both) are specified, nothing else is
printed out (only the info requested). You can specify as many fields and/or
links as you want by using multiple -f/-l E<lt>ARGE<gt> on the command line.
=head1 AUTHOR - Chris Fields
Chris Fields cjfields at bioperl dot org
=cut
use Getopt::Long;
use Bio::DB::EUtilities;
my ($db, @fields, @links, $outfile, $email);
GetOptions(
'e|email:s' => \$email,
'd|db|database:s' => \$db,
'f|field:s' => \@fields,
'l|link:s' => \@links,
'o|out|outfile:s' => \$outfile,
'h|help' => sub { exec('perldoc',$0); exit; }
);
my $outfh;
if( $outfile ) {
open($outfh, ">$outfile") || die("$outfile: $!");
} else {
$outfh = \*STDOUT;
}
if (!defined $db) {
my $eutil = Bio::DB::EUtilities->new(-eutil => 'einfo',
-email => $email);
print $outfh join("\n",$eutil->get_available_databases);
exit;
} else {
my $eutil = Bio::DB::EUtilities->new(-eutil => 'einfo',
-db => $db,
-email => $email);
if (@links || @fields) {
for my $fi ($eutil->get_FieldInfo) {
my $code = $fi->get_field_code;
if (grep {$_ eq $code} @fields) {
print $outfh $fi->to_string."\n";
}
}
for my $li ($eutil->get_LinkInfo) {
my $nm = $li->get_link_name;
if (grep {$_ eq $nm} @links) {
print $outfh $li->to_string."\n";
}
}
} else {
$eutil->print_FieldInfo;
$eutil->print_LinkInfo;
}
}
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