#!/usr/bin/env perl -w

# 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 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<

# Read tabular data.

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


use strict;
use Maasha::Common;
use Maasha::Fasta;
use Maasha::Biopieces;


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


my ( $run_time_beg, $run_time_end, $options, $in, $out, $record, $data_in, $num, $skip, $line, @fields, @fields2, $i );

$options = Maasha::Biopieces::parse_options(
    [
        { long => 'data_in', short => 'i', type => 'files!', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
        { long => 'delimit', short => 'd', type => 'string', mandatory => 'no', default => '\s+', allowed => undef, disallowed => undef },
        { long => 'cols',    short => 'c', type => 'list',   mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
        { long => 'keys',    short => 'k', type => 'list',   mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
        { long => 'skip',    short => 's', type => 'uint',   mandatory => 'no', default => '0',   allowed => undef, disallowed => undef },
        { long => 'num',     short => 'n', type => 'uint',   mandatory => 'no', default => undef, allowed => undef, disallowed => '0' },
    ]   
);

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

while ( $record = Maasha::Biopieces::get_record( $in ) ) {
    Maasha::Biopieces::put_record( $record, $out );
}

if ( $options->{ 'data_in' } )
{
    $data_in = Maasha::Common::read_open_multi( $options->{ 'data_in' } );

    $num  = 1;
    $skip = $options->{ 'skip' };

    while ( $line = <$data_in> ) 
    {
        if ( $skip )
        {
            $skip--;
            next;
        }

        next if $line =~ /^#|^$/;

        chomp $line;

        undef $record;
        undef @fields2;

        @fields = split /$options->{'delimit'}/, $line;

        if ( $options->{ "cols" } ) {
            map { push @fields2, $fields[ $_ ] } @{ $options->{ "cols" } };
        } else {
            @fields2 = @fields;
        }

        for ( $i = 0; $i < @fields2; $i++ )
        {
            if ( $options->{ "keys" }->[ $i ] ) {
                $record->{ $options->{ "keys" }->[ $i ] } = $fields2[ $i ];
            } else {
                $record->{ "V" . $i } = $fields2[ $i ];
            }
        }

        Maasha::Biopieces::put_record( $record, $out );

        last if $options->{ "num" } and $num == $options->{ "num" };

        $num++;
    }

    close $data_in;
}


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


BEGIN
{
    $run_time_beg = Maasha::Biopieces::run_time();

    Maasha::Biopieces::log_biopiece();
}

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

    $run_time_end = Maasha::Biopieces::run_time();

    Maasha::Biopieces::run_time_print( $run_time_beg, $run_time_end, $options );
}


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


__END__