Warning: Use of uninitialized value $count in concatenation (.) or string at p3_in .pl line 34，<SRC> chunk 140

Question

I cannot figure out why the output complains that $count is not initialized, and what should I do? Here is my code:

#!/usr/bin/perl -w
# Author: Thomas Thiel
# Program name: primer3_in.pl
# Description: creates a PRIMER3 input file based on SSR search results

open (IN,"<$ARGV[0]") || die ("\nError: Couldn't open misa.pl results file (*.misa) !\n\n");

my $filename = $ARGV[0];
$filename =~ s/\.misa//;
open (SRC,"<$filename") || die ("\nError: Couldn't open source file containing original FASTA sequences !\n\n");
open (OUT,">$filename.p3in");

undef $/;
$in = <IN>;
study $in;

$/= ">";

my $count;
while (<SRC>)
  {
  next unless (my ($id,$seq) = /(.*?)\n(.*)/s);
  $seq =~ s/[\d\s>]//g;#remove digits, spaces, line breaks,...
  while ($in =~ /$id\t(\d+)\t\S+\t\S+\t(\d+)\t(\d+)/g)
    {
    my ($ssr_nr,$size,$start) = ($1,$2,$3);
    $count++;
    print OUT "SEQUENCE_ID=$id"."_$ssr_nr\nSEQUENCE_TEMPLATE=$seq\n";
    print OUT "PRIMER_PRODUCT_SIZE_RANGE=100-280\n";
    print OUT "TARGET=",$start-3,",",$size+6,"\n";
    print OUT "PRIMER_MAX_END_STABILITY=250\n=\n"
    };
  };
print "\n$count records created.\n";

How can I initialize $count?

Answer 1

Your code does not initialize the $count variable; it is undefined.

To initialize $count to a numeric value (like 0), change:

my $count;

to:

my $count = 0;

Answer 2

There are multiple paths through the code that do not result in $count++ being called. One or more of these may never be true:

• while (<SRC>)
• unless (my ($id,$seq) = /(.*?)\n(.*)/s)
• while ($in =~ /$id\t(\d+)\t\S+\t\S+\t(\d+)\t(\d+)/g)

Before the first use, unconditionally initialise $count. The obvious place would be in the my $count statement.

---

perldoc perlsyn explains:

The only things you need to declare in Perl are report formats and subroutines (and sometimes not even subroutines). A scalar variable holds the undefined value ("undef") until it has been assigned a defined value, which is anything other than "undef". When used as a number, "undef" is treated as 0; when used as a string, it is treated as the empty string, ""; and when used as a reference that isn't being assigned to, it is treated as an error. If you enable warnings, you'll be notified of an uninitialized value whenever you treat "undef" as a string or a number. Well, usually.