Refactors make_nr loop with SeqIO.write call

[ShriramK]

TODO: Refactor as generator with single SeqIO.write(...) call

[peterjc]

I'm not sure if you understand how generator functions work, so it is hard for me to explain this without writing all the code, but if you want to work on this a bit more that's fine.

The goal is something like this:

    if duplicates:
        count = SeqIO.write(pick_records(input_fasta), output_fasta, "fasta")
        print("%i unique entries; removed %i duplicates leaving %i representative records"
              % (unique, len(duplicates), len(representatives)))
        assert count == unique + len(representatives)

where you have defined a generator function:

def pick_records(input_fasta_file):
    global representatives
    global duplicates
    for record in SeqIO.parse(input_fasta, "fasta"):
        # TODO, sometimes yield a record

[ShriramK]

Thanks Peter for your comment. It helped.
I had the right idea for the generator but lacked clarity on how it fits into the refactoring, or focus of the refactoring here, and SeqIO methods and their input arguments.
I'll come up with a revised fix.

[peterjc]

As an aside, one of the reasons for making this change goes away in Biopython 1.72, see biopython/biopython#1223