def getDistance(virus_d, host_d):
seqs = utils_graph.unionLists([virus_d,
host_d])
#virus_d_rn = renorm(seqs, virus_d)
#host_d_rn = renorm(seqs, host_d)
host_v = []
virus_v = []
for seq in seqs:
for v,d in ( (host_v, host_d),
(virus_v, virus_d) ):
if seq in d:
v.append(d[seq])
else:
v.append(float(0))
# host_norm = norm(host_v)
# virus_norm = norm(virus_v)
# if host_norm:
# host_u = host_v/host_norm
# else:
# host_u = host_v
# if virus_norm:
# virus_u = virus_v/virus_norm
# else:
# virus_u = virus_v
dis = distance.cosine(host_v, virus_v)
#print dis, virus_v, host_v
return dis
def getDistance(virus_d, host_d):
seqs = utils_graph.unionLists([virus_d,
host_d])
host_v = []
virus_v = []
for seq in seqs:
for v,d in ( (host_v, host_d),
(virus_v, virus_d) ):
if seq in d:
v.append(d[seq])
else:
v.append(0)
return distance.cosine(host_v, virus_v)
# flu + '.H5N1.simpleELMs')
utils.count_flu_sampled(flu, flu_elm_file, flu_counts,
seen_seqs, {}, False)
use_seqs = {}
for elmSeq in seen_seqs[flu]:
elm, seq = elmSeq.split(':')
if elm == use_elm:
if flu_counts[flu][elmSeq] > 0:
use_seqs[elmSeq] = True
seen_seqs_ls.append(use_seqs)
# remove seqs seen less than 10x
#for flu in flu_counts:
# for elmSeq in
use_seqs_pre = utils_graph.unionLists(seen_seqs_ls)
counts = utils.count_host_elmSeqs(('Gallus_gallus','H_sapiens'),
False, {},
'working/Jun29/', {use_elm:True},
'.init')
use_seqs = utils_graph.unionLists([use_seqs_pre, counts['Gallus_gallus'],
counts['H_sapiens']])
host_vecs = utils.mk_count_vecs(counts, use_seqs)
host_dists = utils.mk_count_dists(host_vecs)
flu_vecs = utils.mk_count_vecs(flu_counts, use_seqs)
flu_dists = utils.mk_count_dists(flu_vecs)
# for flu in flu_dists:
# print sum(flu_dists[flu])
for host in species:
host2elmFreqs[host] = utils.get_seq2count_dict(os.path.join(local_settings.RESULTSDIR,
'elmdict_' + host + suffix),
float(0))
tmp_input = 'plots/for_aydin_2/cos_host_host' + suffix + '.tab'
with open(tmp_input, 'w') as f:
f.write('Host1\tHost2\tDistance\n')
for i in xrange(len(species)):
for j in xrange(len(species)):
if i != j:
host1 = species[i]
host2 = species[j]
sum = float(0)
elms_compared = 0
for elm in utils_graph.unionLists([host2elmFreqs[host1],
host2elmFreqs[host2]]):
for h in (host1, host2):
if elm not in host2elmFreqs[h]:
host2elmFreqs[h][elm] = {}
if len(host2elmFreqs[host1][elm].keys()) != 0 and len(host2elmFreqs[host2][elm].keys()) != 0:
sum += utils.getDistance(host2elmFreqs[host1][elm],
host2elmFreqs[host2][elm])
elms_compared += 1
f.write('%s\t%s\t%.10f\n'
% (short_names[host1],
short_names[host2],
float(sum)/float(elms_compared)))
out_file = 'plots/for_aydin_2/cos_dis_sum_host' + suffix + '.png'
tmp_r = 'tmp_r' + str(random.randint(0,100))
with open(tmp_r, 'w') as f:
common_mammal_controled)
utils_graph.dumpNodes('mammal_controled' + str(cut), use_mammal_controled)
utils_graph.dumpNodes('bird_controled' + str(cut), use_bird_controled)
utils_graph.dumpNodes('common_controled' + str(cut), common_all_elms_controled)
for k in use_mammal_controled.keys():
if 'FAIL' in k:
del use_mammal_controled[k]
for k in use_bird_controled.keys():
if 'FAIL' in k:
del use_bird_controled[k]
for k in common_all_elms_controled.keys():
if 'FAIL' in k:
del common_all_elms_controled[k]
test_elms = utils_graph.unionLists([use_mammal, use_bird])
virus_elms_same = 0
virus_elm_count = 0
non_virus_elms_same = 0
with open('mammal_bird.different.' + str(cut) + '.test', 'w') as f:
for elm in test_elms:
if elm not in ignore_elms:
count,same = test_it(elm, elm2freq, f)
virus_elms_same += same
virus_elm_count += count
non_virus_elms = 0
non_virus_elms_all = 0
control_elms = {}
with open('mammal_bird.different.' + str(cut) + '.notest', 'w') as f:
for elm in elm2freq:
""" What is the Jensen-shannon distance
between 2 flu groups?
"""
import utils, sys, utils_graph
flu_group_1_file = sys.argv[1]
flu_group_2_file = sys.argv[2]
flu_counts = {}
seen_elmSeqs = {}
seen_seqs_ls = []
for name, file in (('g1', flu_group_1_file),
('g2', flu_group_2_file)):
utils.count_flu_sampled(name, file,
flu_counts,
seen_elmSeqs, {}, False)
seen_seqs_ls.append(seen_elmSeqs[name])
use_elmSeqs = utils_graph.unionLists(seen_seqs_ls)
flu_vecs = utils.mk_count_vecs(flu_counts, use_elmSeqs)
flu_dists = utils.mk_count_dists(flu_vecs)
js_dis = utils.jensen_shannon_dists(flu_dists['g1'],
flu_dists['g2'])
print js_dis
for hp in h2_noRestrictions.keys():
for hp_neigh in network[hp].keys():
for cd in matching_cds.keys():
if human_cd2protein[cd].has_key(hp_neigh):
h1[hp_neigh] = True
h2[hp] = True
h1_to_h2[hp_neigh + ":" + hp] = True
for vp in virus_elm2protein[elm].keys():
for pred in h1.keys():
if version2geneid.has_key(pred):
f.write(vp + "\t" + elm + "\t" + version2geneid[pred] + "\th1\n")
for pred in h2.keys():
if version2geneid.has_key(pred):
f.write(vp + "\t" + elm + "\t" + version2geneid[pred] + "\th2\n")
for pred in utils_graph.unionLists([h1, h2]).keys():
if version2geneid.has_key(pred):
f.write(vp + "\t" + elm + "\t" + version2geneid[pred] + "\th1h2\n")
for pred in h2_noRestrictions.keys():
if version2geneid.has_key(pred):
f.write(vp + "\t" + elm + "\t" + version2geneid[pred] + "\th2All\n")
for pair in h1_to_h2.keys():
if not vp_to_h1_to_h2.has_key(vp):
vp_to_h1_to_h2[vp] = {}
vp_to_h1_to_h2[vp][pair] = True
with open(outf2, "w") as f:
for vp in vp_to_h1_to_h2.keys():
for pair in vp_to_h1_to_h2[vp]:
[h1_gene, h2_gene] = pair.split(":")
if version2geneid.has_key(h1_gene) and version2geneid.has_key(h2_gene):
mapping = {}
hosts = global_settings.TEST_GENOMES
#all_elmSeqs = {}
flus = ('human',)
flu_counts = {}
seen_seqs = {}
seen_seqs_ls = []
for flu in flus:
flu_elm_file = os.path.join('results/',
flu + '.H5N1.elms')
utils.count_flu_sampled(flu, flu_elm_file, flu_counts,
seen_seqs, mapping, do_clustering)
seen_seqs_ls.append(seen_seqs[flu])
if len(seen_seqs_ls) > 1:
all_elmSeqs = utils_graph.unionLists(seen_seqs_ls)
else:
all_elmSeqs = seen_seqs_ls[0]
host_counts = utils.count_host_elmSeqs(hosts, do_clustering, mapping,
elm_count_dir)
host_found_seqs = utils_graph.unionLists([host_counts['H_sapiens'],
host_counts['Gallus_gallus']])
use_seqs = utils_graph.unionLists([all_elmSeqs, host_found_seqs])
flu_vecs = utils.mk_count_vecs(flu_counts, use_seqs)
host_vecs = utils.mk_count_vecs(host_counts, use_seqs)
host_dists = utils.mk_count_dists(host_vecs)
flu_dists = utils.mk_count_dists(flu_vecs)