Use of uninitialized value error

birdy has asked for the wisdom of the Perl Monks concerning the following question:

Hello,

i am facing the following error in the cgi.log file:

Use of uninitialized value $FastaSeqOfDataBase in string at anagnos43.pl line 549, <YEASTFASTA> chunk 6408.

The error has to do with this line of my code:

$HashOfDataBase {"$IdFasta"} = "$FastaSeqOfDataBase";
[download]

I am trying to understand why is that happening since i have initiliaze all the values (or at least that i think).

my %HashOfDataBase = ();
my $IdFasta = "";

if($Data=~/^(\S+)\s+\S+\s+.*/) 
{
  $IdFasta=$1;#storing name
}

@ArrayFasta=split '"',$Data;
$FastaSeqOfDataBase = $ArrayFasta[2];#storing letters of the alphabet 
+like a,b,d,e..

#use this if to initiliaze the "$HashOfDataBase {$IdFasta}"
if ($Flag == 0)
{
   $Flag = 1;
   $HashOfDataBase {"$IdFasta"} = "";
}
                            $HashOfDataBase {"$IdFasta"} = "$FastaSeqO
+fDataBase";#that is the line of the error
[download]

Really many thanks in advance

Comment on Use of uninitialized value error Select or Download Code

Replies are listed 'Best First'.
Re: Use of uninitialized value error by ikegami (Patriarch) on Jul 04, 2011 at 20:05 UTC
The warning simply means the variable's value is undef. If `$FastaSeqOfDataBase` is undefined, then `$ArrayFasta[2]` is undefined. If `$ArrayFasta[2]` is undefined, then the `split` returned fewer than three strings. If the `split` returned fewer than three strings, then `$Data` contains fewer than two double quotes.	[reply] [d/l] [select]
Re^2: Use of uninitialized value error by sumeetgrover (Monk) on Jul 04, 2011 at 20:14 UTC
Have you used strict at the beginning of the program? I would suggest that. If you already have used strict at the beginning of the program, then I do not see you having 'declared' the variable `$FastaSeqOfDataBase` with `my`. If this doesn't help, I'd suggest the classic 'Static Verification' technique to dry-run the code with sample data and determine what might cause the error. Hope this helps!	[reply] [d/l] [select]
Re^2: Use of uninitialized value error by birdy (Initiate) on Jul 04, 2011 at 20:20 UTC
	[reply]
Re^3: Use of uninitialized value error by ikegami (Patriarch) on Jul 04, 2011 at 20:36 UTC
And what are you proposing to do as a solution? You haven't said enough for us to identify the problem, much less give a solution. I'm guessing the problem is either a bad assumption about the format of the file or an incorrect parsing of the file.	[reply]
Re^4: Use of uninitialized value error by birdy (Initiate) on Jul 04, 2011 at 20:42 UTC
Re^5: Use of uninitialized value error by ikegami (Patriarch) on Jul 04, 2011 at 20:57 UTC
Re^5: Use of uninitialized value error by ikegami (Patriarch) on Jul 04, 2011 at 20:52 UTC
Re^3: Use of uninitialized value error by birdy (Initiate) on Jul 04, 2011 at 20:35 UTC
I forget to write it down but i do `my $FastaSeqOfDataBase = "";` in some lines before i call it.	[reply] [d/l]
Re^4: Use of uninitialized value error by sumeetgrover (Monk) on Jul 04, 2011 at 20:46 UTC
Re: Use of uninitialized value error by bimleshsharma (Beadle) on Jul 05, 2011 at 06:44 UTC
Man, you did little mistake at last line. Variable should not put into double/single quote during assignment to another variable. Here last line should be ... $HashOfDataBase {"$IdFasta"} = $FastaSeqOfDataBase; instead of .... $HashOfDataBase {"$IdFasta"} = "$FastaSeqOfDataBase";#that is the line of the error Hopefully this will resolve your issue.	[reply]
Re^2: Use of uninitialized value error by chromatic (Archbishop) on Jul 05, 2011 at 06:54 UTC
Variable should not put into double/single quote during assignment to another variable. Here last line should be ... That's generally good advice, but it's sometimes wrong (sometimes forcing string interpolation of a regex capture is the safest approach) and it won't make a difference in this case.	[reply]
Re^3: Use of uninitialized value error by lidden (Curate) on Jul 05, 2011 at 14:28 UTC
You do get a warning if you try to interpolate an undefined variable into a string, but not from assigning it to another variable. If that is good or bad in OPs case depends on if it is ok for the variable to be undefined or not.	[reply]