ibol.py

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*', open(fname).read()):
        names.append(name)
        species.append(name.split('|')[-1])
        genomes.append(g)
    return names, species, genomes

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 open(fname):
        i,j,d = map(int, line.split())
        neighbors[i][j] = neighbors[j][i] = d
    return neighbors
        
def cluster(neighbors, d, dc):
    """Return a list of clusters, each cluster element is within d of another
    and within dc of every other cluster element."""
    unclustered = set(neighbors) ## set of g's not yet clustered
    return [closure(g, set(), unclustered, d, dc)
            for g in neighbors if g in unclustered]

def closure(g, s, unclustered, d, dc):
    "Accumulate in set s the transitive closure of 'near', starting at g"
    if g not in s and g in unclustered and near(g, s, d, dc):
        s.add(g); unclustered.remove(g)
        for g2 in neighbors[g]:
            closure(g2, s, unclustered, d, dc)
    return s

def dist(i, j):
    "Distance between two genomes."
    if i == j: return 0
    return neighbors[min(i, j)].get(max(i, j), max_distance)

def near(g, cluster, d, dc):
    "Is g within d of some member of c, and within dc of every member of c?"
    distances = [dist(g, g2) for g2 in cluster] or [0]
    return min(distances) <= d and max(distances) <= dc

def diameter(cluster):
    "The largest distance between two elements of the cluster"
    return max([dist(i, j) for i in cluster for j in cluster] or [0])

def margin(cluster):
    "The distance from a cluster to the nearest g2 outside this cluster."
    return min([d for g in cluster for g2,d in neighbors[g].items()
                if g2 not in cluster] or [max_distance])

################################################################ Analysis

def pct(num, den):
    "Return a string representing the percentage. "
    if '__len__' in dir(den): den = len(den)
    if num==den: return ' 100%'
    return '%.1f%%' % (num*100.0/den)

def histo(items):
    "Make a histogram from a sequence of items or (item, count) tuples."
    D = defaultdict(int)
    for item in items:
        if isinstance(item, tuple): D[item[0]] += item[1]
        else: D[item] += 1
    return D

def showh(d):
    "Show a histogram"
    if not isinstance(d, dict): d = histo(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))))
    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])))
    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))
    
def nreport(neighbors):
    NN, NumN = defaultdict(int), defaultdict(int) ## Nearest, Number of neighbors
    for n in neighbors:
        nn = min(neighbors[n].values() or ['>25'])
        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))

def nspecies(c): return len(set(species[g] for g in c))

def showc(c):
    return "N=%d, D=%d, M=%d: %s %s" % (
        len(c), diameter(c), margin(c), list(c), showh(species[g] for g in c))

def creport(drange, dcrange):
    def table(what, fn):
        print("\n" + what)
        print(' '*8, ' '.join([' '+pct(dc, glen) for dc in dcrange]))
        for d in drange:
            print('%s (%2d)' % (pct(d, glen), d), end=' ')
            for dc in dcrange:
                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))
    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 c in cluster1:
        if margin(c) <= 16:
            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):')
    #table(lambda cl: pct(len(cluster1)-compare(cluster1, cl),max(len(cluster1),len(cl))))
    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
        for c in clusters:
            d = diameter(c)
            for g in c:
                for g2 in neighbors[g]:
                    if g2 not in c and dist(g, g2) < P*d:
                        total += 1
        return pct(total, n)
    def f(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()
    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)))
        SS[d] += 1
    print('Diameters of %d labeled clusters: %s' % (len(set(species)), showh(SS)))
    
def compare(cl1, cl2):
    "Compare two lists of clusters"
    return sum(c1==c2 or 0.5*(abs(len(c1)-len(c2))==1 and
                              (c1.issubset(c2) or c2.issubset(c1)))
               for c1 in cl1 for c2 in cl2)

def unit_tests():
    assert set(len(g) for g in genomes) == set([glen])
    clusters = cluster(neighbors, 11, 11)
    assert sum(len(c) for c in clusters) == len(genomes)
    assert len(set(g for c in clusters for g in c)) == len(genomes)
    assert dist(17, 42) == dist(42, 17)
    assert diameter(set()) == 0
    assert diameter([17, 42]) == dist(17, 42)
    assert pct(1, 2) == '50.0%'
    print('\nAll tests pass.\n')

    

################################################################ Main body
 
max_distance = 26
names, species, genomes = get_genomes() ## genomes = ['ACT...', ...]
n = len(genomes)
glen = len(genomes[0])
neighbors = get_neighbors() ## neighbor[g] = {g2:d2, g3:g3, ...}
greport(genomes)
nreport(neighbors)
creport(range(6, 15), [glen,16,15,14,13, 12, 11])
#sreport(species)

unit_tests()