Question

I have a program that creates an array of hashes while parsing a FASTA file. Here is my code

use strict;
use warnings;

my $docName = "A_gen.txt";
my $alleleCount = 0;
my $flag = 1;

my $tempSequence;
my @tempHeader;
my @arrayOfHashes = ();

my $fastaDoc = open(my $FH, '<', $docName);
my @fileArray = <$FH>;

for (my $i = 0; $i <= $#fileArray; $i++) {
    if ($fileArray[$i] =~ m/>/) { # creates a header for the hashes
    $flag = 0;
    $fileArray[$i] =~ s/>//;
    $alleleCount++;
    @tempHeader = split / /, $fileArray[$i];
    pop(@tempHeader); # removes the pointless bp
    for (my $j = 0; $j <= scalar(@tempHeader)-1; $j++) {
        print $tempHeader[$j];
        if ($j < scalar(@tempHeader)-1) {
            print " : "};
            if ($j == scalar(@tempHeader) - 1) {
                print "\n";
            };
        }
    }
    # push(@arrayOfHashes, "$i");

    if ($fileArray[$i++] =~ m/>/) { # goes to next line
        push(@arrayOfHashes, {
            id => $tempHeader[0],
            hla => $tempHeader[1], 
            bpCount => $tempHeader[2],
            sequence => $tempSequence
        });
        print $arrayOfHashes[0]{id};
        @tempHeader = ();
        $tempSequence = "";
    }
    $i--; # puts i back to the current line

    if ($flag == 1) {
        $tempSequence = $tempSequence.$fileArray[$i];
    }
}

print $arrayOfHashes[0]{id};
print "\n";

print $alleleCount."\n";
print $#fileArray +1;

My problem is when the line

print $arrayOfHashes[0]{id};

is called, I get an error that says

Use of uninitialized value in print at fasta_tie.pl line 47, line 6670.

You will see in the above code I commented out a line that says

push(@arrayOfHashes, “$i”);

because I wanted to make sure that the hash works. Also the data prints correctly in the
desired formatting. Which looks like this

HLA:HLA00127 : A*74:01 : 2918

Answer 1

try to add

print "Array length:" . scalar(@arrayOfHashes) . "\n"; 

before

print $arrayOfHashes[0]{id};

So you can see, if you got some content in your variable. You can also use the module Data::Dumper to see the content.

use Data::Dumper;
print Dumper(\@arrayOfHashes);

Note the ‘\’ before the array!

Output would be something like:

$VAR1 = [
{
‘sequence’ => ‘tempSequence’,
‘hla’ => ‘hla’,
‘bpCount’ => ‘bpCount’,
‘id’ => ‘id’
}
];

But if there’s a Module for Fasta, try to use this. You don’t have to reinvent the wheel each time 😉