I have two files that look like this

file 1

1gtiA 7
1jpeA 4
1jpeA 6
1jpeA 7
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file 2

0.333           #              VF
0.267           #              TE
0.200           #              YD
0.267           #              QG
0.000           #              G-
0.000           #              C-
0.000           #              A-
0.000           #              D-
0.000           #              A-
0.000           #              --
0.000           #              C-
0.000           #              Y-
0.000           #              P-
0.200           #              PD
0.067           #              EL
1.000           #              TT
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I need to map the information from the first file onto the second by changing the relevant position on the second file to a small case letter. So the result should be

0.333           #              VF
0.267           #              TE
0.200           #              YD
0.267           #              Qg
0.000           #              G-
0.000           #              C-
0.000           #              a-
0.000           #              D-
0.000           #              A-
0.000           #              --
0.000           #              C-
0.000           #              Y-
0.000           #              P-
0.200           #              PD
0.067           #              El
1.000           #              Tt
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As you can see, one has to disregard the "-" when doing the mapping. The information for the two items of interest in file 2 are presented vertically. There could be many more such items but I'll only include two for the example.

score hash_character item1 item2 
0.333           #      V     F
etc
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Item 1 corresponds to the item called 1gtiA in file 1 and item 2 1jpeA. I've got some code but its not working at all so any help much appreciated. Apologies for the number of posts recently. I'm just trying to complete a project and its not going too smoothly! As you can see its very much a work in progress!

#! /usr/local/bin/perl -w

use FileHandle;
use strict;

my $scorecons_file = shift;
#my $alignment_file = shift;
my $csa_file = shift;

my $column_count;

my $res_count1 = 0;
my $res_count2 = 0;

warn "# Reading CSA data";
my $hCSAData = getCSAData($csa_file);
warn "# Got CSA data: ".scalar (keys %$hCSAData);

my $fh_score = new FileHandle($scorecons_file, "r") || die "Cannot ope
+n seq file: $scorecons_file ($!)";

while(my $line = $fh_score->getline)
{
    $column_count++; 
    
    chomp $line;
    
    my @field = split /\s+/, $line;
    
    #print "$field[0] $field[2]\n"; # test print
    
    my $score = $field[0];
    
    my $sequence = $field[2];

    #print "$sequence\n";
    
    my @sequence_field = split //, $sequence;

    if("$sequence_field[0]" ne "-")
    {
    $res_count1++;
    #print "$sequence_field[0] ";

#    print "$res_count1 $column_count\n";
    
    # if(my $hCSA = $hCSAData->{$column_count}->{$res_count1})
    #    {
        #print "yes";

     #   }

    }

    # if("$sequence_field[1]" ne "-")
    #{
    #$res_count2++;
    #print "$sequence_field[1] \n";
   # }
#
 
}

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

sub getCSAData
{
    my ($fIn) = @_;
    
    my $fh = new FileHandle($fIn)
    or die "";
    
    my $res;
    my $code;
    my $count = 1;
    my $key = 0;
    my $protein = "";
    my $code = 0;
    
    my $hData = {};
    while (my $line = $fh->getline)
    {
    my @cols = split /\s+/, $line;
    
    
    
    #$key = "$cols[0]" . "$cols[1]";

    #print "$cols[0] $cols[1]\n";

    

    $key = $cols[0];

    if("$key" ne "$protein")
    {
        $code++;

    }
    
    $protein = $key;

    #print "$code $cols[1]\n";



    
    my $hEntry = {
        'code' => $code,
        'res' => $cols[1],       
    };
    my ($code, $res) = sort ($hEntry->{code}, $hEntry->{res});
    $hData->{$code}->{$res} = $hEntry;
    #$hData->{$res}->{$code} = $hEntry;

    print "$code $res\n";
    }
    return $hData;
    
}
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