Hi there. Thanks everyone for all your help so far today. I have noe more question if thats ok. At the moment, my perl scripts output is this:

>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
[download]

But I want it to be like this.

0.000           #              -MM
0.331           #              WKT
0.370           #              DNE
[download]

But I'm not sure how to organise the print statements. code so far is as follows.

#!/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);

}
[download]

Any advice much appreciated.

---

---

Posts are HTML formatted. Put <p> </p> tags around your paragraphs. Put <code> </code> tags around your code and data!

Titles consisting of a single word are discouraged, and in most cases are disallowed outright.

Read Where should I post X? if you're not absolutely sure you're posting in the right place.

Please read these before you post! —

• How do I compose an effective node title?
• How do I post a question effectively?
• Markup in the Monastery

Posts may use any of the Perl Monks Approved HTML tags:

a, abbr, b, big, blockquote, br, caption, center, col, colgroup, dd, del, details, div, dl, dt, em, font, h1, h2, h3, h4, h5, h6, hr, i, ins, li, ol, p, pre, readmore, small, span, spoiler, strike, strong, sub, summary, sup, table, tbody, td, tfoot, th, thead, tr, tt, u, ul, wbr

You may need to use entities for some characters, as follows. (Exception: Within code tags, you can put the characters literally.)

	For:		Use:
	&		&
	<		&lt;
	>		&gt;
	[		&#91;
	]		&#93;

Link using PerlMonks shortcuts! What shortcuts can I use for linking?

See Writeup Formatting Tips and other pages linked from there for more info.