I can't access hash values - arrays

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 ;)

Answer 2

First you do this:
$fileArray[$i] =~ s/>//;
Then later you try to match like this:
$fileArray[$i++] =~ m/>/
You step through the file array, removing the first "greater than" sign in the line on each line. And then you want to match the current line by that same character. That would be okay if you only want to push the line if it has a second "greater than", but you will never push anything into the array if you only expect 1, or there turns out to be only one.
Your comment "puts i back to the current line" shows what you were trying to do, but if you only use it once, why not use the expression $i + 1?
Also, because you're incrementing it post-fix and not using it for anything, your increment has no effect. If $i==0 before, then $fileArray[$i++] still accesses $fileArray[0], only $i==1 after the expression has been evaluated--and to no effect--until being later decremented.
If you want to peek ahead, then it is better to use the pre-fix increment:
if ($fileArray[++$i] =~ m/>/) ...