Hmm, just something that might help simplify quite a bit your program.
if ($line =~ m/^A.TL5E00/)
{
$line =~ s/A.TL5E00/+TL\E5C/g;
push @NewSym,$line;
}
might probably be rewritten in a simpler fashion:
push @NewSym, $line if $line =~ s/^A.TL5E00/+TL\E5C/g;
I haven't tested it on real data (you did not supply any), but it seems to work properly, as shown in this session under the Perl debugger:
$ perl -de 42
Loading DB routines from perl5db.pl version 1.33
Editor support available.
Enter h or `h h' for help, or `man perldebug' for more help.
main::(-e:1): 42
DB<1> $line = "A.TL5E00xxxx";
DB<2> push @NewSym, $line if $line =~ s/^A.TL5E00/+TL\E5C/g;
DB<3> x @NewSym
0 '+TL5Cxxxx'
If the substitution does not find a match, it will report a false value and the push will not be executed.
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