open my $infh, '<', 'input.txt' or die $!;
# open output file here
while( my $line = <$infh> ) {
    # do calculations and write to output file here
    # example warning:
    warn "found a z" if $line=~/z/;
}
close $infh;

__END__
# Script Output:
found a z at - line 6, <$infh> line 3.
found a z at - line 6, <$infh> line 4.