Victory! I made the code work properly. Nevertheless, I do probably have efficiency problems. I would appreciate if you can comment on points where I can improve my code (in terms of both performance and appropriate style). Thanks guys, I could not do it without your help! 

Here is the final ugly code.

#!/usr/bin/perl -w
use strict;
use Data::Dumper;

my %info = (); 
my ($gi, $humangi, $accession);

my $data = '/DATA/proteinfile.txt'; 
open INFILE, '<', $data or die "Failed at opening $data!\n";

# Construct the hash with GIs as keys and sequences as values
while ( <INFILE> ) {
my $line = $_;
chomp($line);
    last if m!END!;
    
    if($line=~m/HUMAN/){
        
        ($humangi) = ($line=~m/^\S+\|(\d+)/);
        
       ($accession) = ($line=~m/^\S+\|\d+\|\w+\|(\S{6}?)/);
       
          }
    
    if($line=~m/^\S+\|(\d+)/)
       {
        if(defined($1))
         { 
          $gi=$1;
         }    
       }
    else
       {
        $info{$gi} = $line;
        }
}
    #print Dumper (\%info);

    print "$humangi\n";
    print "$accession\n";

close(INFILE);

my $data2 = '/DATA/variantlist.txt'; 
open INFILE2, '<', $data2 or die "Failed at opening $data2!\n";

my $data3 = '/DATA/VariantOutput.txt'; 
open OUTFILE, '>', $data3 or die "Failed at opening $data3!\n";

print OUTFILE "This is [GI: $humangi] and [Accession: $accession]\nVAR
+IANT\t\tPOTENTIAL\t\tPD\n";

while ( <INFILE2>){
# Grab a variant from the file (in this example: P82L)
my $line2 = $_;
chomp($line2);
my $Variant = $line2;

# Split the variant into three parts
my ($source, $position, $sink) = split(/(\d+)(\w)/, $Variant);

#print "$source\t$position\t$sink\n";
# Check whether HS has the source (i.e., P) at the given position (i.e
+., 82)
my $temp = $info{$humangi};

    #print "Temp contains $temp" . "\n";
    
my @char = split //, $temp;    

    #print "Now \@char contains: @char";

    #print "Inside the temp: $char[0] and $char[1]\n";

my $target = $char[$position-1];
    
    #print "This is the target: $target" . "\n";

if ( $target eq $source) {
    
     print "Yep!\n";
    }
    
my @VariantList = ();
my @PDList = ();
    
# Scan the rest of the sequences to check what amino acid they have at
+ the given position
for my $gi ( keys %info ) {
        my $value = $info{$gi};
        
        my @char2 = split //, $value;
        
        my $potential = $char2[$position-1];
        
        push (@VariantList, $potential); 
        
        
        if ($potential eq $sink){ # Note the cases where we observe th
+e sink (i.e., L) at this position
            
            my $pd = "$potential" . "{" . "$gi" . "}";
            
            push (@PDList, $pd)             
            #print "A pathogenic deviation has been found at site $pos
+ition - from $source to $sink !\n" . " And the corresponding gi for t
+his deviation is: $gi\n";
            
            }
            }

print OUTFILE "$Variant\t\t@VariantList\t\t@PDList\n";
}
close(INFILE2);

[download]

In reply to Re^4: Use of uninitialized value in string eq by sophix
in thread Use of uninitialized value in string eq by sophix

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