libbio-eutilities-perl 1.75-3 / usr / bin / bp_einfo

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#!/usr/bin/perl

use strict;
use warnings;

# PODNAME:  bp_einfo
# ABSTRACT: Query einfo to find all available databases or information about a specific database (field information or links to other NCBI databases).
# AUTHOR:   Chris Fields <cjfields@bioperl.org>
# OWNER:    2009-2012 Chris Fields
# LICENSE:  Perl_5


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;
    }
}

__END__

=pod

=encoding utf-8

=head1 NAME

bp_einfo - Query einfo to find all available databases or information about a specific database (field information or links to other NCBI databases).

=head1 VERSION

version 1.75

=head1 SYNOPSIS

 bp_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 FEEDBACK

=head2 Mailing lists

User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to
the Bioperl mailing list.  Your participation is much appreciated.

  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

=head2 Support

Please direct usage questions or support issues to the mailing list:
I<bioperl-l@bioperl.org>

rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.

=head2 Reporting bugs

Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via the
web:

  https://github.com/bioperl/%%7Bdist%7D

=head1 AUTHOR

Chris Fields <cjfields@bioperl.org>

=head1 COPYRIGHT

This software is copyright (c) 2009-2012 by Chris Fields.

This software is available under the same terms as the perl 5 programming language system itself.

=cut

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