return True
results_dir = sys.argv[1]
suffix = sys.argv[2]
elmfile = sys.argv[3]
elms = {}
with open(elmfile) as f:
for line in f:
elm, exp = line.strip().split('\t')
elms[elm] = True
for elm in elms:
counts = utils.count_host_elmSeqs(global_settings.TEST_GENOMES,
False, {},
results_dir, {elm:True}, suffix)
all_elmSeqs = {}
for host in counts:
for elmSeq in counts[host]:
all_elmSeqs[elmSeq] = True
host_vecs = utils.mk_count_vecs(counts, all_elmSeqs)
host_dists = utils.mk_count_dists(host_vecs)
js = defaultdict(dict)
for host1, host2 in itertools.combinations(host_dists, 2):
dis = utils.jensen_shannon_dists(host_dists[host1],
host_dists[host2])
js[host1][host2] = dis
js[host2][host1] = dis
if check_phylogeny(js):
print elm
# (protein, st, stp,
# elm, seq, junk) = line.strip().split('\t')
# elmSeq = elm + ':' + seq
# all_elmSeqs[elmSeq] = True
# flu_counts[flu][elmSeq] += 1
for host in hosts:
host_counts[host] = defaultdict(utils.init_zero)
with open('results/roundup_all/elmdict_' + host + '.init') as f:
for line in f:
(elm, seq, count, fq) = line.strip().split('\t')
elmSeq = elm + ':' + seq
all_elmSeqs[elmSeq] = True
host_counts[host][elmSeq] += int(count)
flu_vecs = utils.mk_count_vecs(flu_counts, all_elmSeqs)
flu_dists = utils.mk_count_dists(flu_vecs)
host_vecs = utils.mk_count_vecs(host_counts, all_elmSeqs)
host_dists = utils.mk_count_dists(host_vecs)
def print_it(name, vec):
print name, float(count_0s(vec))/float(len(vec))
print_it('chicken_flu', flu_vecs['chicken'])
print_it('human flu', flu_vecs['human'])
print_it('H sapiens', host_vecs['H_sapiens'])
print_it('Gallus gallus', host_vecs['Gallus_gallus'])
flu_dists['chicken'].sort()
print flu_dists['chicken'][-3], flu_dists['chicken'][-2], flu_dists['chicken'][-1]
flu_counts['chicken'] = utils.count_flu(new_chicken_counts, all_elmSeqs)
for host in hosts:
host_counts[host] = defaultdict(utils.init_zero)
with open('working/runs/Jun24/elmdict_' + host + '.init') as f:
for line in f:
(elm, seq, count, fq) = line.strip().split('\t')
elmSeq = elm + ':' + seq
if elmSeq in host_flu_elmSeq_mapping:
for a_flu_elmSeq in host_flu_elmSeq_mapping[elmSeq]:
host_counts[host][a_flu_elmSeq] += int(count)
# else:
# host_counts[host][elmSeq] += int(count)
# all_elmSeqs[elmSeq] = True
flu_vecs = utils.mk_count_vecs(flu_counts, mapped)
flu_dists = utils.mk_count_dists(flu_vecs)
host_vecs = utils.mk_count_vecs(host_counts, mapped)
host_dists = utils.mk_count_dists(host_vecs)
js_distances = defaultdict(dict)
for host in hosts:
for flu in flus:
js_dis = utils.jensen_shannon_dists(host_dists[host],
flu_dists[flu])
js_distances[host][flu] = js_dis
print host, flu, js_dis
def print_it(name, vec):
print name, float(count_0s(vec))/float(len(vec))
seen_elms = defaultdict(dict)
for host in ls_of_hosts:
host_elmCounts[host] = defaultdict(utils.init_zero)
with open(results_dir + 'elmdict_' + host + '.redo') as f:
for line in f:
(elm, seq, count, fq) = line.strip().split('\t')
if elm in use_elms:
host_elmCounts[host][elm] += int(count)
seen_elms[elm][host] = True
#use_elms = {}
#for elm in seen_elms:
# if len(seen_elms[elm]) == len(ls_of_hosts):
# use_elms[elm] = True
# print len(use_elms)
return (host_elmCounts, use_elms)
use_elms = {}
with open(use_elms_file) as f:
for line in f:
(elm, stuff) = line.strip().split('\t')
use_elms[elm] = True
hosts = global_settings.GENOMES
if use_freqs == 'T':
host_elmCounts, elms = get_host_freqs(hosts, use_elms)
else:
host_elmCounts, elms = get_host_counts(hosts, use_elms)
host_vecs = utils.mk_count_vecs(host_elmCounts, elms)
host_dists = utils.mk_count_dists(host_vecs)
utils_plot.phylogeny_js(out_file, host_dists)
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])
# sys.exit(0)
for seq, hhuman, hchicken, hf, cf in zip(use_seqs, host_dists['Gallus_gallus'],
host_dists['H_sapiens'],
flu_dists['human'],
flu_dists['chicken']):
print seq + '\t' + str(hhuman) + '\t' + str(hchicken) + '\t' + str(hf) + '\t' + '\t' + str(cf)
for host in host_dists:
for flu in flu_dists:
""" 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
