geinf/swp2.py

import matplotlib.pyplot as plt
import os

def return_x_y_from_stwp_theta_file(stwp_theta_file, breaks, mu, tgen):
    with open(stwp_theta_file, "r") as swp_file:
        # Read the first line
        line = swp_file.readline()
        L = float(line.split()[2])
        # Process lines until the end of the file
        while line:
            # check at each line
            if line.startswith("dim") :
                dim = int(line.split()[1])
                if dim == breaks+1:
                    likelihood = line.split()[5]
                    groups = line.split()[6:6+dim]
                    theta_site = line.split()[6+dim:6+dim+1+dim]
                elif dim < breaks+1:
                    line = swp_file.readline()
                    continue
                elif dim > breaks+1:
                    break
                    #return 0,0,0
            # Read the next line
            line = swp_file.readline()
    #### END of parsing
    # quit this file if the number of dimensions is incorrect
    if dim < breaks+1:
        return 0,0,0
    # get n, the last bin of the last group
    #n = int(groups[-1].split(",")[-1])
    # revert the list of groups as the most recent times correspond
    # to the closest and last leafs of the coal. tree.
    groups = groups[::-1]
    # initiate the dict of times
    t = {}
    # list of thetas 
    theta_L = []
    sum_t = 0
    for group_nb, group in enumerate(groups):
        print(group_nb, group, theta_site[group_nb], len(theta_site))
        # store all the thetas one by one, with one theta per group
        theta_L.append(float(theta_site[group_nb]))
        # if the group is of size 1
        if len(group.split(',')) == 1:
            i = int(group)
        # if the group size is >1, take the first elem of the group
        # i is the first bin of each group, straight after a breakpoint
        else:
            i = int(group.split(",")[0])
            j = int(group.split(",")[-1])
        t[i] = 0
        if len(group.split(',')) == 1:
            k = i
            t[i] += ((theta_L[group_nb] ) / (k*(k-1)) * tgen) / mu
        else:
            for k in range(i, j+1):
                t[i] += ((theta_L[group_nb] ) / (k*(k-1)) * tgen) / mu
        # we add the cumulative times at the end
        t[i] += sum_t
        sum_t = t[i]
    # build the y axis (sizes)
    y = []
    #theta_L.sort(reverse=True)
    for theta in theta_L:
        # with size N = theta/4mu
        size = theta / (4*mu)
        y.append(size)
        y.append(size)
    
    # build the time x axis
    x = [0]
    # need to fix: t.values are sorted? and in reverse order because the groups and the times are sorted in opposite order
    for time in range(0, len(t.values())-1):
        x.append(list(t.values())[time])
        x.append(list(t.values())[time])
    x.append(list(t.values())[len(t.values())-1])

    #x = x[::-1]
    #y = y[::-1]
    #x.sort(reverse=True)
    #y.sort(reverse=True)
    
    return x,y,likelihood

def plot_3epochs_thetafolder(folder_path, mu, tgen, breaks = 2, title = "Title"):
    
    scenari = {}
    cpt = 0
    
    for file_name in os.listdir(folder_path):
        if os.path.isfile(os.path.join(folder_path, file_name)):
            # Perform actions on each file
            x,y,likelihood = return_x_y_from_stwp_theta_file(folder_path+file_name, breaks = breaks, 
                                                             tgen = tgen,
                                                             mu = mu)
            if x == 0 or y == 0:
                continue
            cpt +=1
            scenari[likelihood] = x,y
    print("\n*******\n"+title+"\n--------\n"+"mu="+str(mu)+"\ntgen="+str(tgen)+"\nbreaks="+str(breaks)+"\n*******\n")
    print(cpt, "theta files have been scanned.")
    # sort starting by the smallest -log(Likelihood)
    best10_scenari = (sorted(list(scenari.keys())))[:10]
    print("10 greatest Likelihoods", best10_scenari)
    greatest_likelihood = best10_scenari[0]
    x, y = scenari[greatest_likelihood]
    my_dpi = 300
    plt.figure(figsize=(5000/my_dpi, 2800/my_dpi), dpi=my_dpi)
    plt.plot(x, y, 'r-', lw=2, label = 'Lik='+greatest_likelihood)
    for scenario in best10_scenari[1:]:
        x,y = scenari[scenario]
        print("\n----  Lik:",scenario,"\n\nt=", x,"\n\nN=",y, "\n\n")
        plt.plot(x, y, '--', lw=1, label = 'Lik='+scenario)
    plt.ylabel("Individuals (N)")
    plt.xlabel("Time (years)")
    plt.legend(loc='upper right')
    plt.title(title)
    #plt.gcf().set_size(1000, 500)
    plt.savefig(title+'_b'+str(breaks)+'.pdf')
    #plt.show()

if __name__ == "__main__":
            
    if len(sys.argv) != 4:
        print("Need 3 args: ThetaFolder MutationRate GenerationTime")
        exit(0)
        
    folder_path = sys.argv[1]
    mu = sys.argv[2]
    tgen = sys.argv[3]

    plot_3epochs_thetafolder(folder_path, mu, tgen)