Thank you, GrandFather. Particularly I appreciate your advise regarding the initialization of variables. Plus, I have not heard the hash slice before, that was very helpful too!

chomp @INFILE2 loop. You are right, I should have chomped the lines. Because I get that file by using another script where I add \n at the end. Thanks for pointing it out.

I revised the code in line with your suggestions, and get the following errors:

Possible unintended interpolation of @VariantList in string at PD.pl line 91.

I have no idea why I am getting this error. I thought I can safely use an array to print it out in this way.

Type of arg 1 to push must be array (not hash slice) at PD.pl line 33, near "$line;"

This is weird?!

Global symbol "@VariantList" requires explicit package name at PD.pl l
+ine 91.
Execution of PD.pl aborted due to compilation errors.

[download]

And here is the code.

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

my %info = (); 
my $humangi;

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+)/)
    
        }
    
    if($line=~m/^\S+\|(\d+)/)
       {
        if(defined($1))
         { 
          my $gi=$1;
         }    
       }
    else
       {
        if (defined(my $gi))
          {
          push (@info{$gi}, $line);
          }
        else
          {
          die "Badly formatted file. Failed at reading the GI!\n";
          }
       }
}
    #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 $line2 = $_;
chomp($line2);
my $Variant = $line2;

# 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);

[download]

In reply to Re^2: Use of uninitialized value in string eq by sophix
in thread Use of uninitialized value in string eq by sophix

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