def main(args):
suffix = sys.argv[1]
elms = sys.argv[2:]
file_species_pairs = []
for g in global_settings.GENOMES:
file_species_pairs.append(('results/elmdict_'
+ g + suffix, g))
plot_dir = 'plots/for_aydin/'
species2elms = {}
for file, species in file_species_pairs:
species2elms[species] = utils.get_seq2count_dict(file, float(0))
for elm in elms:
utils_plot.elm_host_barplot(species2elms, elm,
os.path.join(plot_dir,
elm + '.hosts'
+ suffix + '.png'))
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 = {}
for file, species in file_species_pairs:
species2elms[species] = utils.get_seq2count_dict(file, cutoff)
elms = {}
for species in species2elms:
for elm in species2elms[species]:
elms[elm] = True
for elm in elms:
if utils.check_ones(species2elms, elm) and (elm in species2elms['swine'] or elm in species2elms['human'] or elm in species2elms['chicken']) and elm in species2elms['H_sapiens'] :
utils_plot.elm_host_barplot(species2elms, elm,
os.path.join(plot_dir,
elm + '.hosts.png'))
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'))
dis[g] = utils_distance.distance_elms(species2dict[g][elm],
virus2dict[v][elm])
is_less = True
is_gtr = True
for g in genomes:
if g != v2h[v]:
if dis[v2h[v]] > dis[g]:#it is not less than at least one
is_less = False
if is_less:
right_count[v] += 1
new_d = {}
for h in species2dict:
new_d[h] = species2dict[h]
for v in virus2dict:
new_d[v] = virus2dict[v]
utils_plot.elm_host_barplot(new_d,
elm, elm + '.png')
for v in right_count:
print v, right_count[v]
#for elm in use_elms:
# utils_plot.elm_host_barplot(virus2dict, elm, elm + '.png')
# v = 'human'
# for elm in use_elms:
# if elm in host_elms:
# dis = {}
# for g in genomes:
# dis[g] = utils_distance.distance_elms(species2dict[g][elm],
import utils, utils_plot, utils_distance
d = {'web':utils.get_seq2count_dict('results/human.website.elm.elmdict',
float(.01)),
'regex':utils.get_seq2count_dict('results/hprd_new.regex.elms.elmdict',
float(.01))}
elms = utils_distance.get_elements(d['web'], d['regex'])
for elm in elms:
utils_plot.elm_host_barplot(d, elm, 'plots/hprd/' + elm + '.png')