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#!perl
use strict;
use Data::Dumper;
use Carp;
#
# This is a SAS Component
#
HideShow 99 lines of Pod
=head1 genomes_to_genome_data
Example:
    genomes_to_genome_data [arguments] < 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 subsystem.
This is a pipe command. The input is taken from the standard input, and the
output is to the standard output.
=head2 Documentation for underlying call
This script is a wrapper for the CDMI-API call genomes_to_genome_data. It is documented as follows:
  $return = $obj->genomes_to_genome_data($genomes)
=over 4
=item Parameter and return types
=begin html
<pre>
$genomes is a genomes
$return is a reference to a hash where the key is a genome and the value is a genome_data
genomes is a reference to a list where each element is a genome
genome is a string
genome_data is a reference to a hash where the following keys are defined:
        complete has a value which is an int
        contigs has a value which is an int
        dna_size has a value which is an int
        gc_content has a value which is a float
        genetic_code has a value which is an int
        pegs has a value which is an int
        rnas has a value which is an int
        scientific_name has a value which is a string
        taxonomy has a value which is a string
        genome_md5 has a value which is a string
</pre>
=end html
=begin text
$genomes is a genomes
$return is a reference to a hash where the key is a genome and the value is a genome_data
genomes is a reference to a list where each element is a genome
genome is a string
genome_data is a reference to a hash where the following keys are defined:
        complete has a value which is an int
        contigs has a value which is an int
        dna_size has a value which is an int
        gc_content has a value which is a float
        genetic_code has a value which is an int
        pegs has a value which is an int
        rnas has a value which is an int
        scientific_name has a value which is a string
        taxonomy has a value which is a string
        genome_md5 has a value which is a string
=end text
=back
=head2 Command-Line Options
=over 4
=item -c Column
This is used only if the column containing the subsystem is not the last column.
=item -i InputFile    [ use InputFile, rather than stdin ]
=back
=head2 Output Format
The standard output is a tab-delimited file. It consists of the input
file with extra columns added in this order: rnas gc_content dna_size taxonomy scientific_name contigs genome_md5 pegs genetic_code complete.
Input lines that cannot be extended are written to stderr.
=cut
my $usage = "usage: genomes_to_genome_data [-c column] < input > output";
use Bio::KBase::CDMI::CDMIClient;
use Bio::KBase::Utilities::ScriptThing;
my $column;
my $input_file;
my $kbO = Bio::KBase::CDMI::CDMIClient->new_for_script('c=i' => \$column,
                                      'i=s' => \$input_file);
if (! $kbO) { print STDERR $usage; exit }
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 = $kbO->genomes_to_genome_data(\@h);
    for my $tuple (@tuples) {
        #
        # Process output here and print.
        #
        my ($id, $line) = @$tuple;
        my $v = $h->{$id};
        if (! defined($v))
        {
            print STDERR $line,"\n";
        }
        elsif (ref($v) eq 'ARRAY')
        {
            foreach $_ (@$v)
            {
                print "$line\t$_\n";
            }
        }
        else
        {
            my $rna = $v->{rnas};
            my $gc = $v->{gc_content};
            my $dna_size = $v->{dna_size};
            my $tax = $v->{taxonomy};
            my $name = $v->{scientific_name};
            my $contigs = $v->{contigs};
            my $md5 = $v->{genome_md5};
            my $pegs = $v->{pegs};
            my $gcode = $v->{genetic_code};
            my $complete = $v->{complete};
            print "$line\t$rna\t$gc\t$dna_size\t$tax\t$name\t$contigs\t$md5\t$pegs\t$gcode\t$complete\n";
        }
    }
}