Hey guys, Last time when I had an error of uninitialized value, I was able to fix it by simply initializing the variable. In this case, I could not figure our what is particularly wrong with my use of string comparison. I would appreciate any comment. ps. I get the errors where I use 'eq' operator. 
#!/usr/bin/perl -w
use strict;
use Data::Dumper;

my ( $data, $line, $gi, $humangi, %info); 

$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> ) {
$line = $_;
chomp($line);
    last if m!END!;
    
    if($line=~m/HUMAN/){
        
        ($humangi) = ($line=~m/^\S+\|(\d+)/)
    
        }
    
    if($line=~m/^\S+\|(\d+)/)
       {
        if(defined($1))
         { 
          $gi=$1;
         }    
       }
    else
       {
        $info{$gi}=$line;
       }
}
    #print Dumper (\%info);

    print "$humangi\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";

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

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

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

    if ( $temp[$position] eq $source) {
    
     print "Yep, $source has been confirmed!\n";
    }
    
    else {
        
    print "There is something wrong!\n";
    }

# 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 @VariantList = ();
        
        push ( @VariantList, $value[$position]); 
        
        if ($value[$position] eq $sink){ # Note the cases where we obs
+erve the sink (i.e., L) at this position
            
            print OUTFILE "A pathogenic deviation has been found at si
+te $position - from $source to $sink !\n" . " And the corresponding g
+i for this deviation is: $gi\n";
            
            }
}

#print OUTFILE "Variant list contains: @VariantList\n";
}
close(INFILE2);

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In reply to Use of uninitialized value in string eq by sophix

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