#!perl
use strict;
use Data::Dumper;
use Carp;
use Getopt::Long;

#
# This is a SAS Component
#

=head1 kbase_ids_to_external_ids

Given a set of KBase identifiers, look up the associated external identifiers.

Example:

    kbase_ids_to_external_ids  < input > output

The standard input should be a tab-separated table (i.e., each line
is a tab-separated set of fields).  Normally, the last field in each
line would contain the identifer. If another column contains the identifier
use

    -c N

where N is the column (from 1) that contains the identifier.

This is a pipe command. The input is taken from the standard input, and the
output is to the standard output.

=head2 Command-Line Options

=over 4

=item -c Column

This is used only if the column containing the identifier is not the last column.

=item -i InputFile

Read data from InputFile instead of from the standard input.

=back

=head2 Output Format

The standard output is a tab-delimited file. It consists of the input
file with extra columns added.

Input lines that cannot be extended are written to stderr.

=cut

my $usage = "usage: kbase_ids_to_external_ids [-c column]  < input > output\n";

use Bio::KBase;
use Bio::KBase::Utilities::ScriptThing;

my $column;

my $input_file;

my $kb = Bio::KBase->new();
my $idserver = $kb->id_server();

my $rc = GetOptions('c=i' => \$column,
		    'i=s' => \$input_file);


(@ARGV == 0 && $rc) or die $usage;

my $ih;
if ($input_file)
{
    open $ih, "<", $input_file or die "Cannot open input file $input_file: $!";
}
else
{
    $ih = \*STDIN;
}

while (my @tuples = Bio::KBase::Utilities::ScriptThing::GetBatch($ih, undef, $column)) {
    my @h = map { $_->[0] } @tuples;
    my $h = $idserver->kbase_ids_to_external_ids(\@h);
    for my $tuple (@tuples) {
        #
        # Process output here and print.
        #
        my ($id, $line) = @$tuple;
        my $v = $h->{$id};

        if (! defined($v))
        {
            print STDERR $line,"\n";
        }
	else
	{
	    print join("\t", $line, @$v), "\n";
	}
    }
}