Comparing two multi-fasta files of the same set of proteins with parser - to find and count mutations after treatment
from Bio import SeqIO
for normal, treated in zip(SeqIO.parse("/data/statistic/normal_samples", "fasta"),
                           SeqIO.parse("/data/statistic/with_treatment", "fasta")):
    ... do stuff...


That's generally how you zip iterators together in python.