def run(species_registry, env, pct_env, pct_pool, rep):
population = Population(species_registry, env, population_size, microbe_size, pct_env, pct_pool)
prefix = str(rep + 1) + "_"
sufix = "_E" + str(pct_env) + "_P" + str(pct_pool) + ".txt"
print "Output 5 result files in the format of: %s[****]%s" % (prefix, sufix)
file1 = open(prefix + "fixation" + sufix, 'w')
file2 = open(prefix + "gamma_diversity" + sufix, 'w')
file3 = open(prefix + "beta_diversity" + sufix, 'w')
file4 = open(prefix + "sum" + sufix, 'w')
file6 = open(prefix + "alpha_diversity" + sufix, 'w')
while population.number_of_generation <= number_of_generation:
population.sum_species()
if population.number_of_generation % number_generation_for_observation == 0:
# NOTE: separate summarise and get stats
# population.calcalute_all_stats()
# then use accessor to get values.
print >> file1, population.ratio_of_fixation()
print >> file4, population
print >> file6, population.get_alpha_diversity()
print >> file2, population.get_gamma_diversity()
population.microbiome_sequence_alignment()
population.segregating_site()
print >> file3, str(population.get_beta_diversity()) + '\t' + str(population.number_of_segregating_site)
population.get_next_gen()
