Can't use string("72")as an array reference while "strict refs" in use
+ at test.pl line 21, <$fh> line 2
[download]

#!/usr/bin/perl

use strict;
use warnings;

my $qfn1 = "wah.txt";
my $qfn2 = "taj.txt";

my %positions;
{
   open(my $fh, '<', $qfn1)
      or die("Cannot open file \"$qfn1\": $!\n");

  while (<$fh>) {
   chomp; 
   my ($key, $pos) = split /\s+/;
   if (!$positions{$key}) {
     $positions{$key} = $pos;
   } else {
     my $ref = $positions{$key};
     push @$ref,$pos;
   }
}
}

my %sequences;
{
   open(my $fh, '<', $qfn2)
      or die("Cannot open file \"$qfn2\": $!\n");

   my $key;
   while (<$fh>) {
       if ( s/^>// ) {
           $key = ( split /\|/ )[1];
       }
       else {
           chomp;
           $sequences{$key} .= $_;
       }
   }
}

for my $key ( sort keys %positions ) {
   my $ref = $positions{$key};
   foreach my $value (@$ref) {
    if ( ! exists( $sequences{$key} )) {
        warn "KEY $key in File1 not found in File2\n";
        next;
    }
    if ( length( $sequences{$key} ) < $positions{$key} ) {
        warn "KEY $key: File2 string length too short for File1 positi
+on value\n";
        next;
    }
    my $index = rindex( $sequences{$key}, "ATG", $positions{$key} );
    if ( $index < 0 ) {
        warn sprintf( "KEY %s: No ATG in File2 string prior to positio
+n %d\n",
                      $key, $positions{$key} );
        next;
    }
    $index += 3 while ( ($index + 3) < $positions{$key} );
    print "$key $positions{$key} " . substr($sequences{$key}, $index, 
+3) . "\n";
}

}
[download]

There was a formatting error in u671296's code. The line $positions{$key} = $pos; should read $positions{$key} = [$pos];, in order to create an array reference. Then the push in the else branch will have an array reference to push into, rather than just a scalar number.

I wonder why the square brackets disappeared ? Perhaps because I possibly didn't put the code in a c tag ?