#!/usr/bin/env perl

# Copyright (C) 2007-2009 Martin A. Hansen.

# This program is free software; you can redistribute it and/or
# modify it under the terms of the GNU General Public License
# as published by the Free Software Foundation; either version 2
# of the License, or (at your option) any later version.

# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
# GNU General Public License for more details.

# You should have received a copy of the GNU General Public License
# along with this program; if not, write to the Free Software
# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.

# http://www.gnu.org/copyleft/gpl.html


# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DESCRIPTION <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<

# Write tabular output from the stream.

# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<


use warnings;
use strict;
use Maasha::Fasta;
use Maasha::Biopieces;


# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<


my ( $options, $in, $out, $record, $data_out, @vals, $ok, $key, @keys, $A, $B, %no_keys, $sort_keys, $check_sort );

$options = Maasha::Biopieces::parse_options(
    [
        { long => 'no_stream', short => 'x', type => 'flag',   mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
        { long => 'data_out',  short => 'o', type => 'file',   mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
        { long => 'comment',   short => 'c', type => 'flag',   mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
        { long => 'delimit',   short => 'd', type => 'string', mandatory => 'no', default => "\t",  allowed => undef, disallowed => undef },
        { long => 'keys',      short => 'k', type => 'list',   mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
        { long => 'no_keys',   short => 'K', type => 'list',   mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
        { long => 'compress',  short => 'Z', type => 'flag',   mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
    ]   
);

$in       = Maasha::Biopieces::read_stream( $options->{ "stream_in" } );
$out      = Maasha::Biopieces::write_stream( $options->{ "stream_out" } );
$data_out = Maasha::Biopieces::write_stream( $options->{ "data_out" }, $options->{ "compress" } );

map { $no_keys{ $_ } = 1 } @{ $options->{ "no_keys" } };

while ( $record = Maasha::Biopieces::get_record( $in ) ) 
{
    undef @vals;
    $ok = 1;
    
    if ( $options->{ "keys" } )
    {
        map { $ok = 0 if not exists $record->{ $_ } } @{ $options->{ "keys" } };

        if ( $ok )
        {
            foreach $key ( @{ $options->{ "keys" }  } )
            {
                if ( exists $record->{ $key } )
                {
                    push @keys, $key if $options->{ "comment" };
                    push @vals, $record->{ $key };
                }
            }
         }
    }
    else
    {
        if ( not $check_sort )
        {
            $sort_keys = 1;

            map { $sort_keys = 0 if $_ !~ /^V(\d+)$/ } keys %{ $record };

            $check_sort = 1;
        }

        if ( $sort_keys )
        {
            foreach $key ( sort { $A = $a; $B = $b; $A =~ s/^V(\d+)$/$1/; $B =~ s/^V(\d+)$/$1/; $A <=> $B } keys %{ $record } )
            {
                next if exists $no_keys{ $key };

                push @keys, $key if $options->{ "comment" };
                push @vals, $record->{ $key };
            }
        }
        else
        {
            foreach $key ( keys %{ $record } )
            {
                next if exists $no_keys{ $key };

                push @keys, $key if $options->{ "comment" };
                push @vals, $record->{ $key };
            }
        
        }
    }

    if ( @keys and $options->{ "comment" } )
    {
        print $data_out "#", join( $options->{ "delimit" }, @keys ), "\n";

        delete $options->{ "comment" };
    }

    print $data_out join( $options->{ "delimit" }, @vals ), "\n" if @vals;

    Maasha::Biopieces::put_record( $record, $out ) if not $options->{ "no_stream" };
}

close $data_out;

Maasha::Biopieces::close_stream( $in );
Maasha::Biopieces::close_stream( $out );


# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<


BEGIN
{
    Maasha::Biopieces::status_set();
}


END
{
    Maasha::Biopieces::status_log();
}


# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<


__END__