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

#
# This is a SAS Component
#

=head1 fids_to_dna_sequences


fids_to_dna_sequences allows the user to look up the DNA sequences
corresponding to each of a set of fids.


Example:

    fids_to_dna_sequences [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 fids_to_dna_sequences. It is documented as follows:

  $return = $obj->fids_to_dna_sequences($fids)

=over 4

=item Parameter and return types

=begin html

<pre>
$fids is a fids
$return is a reference to a hash where the key is a fid and the value is a dna_sequence
fids is a reference to a list where each element is a fid
fid is a string
dna_sequence is a string

</pre>

=end html

=begin text

$fids is a fids
$return is a reference to a hash where the key is a fid and the value is a dna_sequence
fids is a reference to a list where each element is a fid
fid is a string
dna_sequence 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 ]

=item -fasta

This is used to request a fasta output file (dropping all of the other columns in the input lines).
It defaults to outputing just a fasta entry.

=back

=head2 Output Format

The standard output is just a fasta file with the sequence.  You can also get
a tab-delimited file by using -fasta=0.  The tab-delimited format consists of the input
file with an extra column of sequence  added.

Input lines that cannot be extended are written to stderr.

=cut


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

use Bio::KBase::CDMI::CDMIClient;
use Bio::KBase::Utilities::ScriptThing;

my $column;

my $input_file;
my $fasta = 1;
my $kbO = Bio::KBase::CDMI::CDMIClient->new_for_script('c=i' => \$column,
				     'fasta=i' => \$fasta,
				      '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;
}

my %fasta_written;   # to remove any possible duplicates
while (my @tuples = Bio::KBase::Utilities::ScriptThing::GetBatch($ih, undef, $column)) {
    my @h = map { $_->[0] } @tuples;
    my $h = $kbO->fids_to_dna_sequences(\@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)
            {
		if ($fasta)
		{
		    if (! $fasta_written{$id})
		    {
			$fasta_written{$id} = 1;
			print ">$id\n$_\n";
		    }
		}
		else
		{
		    print "$line\t$_\n";
		}
            }
        }
        else
        {
	    if ($fasta)
	    {
		if (! $fasta_written{$id})
		{
		    $fasta_written{$id} = 1;
		    print ">$id\n$v\n";
		}
	    }
	    else
	    {
		print "$line\t$v\n";
	    }
        }
    }
}