def show_distance(num=0): genomes = PPR.load_genomes() ppr = genomes[0].pprs[num] closest = minima(ppr, genomes) left = range(len(closest[0])) plt.bar(left, closest[1], width=1.0) plt.xticks([l+0.5 for l in left], closest[0], rotation=90) plt.show()
def ppr_distance():
genomes = PPR.load_genomes()
genomes = [g for g in genomes if len(g) > 50]
data = []
for i,g in enumerate(genomes, 1):
print "Genome {}/{}: {} ({})".format(i, len(genomes),
g.name,short_name(g.name))
data.append([short_name(g.name),] + get_average(g,genomes))
utils.write_data(['',] + [reduce_name(g.name) for g in genomes],
data,
'output/Average_PPR_distance.dat')
def get_groups(threshold=0.3):
"""Attempt to group similar PPRs"""
stdout.write("\rLoading...")
stdout.flush()
genomes = PPR.load_genomes()
groups = []
total = sum([sum([1 for p in g.pprs]) for g in genomes])
done = 0
fmt = "\rGrouping ({{:{}d}}/{{}}) | {{:2.1f}}%, {{:.1f}} per group ".format(
len(str(total)))
for genome in genomes:
for ppr in genome.pprs:
#find the best group
possible = []
#groups are possible if the distance to each member is lte threshold
for group in groups:
if max([ppr.distance(p2, 'MSE')[0] for p2 in group]) <= threshold:
possible.append(group)
#if there are no possible groups, start a new one
if not possible:
groups.append([ppr,])
#otherwise, append to the group with the lowest average distance
else:
avg = [sum([ppr.distance(p2, 'MSE')[0] for p2 in group])/float(len(group))
for group in possible]
possible[avg.index(min(avg))].append(ppr)
#Write progress info
done += 1
stdout.write(fmt.format(done,total, 100.0 * done / float(total),
done / float(len(groups))))
stdout.flush()
stdout.write("\r" + (" "*60) + "\r")
stdout.flush()
return groups
