daoyuanSN.py

import re, glob, os, collections,sys
from decimal import Decimal
from math import log
from string import ascii_lowercase

# parameters = [ 'TL{all}', 'r(A<->C){1}', 'r(A<->G){1}', 'r(A<->T){1}', 'r(C<->G){1}', 'r(C<->T){1}', 'r(G<->T){1}', 'r(A<->C){2}', 'r(A<->G){2}', 'r(A<->T){2}', 'r(C<->G){2}', 'r(C<->T){2}', 'r(G<->T){2}', 'r(A<->C){3}', 'r(A<->G){3}', 'r(A<->T){3}', 'r(C<->G){3}', 'r(C<->T){3}', 'r(G<->T){3}', 'pi(A){1}', 'pi(C){1}', 'pi(G){1}', 'pi(T){1}', 'pi(A){2}', 'pi(C){2}', 'pi(G){2}', 'pi(T){2}', 'pi(A){3}', 'pi(C){3}', 'pi(G){3}', 'pi(T){3}', 'alpha{1}', 'alpha{2}', 'alpha{3}', 'm{1}', 'm{2}', 'm{3}']

# parameter = 'speciation'
# parameter = parameters[1]

contain = []
gene_list = ['Prior1.log.txt', 'Posterior1.log.txt']

angio = {}
for fname in gene_list:
    lines = open(fname, 'r').readlines()
#     print lines
    headers = lines[0].strip().split()
    i = headers.index('tmrca(Anacostia)')
#     print i
    angio[fname] = []
    for line in lines[1:]:
        parts = line.strip().split()
        angio[fname].append(float(parts[i]))
#     print fname,len(angio[fname])
    # angio['Prior.log'] = [127.1125949594009,127.58479381380802,...]
# sys.exit('aborted')

# print angio['Prior.log.txt']
# print angio['Posterior.log.txt']
##################################
##partitioning specific parameter values into 3 groups 
def partition(values_1, values_2, k):
    ###sorting values of chosen key
    values = sorted(values_1)
#     print 'values=', values
    values2 = sorted(values_2) 
    length_values2 = len(values2)
    length = int(len(values))
#     print
#     print 'length=', length
    ###creating 3 partitons of values
    parts = [(length/k)*(i+1) for i in range(k-1)]
#     parts = [length/3, (length/3)*2]
#     print 'parts=', parts
    all_list = []
    for n in parts:
        i=0
        ###creates lists of n, n*2, n*3 values
        diff = 200000.0
        diff_list = None
        while int(len(values[i+1:])) >= n:
            a_diff = values[i+n-1]-values[i]
            
            b_diff = values[i+n]-values[i+1]
            if a_diff < diff:
                diff = a_diff
                diff_list = values[i:i+n]
            elif b_diff < diff: 
                diff = b_diff
                diff_list = values[i+1:i+n+1]
            i+=1
        n+=length/k 
        all_list.append(diff_list)
    
#     print 'all_list=', all_list
    collect2 = [0.0]*(length/k)
#     print collect2
    collect = []
    i =0
#     print 'len=', all_list[0], all_list[1]
    
    collect.append(all_list[0])
   
    for i in range(len(all_list)-1):
        a = [e for e in all_list[i+1] if e not in all_list[i]]
        collect.append(a)
    collect.append([e for e in values if e not in all_list[-1]])
    
    collect2 = [0.0]*(k-1)
    i=0
    while i <= k-2:
        tmp = []
        for m in values2:
            if (m >= collect[i][0]) and (m<=collect[i][-1]):
                tmp.append(m)
                collect2[i]+=1

#             print values2
        values2 = [e for e in values2 if e not in tmp]
#         print 'tmp==', tmp, values2      
        i+=1
#     print collect2, length_values2, sum(collect2)   
    collect2.append(length_values2-sum(collect2))
#     print 'collect2', collect2       
    
    Hp1 = log(k)
    Hp2_list = []
    
#     if float(collect2
    for i in collect2:
        if i !=0:
            Hp2_list.append((-i/length) * log(i/length))
    
#     print Hp2_list
    Hp2 = sum(Hp2_list)
#     Hp2 = ((-A2/Total_len) * log(A2/Total_len))+((-B2/Total_len) * log(B2/Total_len))+((-C2/Total_len) * log(C2/Total_len))
    M = 100*(1.-(Hp1-Hp2)/log(k))
    for i,m in enumerate(collect):
        print 'D1 k=%d has n=%d' % (i, len(m))
    print '*********************'
    for i,m in enumerate(collect2):
        print 'D2 k=%d has n=%d' % (i, int(m))
    print '*******************************************'
#     print 'Compatability of D1 and D2, M(D2|D1) =', M
    return M

#     print
    
    
k = 5
result1 = partition(angio['Prior1.log.txt'], angio['Posterior1.log.txt'], k) 
result2 = partition(angio['Posterior1.log.txt'], angio['Prior1.log.txt'], k)
print 'Compatability of D1 and D2, M(D2|D1) =%d', result1 
print 'Compatability of D1 and D2, M(D1|D2) =%d', result2 
print
print 'Average Compatability of D1 and D2, {M(D2|D1)+ M(D1|D2)}/2 =', (result1+result2)/2.