>ca106a84b6c03260e9e38b730b137664/1-17_107-243 1283
0.000           #              -
0.331           #              W
0.370           #              D
>a1b9ed2221c16448ebe19883994fa2db/1-95_130-213 1026
0.000           #              M
0.331           #              K
0.370           #              N
>fdecbdbac2f7f88b0cb666b87a69753a/76-219 209
0.000           #              M
0.331           #              T
0.370           #              E

##</code><code>##

0.000           #              -MM
0.331           #              WKT
0.370           #              DNE

##</code><code>##

#!/usr/local/bin/perl

use strict;
use English;
use Data::Dumper;
use UNIVERSAL qw(isa);
use FileHandle;
use Exception;

my $names = shift;
my $alignment = shift;
my $scorecons = shift;

#my $lineno = 0;

if (!$names || ! -e $names) {
	die new Exception("couldnt open names file $names");
}

if (!$alignment || ! -e $alignment) {
	die new Exception("couldnt open names file $alignment $!");
}

if (!$scorecons || ! -e $scorecons) {
	die new Exception("couldnt open names file $scorecons");
}


warn "# Reading alignment data";
my $alignData = getAlignData($alignment);
warn "# Got alignment data: ".scalar (keys %$alignData);

#warn "# Reading scorecons data";
#my $scoreData = getScoreData($scorecons);
#warn "# Got scorecons data: ".scalar (keys %$scoreData);

warn "# Reading scorecons data\n";
my $scoreData = getScoreData($scorecons);
warn "# Got scorecons data ".scalar @$scoreData;


my $fhnames = new FileHandle($names)
		or die "Couldn't create file handle for $names";

while(my $line = $fhnames->getline)
{

    my @cols = split /\s+/, $line;

    my $header = $cols[0];

    my $align = $alignData->{$header};

    my $number = $align->{line};

    print "$header $number\n"; 


    foreach my $item(@$scoreData)
    {
	# split each line of array into fields

	my @fields = split(/\s+/, $item);

	my $scorecons = $fields[0];

	my $alignment = $fields[2];

	my $align = substr($alignment, $number, 1);

	print "$scorecons           #              $align\n";

    }
    #print "\n";

     
}

#################################################

sub getAlignData
{
	my ($fIn) = @ARG;

	my $fh = new FileHandle($fIn)
		or die "";

	my $count = 0;

	my $hData = {};

	while (my $line = $fh->getline)
	{
	    my @cols = split /\s+/, $line;

	    # search only for lines with identifier

	    my $field = $cols[0];

	    my $test = substr($field, 0, 1);

	    if("$test" eq ">")
	    {

		# $count++;
		 my $hEntry = {
		    'identifier' => $cols[0],
		    'line' => $count,
		};
		 $count++; 

		 #print "$cols[0] $count\n";

		my ($record) = sort ($hEntry->{identifier});
		$hData->{$record} = $hEntry;
		
	    }
	}

	return $hData;
}

####################################################

sub getScoreData
{
    my ($fIn) = @ARG;
    
    open(FILE, "$fIn") || die "Unable to open file\n";

    my @data = <FILE>;

    return (\@data);

}