def main(args):
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,
elm + '.virus_hosts.png'))
# mouse)
# print utils_distance.distance_species(monkey,
# mouse)
species2dict = {}
virus2dict = {}
virus2dict['swineFlu'] = utils.get_seq2count_dict('results/flu_elmdict_swine',
float(.4))
virus2dict['chickenFlu'] = utils.get_seq2count_dict('results/flu_elmdict_chicken',
float(.4))
virus2dict['humanFlu'] = utils.get_seq2count_dict('results/flu_elmdict_human',
float(.4))
for g in ('H_sapiens', 'Gallus_gallus', 'Sus_scrofa'):
species2dict[g] = utils.get_seq2count_dict_for_seqs('results/elmdict_'
+ g + '.txt',
float(0),
virus2dict)
for v in virus2dict:
species2dict[v] = virus2dict[v]
d = utils_distance.distance_matrix(species2dict)
elm_d = utils_distance.elm_distance_matrix(species2dict)
#for elm in elm_d:
# for species_pair in elm_d[elm]:
# print elm + '\t' + species_pair + '\t' + str(elm_d[elm][species_pair])
for s1, s2 in itertools.combinations(d.keys(), 2):
print s1 + '\t' + s2 + '\t' + str(d[s1][s2])
utils_plot.distance_heatmap(elm_d, 'test.png')
