hmm_head

#!/usr/bin/env python
import ghmm
from ghmm import *

def def_cnps(filename,sample_label,positions, signals, states, ab_states):
    str = 0
    stp = 0
    num_probes = 0
    s = 0
    mean_sig = 0  
    count1 = 0
    count2 = 0
    i = 0;
    fname_cnv = open(filename,'w')
    write_seg(fname_cnv,"str", "stp", "num_probes", "mean_sig")
    while i < len(signals):
	if i>len(states):
            break;			   	
        for j in ab_states:
            if(j == states[i]):
                start = positions[i]
                stp = positions[i]                
                s = signals[i]
                num_probes = 1
                while(1):
                    i=i+1
                    #if i>len(states):
		    if i>=len(states):
                        i = i-1;
                        break;	
		    if(states[i] != j):
			i = i-1;
                        break;
                    #print repr(num_probes);
                    stp = positions[i]
                    s+=signals[i]
                    num_probes=num_probes+1

                mean_sig = s/num_probes		
		write_seg(fname_cnv, start, stp, num_probes, mean_sig)
		
        i=i+1
    
    fname_cnv.close()
      

def write_seg(filename,start, stp, num_probes, mean_sig):
    filename.write(str(start)+"\t"+str(stp)+"\t"+str(num_probes)+"\t"+str(mean_sig)+"\n")

def write_num(filename, num):
    f = open(filename, 'a')
    f.write(str(num)+"\n")        
    f.close()   

def write_states(filename, positions,signals,states, divergence):   
    f = open(filename, 'w')
    for i in range(len(signals)):	
	f.write(str(positions[i])+"\t"+str(signals[i])+"\t"+str(states[i])+"\n")        

    f.close()
    
def write_states(filename, positions,signals,states,clusts):   
    f = open(filename, 'w')
    for i in range(len(signals)):	
#	if(divergence[i]):
#            x = str(divergence[i])             
#        else:
#            x = "0.0"
            
#        f.write(str(positions[i])+"\t"+str(signals[i])+"\t"+str(states[i])+"\t"+x+"\n")
	f.write(str(positions[i])+"\t"+str(signals[i])+"\t"+str(states[i])+"\t"+str(clusts[i])+"\n")        
    f.close()

#write a row of emis probs
def write_emis_row(f, model, nstates):
    f.write("<tr>")
    for i in range(nstates):
        f.write("<td><b>%2.5f</b> " % model.getEmission(i,0)[0])
	f.write("<i>%2.5f </i>\n" % model.getEmission(i,0)[1])
	f.write("<b> %2.5f</b> " % model.getEmission(i,1)[0])
	f.write("<i>%2.5f </i>\n" % model.getEmission(i,1)[1])

#write transistion matrix comprised of rows from state x to states 1 thru j
def write_trans(f, model, nstates):
    for j in range(nstates):
    	f.write("<tr>")
    	for i in range(nstates):
        	f.write("<td> %2.5f " % model.getTransition(j,i))