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ChromosomeIntermingling.py
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ChromosomeIntermingling.py
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#from matplotlib import *
#from pylab import *
import numpy as np
'''
import os
answer = os.path.isdir('ContactPb1')
if answer==True:
pass
else:
os.mkdir('ContactPb1')
answer=os.path.isdir('SpatialDistance')
if answer==True:
pass
else:
os.mkdir('SpatialDistance')
fw=[]
for i in range(46):
fw.append(open('SpatialDistance/Spatial_Chr_'+str(i+1)+'.dat','w'))
'''
asize=[249,243,199,191,182,171,160,146,139,134,136,134,115,107,102,91,84,81,59,65,47,51,157,249,243,199,191,182,171,160,146,139,134,136,134,115,107,102,91,84,81,59,65,47,51,157]
csize=np.cumsum(asize)
natoms=csize[-1]+1
noc=46 ### number of chromosome
tsize=[0]+list(csize)
f=open('GM1.dat')
temp=[]
for line in f:
l=line.split()
temp.append(int(l[1]))
active_inactive=temp+temp
'''
CMatrix=[]
for i in range(noc):
array=[]
for i in range(noc):
array.append(0)
CMatrix.append(array)
'''
startPos=5001
endPos=10001+1
M1=np.zeros((46,250),dtype=np.float)
M2=np.zeros((46,250),dtype=np.float)
M3=np.zeros((46,250),dtype=np.float)
M4=np.zeros((46,250),dtype=np.float)
M5=np.zeros((46,250),dtype=np.float)
M6=np.zeros((46,250),dtype=np.float)
M7=np.zeros((46,250),dtype=np.float)
M8=np.zeros((46,250),dtype=np.float)
value=np.zeros((46),dtype=np.object)
chromosome=np.zeros((46),dtype=np.object)
for i in range(46):
value[i]=np.zeros((asize[i]-1),dtype=np.float)
chromosome[i]=np.zeros((asize[i],3),dtype=np.float)
nof=0.0
for filen in range(startPos,endPos,50):
nof+=1
name='my/file'+str(filen)+'.dat'
f=open(name)
cont=f.readlines()
print filen, "Time", len(cont)
for i in range(5,len(cont)): ###8 check this line
l=cont[i].split()
if len(l)==6:
for chro in range(47):
if int(l[1])==chro:
if chro==1:
start=0
else:
start=csize[chro-2]
#print "ankit",chro,l[0],start,int(l[0])-start-1
chromosome[chro-1][int(l[0])-start-1,:]=[float(l[3]),float(l[4]),float(l[5])]
M=np.zeros((noc,noc,3),dtype=np.float)
for p in range(noc):
for q in range(p+1,noc):
#count=np.zeros((asize[p]),dtype=np.float)
for i in range(asize[p]):
for j in range(asize[q]):
#print p,i,j
sub_vec=np.subtract(chromosome[p][i],chromosome[q][j])
dist=np.linalg.norm(sub_vec)
#print p+1,q+1, i+tsize[p]+1, j+tsize[q]+1
if dist<=2.5:
if (active_inactive[i+tsize[p]]!=1)&(active_inactive[j+tsize[q]]!=1): # AA
M[p][q][0]+=1
if (active_inactive[i+tsize[p]]==1)&(active_inactive[j+tsize[q]]==1): # BB
M[p][q][1]+=1
if (active_inactive[i+tsize[p]]!=1)&(active_inactive[j+tsize[q]]==1): # AB
M[p][q][2]+=1
if (active_inactive[i+tsize[p]]==1)&(active_inactive[j+tsize[q]]!=1): # BA
M[p][q][2]+=1
f1=open('InterminglingAA.dat','w')
f2=open('InterminglingBB.dat','w')
f3=open('InterminglingAB.dat','w')
print "no of frame ", nof
for p in range(noc):
for q in range(noc):
f1.write(str(M[p][q][0]/nof)+'\t')
f2.write(str(M[p][q][1]/nof)+'\t')
f3.write(str(M[p][q][2]/nof)+'\t')
f1.write('\n')
f2.write('\n')
f3.write('\n')