Replacing a column with another column
It would be a whole lot better this way:

import sys


def main(filename_in, filename_out):
    with open(filename_in) as fh_in:
        with open(filename_out, 'w') as fh_out:
            count = 1
            for line in fh_in:
                parts = line.strip().split()
                if count &lt; 10:
                    bra = "Bra100000" + str(count)
                else:
                    bra = "Bra10000" + str(count)
                count += 1
                test = "{:10s}" .format(bra)
                fh_out.write("\t".join(parts[0:3]))
                fh_out.write("\t")
                fh_out.write(parts[1])
                fh_out.write("\t")
                fh_out.write(test)
                fh_out.write("\t")
                fh_out.write("\t".join(parts[4:12]))
                fh_out.write("\n")

if __name__ == '__main__':
    main(sys.argv[1], sys.argv[2])


Improvements:


Use with open(...) as ...:. This way the file handles will be correctly closed when exiting the block
Drop the unused variable final
Also drop the pointless variable dict
Since both branches of the if-else increment count, you can move it outside
Instead of count = count + 1, it's simpler as count += 1
Instead of the repetitive write, simplify with join
Do not just dump the code in the global namespace: put it inside a function. This way the command line arguments will have meaningful names
Instead of stripping and splitting line in 2 steps, do it in one: line.strip().split()
It's not a good practice to overwrite loop variables and function parameters. line is a good name for a line of input, splitting that becomes something else and "line" is no longer an appropriate name, so I called it "parts" instead