file_species_pairs = []

i = 1

while i < len(args)-2:

file_species_pairs.append([args[i], args[i+1]])

i += 2

cutoff = float(sys.argv[-2])

plot_dir = sys.argv[-1]

species2elms = {}

virus2elms = {}

# first grab virus ELMs

for file, species in file_species_pairs:

if file.find('flu') != -1:

virus2elms[species] = utils.get_seq2count_dict(file, cutoff)

else:

species2elms[species] = True

elms = {}

for species in virus2elms:

for elm in virus2elms[species]:

elms[elm] = True

for species in species2elms:

species2elms[species] = utils.get_seq2count_dict_for_seqs(file,

cutoff,

virus2elms)

for virus in virus2elms:

species2elms[virus] = virus2elms[virus]

for elm in elms:

if utils.check_ones(species2elms, elm):

if utils_distance.distance_elms(species2elms['Sus_scrofa'][elm],

species2elms['H_sapiens'][elm]) > float(-1) or utils_distance.distance_elms(species2elms['Sus_scrofa'][elm],

species2elms['Gallus_gallus'][elm]) > float(0):

utils_plot.elm_host_barplot(species2elms, elm,

os.path.join(plot_dir,