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Python 3 fixes

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cclauss
2018-10-17 01:48:46 +02:00
parent 1697ee1c43
commit 6a8e87e17b
13 changed files with 140 additions and 116 deletions
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59
py/ibol.py
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@@ -1,10 +1,11 @@
from __future__ import print_function
from collections import defaultdict
def get_genomes(fname="byronbayseqs.fas.txt"):
"Return a list of genomes, and a list of their corresponding names."
import re
names, species, genomes = [], [], []
for name, g in re.findall('>(.*?)\r([^\r]*)\r*', file(fname).read()):
for name, g in re.findall('>(.*?)\r([^\r]*)\r*', open(fname).read()):
names.append(name)
species.append(name.split('|')[-1])
genomes.append(g)
@@ -14,7 +15,7 @@ def get_neighbors(fname="editdistances.txt"):
"Return dict: neighbors[i][j] = neighbors[j][i] = d means i,j are d apart."
## Read the data pre-computed from the Java program
neighbors = dict((i, {}) for i in range(n))
for line in file(fname):
for line in open(fname):
i,j,d = map(int, line.split())
neighbors[i][j] = neighbors[j][i] = d
return neighbors
@@ -75,15 +76,15 @@ def showh(d):
return ' '.join('%s:%s' % i for i in sorted(d.items()))
def greport(genomes):
print "Number of genomes: %d (%d distinct)" % (len(genomes), len(set(genomes)))
print("Number of genomes: %d (%d distinct)" % (len(genomes), len(set(genomes))))
G = dict((g, set()) for g in genomes)
for i in range(n):
G[genomes[i]].add(species[i])
print "Multi-named genomes:", (
len([s for s in G.values() if len(s) > 1]))
print("Multi-named genomes:", (
len([s for s in G.values() if len(s) > 1])))
lens = map(len, genomes)
print "Genome lengths: min=%d, max=%d" % (min(lens), max(lens))
print "Character counts: ", showh(c for g in genomes for c in g)
print("Genome lengths: min=%d, max=%d" % (min(lens), max(lens)))
print("Character counts: ", showh(c for g in genomes for c in g))
def nreport(neighbors):
NN, NumN = defaultdict(int), defaultdict(int) ## Nearest, Number of neighbors
@@ -92,9 +93,9 @@ def nreport(neighbors):
NN[nn] += 1
for d2 in neighbors[n].values():
NumN[d2] += 1
print
print "Nearest neighbor counts:", showh(NN)
print "Number of neighbors at each distance:", showh(NumN)
print()
print("Nearest neighbor counts:", showh(NN))
print("Number of neighbors at each distance:", showh(NumN))
def nspecies(c): return len(set(species[g] for g in c))
@@ -104,34 +105,34 @@ def showc(c):
def creport(drange, dcrange):
def table(what, fn):
print "\n" + what
print ' '*8, ' '.join([' '+pct(dc, glen) for dc in dcrange])
print("\n" + what)
print(' '*8, ' '.join([' '+pct(dc, glen) for dc in dcrange]))
for d in drange:
print '%s (%2d)' % (pct(d, glen), d),
print('%s (%2d)' % (pct(d, glen), d), end=' ')
for dc in dcrange:
print '%5s' % fn(cluster(neighbors, d, dc)),
print
print '\nNearest neighbor must be closer than this percentage (places). '
print 'Each column: all genomes in cluster within this percentage of each other.'
print('%5s' % fn(cluster(neighbors, d, dc)), end=' ')
print()
print('\nNearest neighbor must be closer than this percentage (places). ')
print('Each column: all genomes in cluster within this percentage of each other.')
table("Number of clusters", len)
cluster1 = cluster(neighbors, 8, 15) ## splits Cleora
print '\nNumber of clusters of different sizes:', showh(len(c) for c in cluster1)
print('\nNumber of clusters of different sizes:', showh(len(c) for c in cluster1))
M, T = defaultdict(int), defaultdict(int)
for c in cluster1:
M[margin(c)] += 1; T[margin(c)] += len(c)
for x in M: print '%d\t%d\t%d'% (x,M[x],T[x])
print '\nMargins', showh(M)
for x in M: print('%d\t%d\t%d'% (x,M[x],T[x]))
print('\nMargins', showh(M))
for c in cluster1:
if margin(c) <= 16:
print showc(c)
print '\nScatter plot of cluster diameter vs. margin.'
print(showc(c))
print('\nScatter plot of cluster diameter vs. margin.')
for c in cluster1:
if diameter(c) > 0:
pass
#print '%d\t%d' % (diameter(c), margin(c))
print '\nDifference from cluster(neighbors, 11, 14):'
print('\nDifference from cluster(neighbors, 11, 14):')
#table(lambda cl: pct(len(cluster1)-compare(cluster1, cl),max(len(cluster1),len(cl))))
print '\nNumber of clusters witth more than one species name:'
print('\nNumber of clusters witth more than one species name:')
#table(lambda cl: sum(nspecies(c) > 1 for c in cl))
def pct_near_another(clusters, P=1.25):
total = 0
@@ -143,21 +144,21 @@ def creport(drange, dcrange):
total += 1
return pct(total, n)
def f(P):
print '\nPercent of individuals within %.2f*diameter of another cluster.'%P
print('\nPercent of individuals within %.2f*diameter of another cluster.'%P)
table(lambda cl: pct_near_another(cl, P))
#map(f, [1.2, 1.33, 1.5])
def sreport(species):
SS = defaultdict(int)
print
print()
for s in set(species):
c = [g for g in range(n) if species[g] == s]
d = diameter(c)
if d > 14:
if d==glen: d = '>25'
print 'diameter %s for %s (%d elements)' % (d, s, len(c))
print('diameter %s for %s (%d elements)' % (d, s, len(c)))
SS[d] += 1
print 'Diameters of %d labeled clusters: %s' % (len(set(species)), showh(SS))
print('Diameters of %d labeled clusters: %s' % (len(set(species)), showh(SS)))
def compare(cl1, cl2):
"Compare two lists of clusters"
@@ -174,7 +175,7 @@ def unit_tests():
assert diameter(set()) == 0
assert diameter([17, 42]) == dist(17, 42)
assert pct(1, 2) == '50.0%'
print '\nAll tests pass.\n'
print('\nAll tests pass.\n')