open my $infh, '<', 'input.txt' or die $!;
my @lines = <$infh>;
close $infh;
# open output file here
my $i;
local $SIG{__WARN__} = sub {     
    my $msg = shift;
    $msg =~ s/\.?\s*$//;
    warn "$msg (input line $i)\n";
};
for($i=0;$i<@lines;$i++) {
    # do calculations and write to output file here
    # example warning:
    warn "found a z" if $lines[$i]=~/z/;
}

__END__
# Script Output:
found a z at - line 14 (input line 2)
found a z at - line 14 (input line 3)