connections between statistics.py and statistical_potential.py and some code mod…

…ifications and optimizations

connections between statistics.py and statistical_potential.py and some code mod…
…ifications and optimizations
Aglaé TABOT
Commit e1843847f31708a5024fd53ee6f8cab67e96d9a0 e1843847 1 parent ad0e234c
Showing 2 changed files with 355 additions and 279 deletions
statistical_potential.py
statistics.py
--- a/statistical_potential.py
View file @e184384
+++ b/statistical_potential.py
View file @e184384
+#!/usr/bin/python3
+
+# RNANet statistics
+# Developed by Aglaé Tabot, 2021 
+
+# This file computes statistical potentials over the produced dataset.
+# THIS FILE IS NOT SUPPOSED TO BE RUN DIRECTLY.
 import getopt, os, pickle, sqlite3, shlex, subprocess, sys, warnings
 import time
@@ -13,88 +20,37 @@ from Bio.PDB.vectors import Vector, calc_angle, calc_dihedral
 from multiprocessing import Pool, Manager
 from os import path
 from tqdm import tqdm
+from collections import Counter
 from setproctitle import setproctitle
-from RNAnet import Job, read_cpu_number, sql_ask_database, sql_execute, warn, notify, init_worker, trace_unhandled_exceptions
+from RNAnet import Job, read_cpu_number, sql_ask_database, sql_execute, warn, notify, init_with_tqdm, trace_unhandled_exceptions
 from sklearn.mixture import GaussianMixture
+import scipy.stats as st
 import warnings
 from pandas.core.common import SettingWithCopyWarning
 from itertools import combinations_with_replacement
 from math import *
-# from geometric_stats import get_euclidian_distance
+from geometric_stats import get_euclidian_distance, GMM_histo
 np.set_printoptions(threshold=sys.maxsize, linewidth=np.inf, precision=8)
 runDir = os.getcwd()
-
+@trace_unhandled_exceptions
-def liste_repres(fpath):
+def pyle_measures_for_potentials(name, s, thr_idx):
-    repres=[]
-    df=pd.read_csv(os.path.abspath(fpath))
-    for i in range(df.shape[0]):
-        up_name=df["representative"][i]
-        if '+' in up_name:
-            up_name=up_name.split('+')
-            for i in range(len(up_name)):
-                chain=up_name[i].split('|')
-                chain=chain[0].lower()+'_'+chain[1]+'_'+chain[2]
-                repres.append(chain+'.cif')
-        else :
-            up_name=up_name.split('|')
-            low_name=up_name[0].lower()+'_'+up_name[1]+'_'+up_name[2]
-            repres.append(low_name+'.cif') 
-        
-    return repres
-
-def measure_from_structure(f): # ou alors on le lance à partir de statistics.py?
-    """
-    Do geometric measures required on a given filename
-    """
-
-    name = f.split('.')[0]
-
-    global idxQueue
-    thr_idx = idxQueue.get()
-    setproctitle(f"RNANet statistics.py Worker {thr_idx+1} measure_from_structure({f})")
-
-    # Open the structure 
-    with warnings.catch_warnings():
-        # Ignore the PDB problems. This mostly warns that some chain is discontinuous.
-        warnings.simplefilter('ignore', Bio.PDB.PDBExceptions.PDBConstructionWarning)
-        warnings.simplefilter('ignore', Bio.PDB.PDBExceptions.BiopythonWarning)
-        parser=MMCIFParser()
-        s = parser.get_structure(f, os.path.abspath(path_to_3D_data+ "rna_only/" + f))
-    
-    measures_heavy_atoms(name, s, thr_idx)
-    if DO_WADLEY_ANALYSIS:
-        pyle_measures(name, s, thr_idx)
-    
-    idxQueue.put(thr_idx) # replace the thread index in the queue
-    setproctitle(f"RNANet statistics.py Worker {thr_idx+1} finished")
-
-def pyle_measures(name, s, thr_idx):
     # measure distances P-P, P-C1', P-C4', C1'-C1', C4'-C4'
-    # between residues 
+    # between residues along the chain
-    # along the chain
+    # Requires a lot of storage space!
-    if (path.isfile(runDir + '/results/geometry/Pyle/distances/distances_pyle_'+name+'.csv')):
+    if (path.isfile(runDir + '/results/geometry/Pyle/distances_i_i+1/distances_pyle_i_i+1'+name+'.csv')):
         return
     liste_dist=[]
-    #classes=[]
+
-    #for i in range(0, 150, 5):
-        #classes.append([i, i+5])
-    #classes.append([150, 300])
-    #occur_p_p=len(classes)*[0]
-    #occur_p_c1=len(classes)*[0]
-    #occur_p_c4=len(classes)*[0]
-    #occur_c1_c1=len(classes)*[0]
-    #occur_c4_c4=len(classes)*[0]
-    #nb_occurs=[]
     setproctitle(f"RNANet statistics.py Worker {thr_idx+1} pyle_measures({name})")
     chain = next(s[0].get_chains())
-    #residues=list(chain.get_residues())
+    
     for res1 in tqdm(chain, position=thr_idx+1, desc=f"Worker {thr_idx+1}: {name} pyle_measures", unit="res", leave=False):
-        #res1=chain[i]
+       
         if res1.get_resname() in ["A", "C", "G", "U"]:
             resnum1=list(res1.get_id())[1]
             atom_p_1 = [ atom.get_coord() for atom in res1 if atom.get_name() ==  "P"]
@@ -109,7 +65,7 @@ def pyle_measures(name, s, thr_idx):
                 p_c1p=np.nan
                 c4p_c4p=np.nan
                 c1p_c1p=np.nan
-                #res2=chain[j]
+                
                 if res2.get_resname() in ["A", "C", "G", "U"]:
                     atom_p_2 = [ atom.get_coord() for atom in res2 if atom.get_name() ==  "P"]
@@ -123,94 +79,218 @@ def pyle_measures(name, s, thr_idx):
                     c1p_c1p= get_euclidian_distance(atom_c1p_1, atom_c1p_2)
                     liste_dist.append([res1.get_resname(), int(resnum1), res2.get_resname(), int(resnum2), p_p, p_c4p, p_c1p, c4p_c4p, c1p_c1p])
-                    '''
-                    for x in range(len(classes)):
-                        if classes[x][0] <= p_p <= classes[x][1]:
-                            occur_p_p[x]=occur_p_p[x]+1
-                        if classes[x][0] <= p_c4p <= classes[x][1]:
-                            occur_p_c4[x]=occur_p_c4[x]+1                        
-                        if classes[x][0] <= p_c1p <= classes[x][1]:
-                            occur_p_c1[x]=occur_p_c1[x]+1
-                        if classes[x][0] <= c4p_c4p <= classes[x][1]:
-                            occur_c4_c4[x]=occur_c4_c4[x]+1
-                        if classes[x][0] <= c1p_c1p <= classes[x][1]:
-                            occur_c1_c1[x]=occur_c1_c1[x]+1
-                    '''
-    #for x in range(len(classes)):
-        # for i in range(len(liste_dist)):
-        #     if classes[x][0] <= liste_dist[i][4] <= classes[x][1]:
-        #         occur_p_p[x]=occur_p_p[x]+1
-        #     if classes[x][0] <= liste_dist[i][5] <= classes[x][1]:
-        #         occur_p_c4[x]=occur_p_c4[x]+1                        
-        #     if classes[x][0] <= liste_dist[i][6] <= classes[x][1]:
-        #         occur_p_c1[x]=occur_p_c1[x]+1
-        #     if classes[x][0] <= liste_dist[i][7] <= classes[x][1]:
-        #         occur_c4_c4[x]=occur_c4_c4[x]+1
-        #     if classes[x][0] <= liste_dist[i][8] <= classes[x][1]:
-        #         occur_c1_c1[x]=occur_c1_c1[x]+1
-        #nb_occurs.append([classes[x], occur_p_p[x], occur_p_c1[x], occur_p_c4[x], occur_c1_c1[x], occur_c4_c4[x]])
-    #df = pd.DataFrame(nb_occurs, columns=["classe", "P-P", "P-C1'", "P-C4'", "C1'-C1'", "C4'-C4'"])
-    # return df
-    # nb_occurs.append([classes, occur_p_p, occur_p_c1, occur_p_c4, occur_c1_c1, occur_c4_c4])
-    # print(nb_occurs)
-    # return nb_occurs
-                    
+                
     df = pd.DataFrame(liste_dist, columns=["res1", "resnum1", "res2", "resnum2", "P-P", "P-C4'", "P-C1'", "C4'-C4'", "C1'-C1'"])
-    df.to_csv(runDir + "/results/geometry/Pyle/distances/distances_pyle_" + name + ".csv")
+    df.to_csv(runDir + "/results/geometry/Pyle/distances_i_i+1/distances_pyle_i_i+1" + name + ".csv")
-def gmm_pyle_type(ntpair, data):
+@trace_unhandled_exceptions
+def gmm_pyle_type(ntpair, data, scan):
     setproctitle(f"GMM (Pyle {ntpair} )")
-    os.makedirs(runDir + "/results/figures/GMM/Pyle/distances/", exist_ok=True)
+    os.makedirs(runDir + "/results/figures/GMM/Pyle/distances_i_i+1/", exist_ok=True)
-    os.chdir(runDir + "/results/figures/GMM/Pyle/distances/")
+    os.chdir(runDir + "/results/figures/GMM/Pyle/distances_i_i+1/")
     p_p=list(data["P-P"][~ np.isnan(data["P-P"])])
     p_c4p=list(data["P-C4'"][~ np.isnan(data["P-C4'"])])
     p_c1p=list(data["P-C1'"][~ np.isnan(data["P-C1'"])])
     c4p_c4p=list(data["C4'-C4'"][~ np.isnan(data["C4'-C4'"])])
     c1p_c1p=list(data["C1'-C1'"][~ np.isnan(data["C1'-C1'"])])
-    #print(len(p_p))
-    # res2=list(data["resnum2"])
-    # res1=list(data["resnum1"])
-    # diff=[]
-    # for i in range(len(res1)):
-    #     diff.append(res2[i]-res1[i])
-    # print(diff[:100])
-    GMM_histo(p_p, f"Distance P-P between {ntpair}", toric=False, hist=False, col="cyan")
+    GMM_histo(p_p, f"Distance P-P between {ntpair}", scan, toric=False, hist=False, col="cyan")
-    GMM_histo(p_c4p, f"Distance P-C4' between {ntpair}", toric=False, hist=False, col="tomato")
+    GMM_histo(p_c4p, f"Distance P-C4' between {ntpair}", scan, toric=False, hist=False, col="tomato")
-    GMM_histo(p_c1p, f"Distance P-C1' between {ntpair}", toric=False, hist=False, col="goldenrod")
+    GMM_histo(p_c1p, f"Distance P-C1' between {ntpair}", scan, toric=False, hist=False, col="goldenrod")
-    GMM_histo(c4p_c4p, f"Distance C4'-C4' between {ntpair}", toric=False, hist=False, col="magenta")
+    GMM_histo(c4p_c4p, f"Distance C4'-C4' between {ntpair}", scan, toric=False, hist=False, col="magenta")
-    GMM_histo(c1p_c1p, f"Distance C1'-C1' between {ntpair}", toric=False, hist=False, col="black")
+    GMM_histo(c1p_c1p, f"Distance C1'-C1' between {ntpair}", scan, toric=False, hist=False, col="black")
-    # GMM_histo(diff, f"Gap between {ntpair} ", toric=False, hist=False, col="tomato")
+    
     plt.xlabel("Distance (Angströms)")
-    # plt.xlabel("Number of residues")
-    #plt.ylabel("Distance (Angströms)")
     plt.title(f"GMM of distances for {ntpair} ", fontsize=10)
-    # plt.savefig(f"Longueurs_Pyle_{ntpair}.png" )
+    plt.savefig(runDir + "/results/figures/GMM/Pyle/distances_i_i+1/" + f"Distances_Pyle_{ntpair}.png" )
-    plt.savefig(f"Distances_Pyle_{ntpair}.png" )
     plt.close()
     setproctitle(f"GMM (Pyle {ntpair} distances) finished")
-
+@trace_unhandled_exceptions
-def gmm_pyle():
+def gmm_pyle_per_type(scan):
     setproctitle("GMM (Pyle model)")
-    df = pd.read_csv(os.path.abspath(runDir + "/results/geometry/Pyle/distances/distances.csv"))
+    df = pd.read_csv(os.path.abspath(runDir + "/results/geometry/Pyle/distances_i_i+1/distances.csv"))
-    # dist = ["P-P", "P-C4'", "P-C1'", "C4'-C4'", "C1'-C1'"]
     data=df
     if len(data):
         for b1 in ['A','C','G','U']:
             for b2 in ['A','C','G','U']:
                 thisbases = data[(data.res1 == b1)&(data.res2 == b2)]
                 if len(thisbases):
-                    gmm_pyle_type(b1+b2, thisbases)
+                    gmm_pyle_type(b1+b2, thisbases, scan)
+    setproctitle("GMM (Pyle model) finished")
+
+# The next 7 functions are used to calculate the statistical potentials with the averaging method (residue-averaging)
+# for the Pyle model from the GMM results, and to plot the corresponding figures
+
+
+def pgaussred(x):
+    """
+    distribution function of the normal distribution (= probability that a random variable distributed according to is less than x)
+    calculation by numerical integration: 2000 slices per standard deviation
+    result rounded to 7 decimal places
+    """
+    if x==0:
+        return 0.5
+    u=abs(x)
+    n=int(u*2000)
+    du=u/n
+    k=1/sqrt(2*pi)
+    u1=0
+    f1=k
+    p=0.5
+    for i in range(0,n):
+        u2=u1+du
+        f2=k*exp(-0.5*u2*u2)
+        p=p+(f1+f2)*du*0.5
+        u1=u2
+        f1=f2
+    if x<0:
+        p = 1.0-p
+    return round(p, 7)
+
+def proba(m, s, xinf, xsup):
+    """
+    calculates the probability for a value to belong to the interval [xinf, xsup]
+    for a normal distribution with mean m and standard deviation s
+    """
+    prob=pgaussred((xsup-m)/s)-pgaussred((xinf-m)/s)
+
+    return prob
+
+def extract_from_json(data, xinf, xsup):
+    """
+    extracts the means and standard deviations of the json obtained with the GMM calculations
+    and calculates from these parameters the probability for a value to belong to the interval [xinf, xsup].
+    """
+    p=[]
+    p_tot=0
+    classes=[]
+    with open(data + '.json') as json_data:
+        data_dict = json.load(json_data)
+
+    for i in range(len(data_dict['means'])):
+        mean = data_dict['means'][i]
+        if mean[0] == '[':
+            mean=float((mean.split('['))[1].split(']')[0])
+        else :
+            mean=float(mean)
+        std = data_dict['std'][i]
+        if std[0] == '[':
+            std=float((std.split('['))[2].split(']')[0])
+        else:
+            std=float(std)
+        prob=proba(mean, std, xinf, xsup)
+        p.append(prob)
+
+    for x in p:
+        p_tot = p_tot+x
+    return p_tot
+
+def averaging(liste_data, name):
+    """
+    creates a json that contains all the means and standard deviations of the parameters
+    that we want to use to create the reference distribution with the averaging method
+    """
+    
+    curves=[]
+ 
+    x = np.linspace(0,250,1000)
+
+    summary_data = {}
+    summary_data["measures"] = []
+    summary_data["means"] = []
+    summary_data["std"] = []
+    for data in  liste_data:
+        s=0
+        mean_tot=0
+        std_tot=0
+        with open(runDir + '/results/geometry/json/' + data + '.json') as json_data:
+            data_dict = json.load(json_data)
+
+        for i in range(len(data_dict['means'])):
+            mean = float(data_dict['means'][i])
+  
+            std = float(data_dict['std'][i])
+            
+            weight = float(data_dict['weights'][i])
+            y = weight*st.norm.pdf(x, mean, std)
+            mean_tot=mean_tot+(weight*mean)
+            std_tot=std_tot+(weight*std)
+          
+            curves.append(y)
+        summary_data["measures"].append(data)
+        summary_data["means"].append(str(mean_tot))
+        summary_data["std"].append(str(std_tot))
+ 
+    with open(runDir + '/results/statistical_potential/json/Pyle/avg_' +name + ".json", 'w', encoding='utf-8') as f:
+        json.dump(summary_data, f, indent=4)
+
+def potential_dist(data_obs, data_ref):
+    name=data_obs.split('/')[-1]
+    l=[]
+    for k in range(0, 400, 5):
+        obs=extract_from_json(data_obs, k, k+5)
+        ref=extract_from_json(data_ref, k, k+5)
+        if obs != 0.0 and ref != 0.0:
+            u = -log(obs/ref)
+            l.append([k, k+5, obs, ref, u])
+            l.append([k+5, k+5, obs, ref, u])
+
+        else:
+            l.append([k, k+5, obs, ref, None])
+            l.append([k+5, k+5, obs, ref, None])
+    df=pd.DataFrame(l, columns=["Xinf", "Xsup", "Pobs", "Pref", "- ln(Pobs/Pref)"])
+    df.to_csv(runDir + '/results/statistical_potential/ratio/Pyle/Statistical potential ' + name + ".csv")
+
+def courbe_stat_pot(f):
+    name=f.split('/')[-1]
+    name=name.split('.')[0]
+    df=pd.read_csv(f)
+    E=list(df["- ln(Pobs/Pref)"][~ np.isnan(df["- ln(Pobs/Pref)"])])
+    max_E=max(E)
+    min_E=min(E)
+    index_with_nan=df.index[df.iloc[:,5].isnull()]
+    for i in index_with_nan:
+        df.iloc[i, 5]=max_E # we replace the nan by the maximum found energy
+     
+    y=list(df["- ln(Pobs/Pref)"])
+    x=list(df["Xinf"])
+
+    x=np.array(x)
+    y=np.array(y)
+    plt.plot(x, y)
+    plt.xlabel("Distance (Angström)")
+    plt.ylabel("- ln(Pobs/Pref)")
+    plt.title(name)
+    plt.savefig(runDir + "/results/statistical_potential/figures/Pyle/avg_statistical_pot_ " + name + ".png")
+    plt.close()
+
+def stat_potential_pyle():
+    pyle = ["P-P", "P-C1'", "P-C4'", "C1'-C1'", "C4'-C4'"]
+    nt = ["A", "C", "G", "U"]
+    for pair in pyle:
+        type_list=[]
+        for res1 in nt:
+            for res2 in nt:
+                setproctitle(f"RNANet statistics.py stat_potential_pyle({pair}, {res1}{res2})")
+                type_list.append(f"Distance {pair} between {res1}{res2}")
+                averaging(type_list, f"{pair}")
+                for dist in type_list:
+                    potential_dist(runDir + '/results/geometry/json/' + dist, runDir + f'/results/statistical_potential/json/Pyle/avg_{pair}')
+                    courbe_stat_pot(runDir + '/results/statistical_potential/ratio/Pyle/Statistical potential ' + dist + '.csv')
+                    setproctitle(f"RNANet statistics.py stat_potential_pyle({pair}, {res1}{res2}) finished")
+
+
+@trace_unhandled_exceptions
 def measures_heavy_atoms(name, s, thr_idx):
     """
     create a list of all possible pairs of atoms among the 85 types of atoms
@@ -312,21 +392,17 @@ def measures_heavy_atoms(name, s, thr_idx):
     df_occur = pd.DataFrame(occurences, columns=["atom_pair_type"] + classes_str)
     # save this
     df_occur.to_csv(runDir + "/results/geometry/all-atoms/distances_classes/distances_classes_occur_" + name + ".csv")
-
+@trace_unhandled_exceptions
 def count_occur_atom_dist(fpath, outfilename):
     """
     After having calculated the number of occurrences of the distances between pairs of atoms
     sorted by distance class and by type of pair for each RNA chain,
     we add these occurrences one by one to obtain a single dataframe with the total number of occurrences
     """
-
+  
-    global idxQueue
+    setproctitle(f"Addition of occurences of {fpath}")
-    thr_idx = idxQueue.get()
-    setproctitle(f"Worker {thr_idx+1} : Addition of occurences of {fpath}")    
-
     liste=os.listdir(fpath)
-    
+
-    pbar = tqdm(total=len(liste), position=thr_idx, desc="Preparing "+outfilename, leave=False)
     df_tot = pd.read_csv(os.path.abspath(fpath + liste.pop()))
     for f in range(len(liste)):
@@ -334,23 +410,20 @@ def count_occur_atom_dist(fpath, outfilename):
         for i in range(df.shape[0]):
             for j in range(2, df.shape[1]):
                 df_tot.iloc[i, j]=df_tot.iloc[i, j] + df.iloc[i, j]
-        pbar.update(1)
+        
     df_tot.to_csv(fpath+outfilename)
-    idxQueue.put(thr_idx) # replace the thread index in the queue
-    setproctitle(f"RNANet statistics.py Worker {thr_idx+1} finished")
+    setproctitle(f"Addition of occurences of {fpath} finished")
+
+@trace_unhandled_exceptions
 def mole_fraction(fpath, outfilename):
     """
     Calculation of the mole fraction of each type of atom within the set of structures
-    """
+    """  
-
+    setproctitle(f"Calculation of mole fractions of {fpath}")
-    global idxQueue
-    thr_idx = idxQueue.get()
-    setproctitle(f"Worker {thr_idx+1} : Calculation of mole fractions of {fpath}")    
-
     liste=os.listdir(fpath)
-    pbar = tqdm(total=len(liste), position=thr_idx, desc="Preparing "+outfilename, leave=False)
+   
     df_tot = pd.read_csv(os.path.abspath(fpath + liste.pop()))
     del df_tot["Unnamed: 0"]
@@ -359,31 +432,29 @@ def mole_fraction(fpath, outfilename):
         del df["Unnamed: 0"]
         for i in range(df.shape[0]):
                 df_tot.iloc[i, 1]=df_tot.iloc[i, 1] + df.iloc[i, 1]
-        pbar.update(1)
+
     total=sum(list(df_tot["count"]))
     fract=[]
     for i in range(df_tot.shape[0]):
-        # df_tot.iloc[i, 1]=df_tot.iloc[i, 1]/total
+       
         fract.append(df_tot.iloc[i, 1]/total)
     df_tot["mole_fraction"]=fract
-    file_list=os.listdir(fpath)
+    # file_list=os.listdir(fpath)
-    file_list=[fpath+x for x in file_list]
+    # file_list=[fpath+x for x in file_list]
     # for f in file_list: #after processing, deletion of csv by structure
     #     os.remove(f)
-    df_tot.to_csv(fpath+outfilename) #ou alors juste un return 
+    df_tot.to_csv(fpath+outfilename) 
-    idxQueue.put(thr_idx) # replace the thread index in the queue
-    setproctitle(f"RNANet statistics.py Worker {thr_idx+1} finished")
+    setproctitle(f"Calculation of mole fractions of {fpath} finished")
+
+@trace_unhandled_exceptions
 def compute_ratio_from_csv(fpath, avg_file, qch_file):
     """
     Calculation of observed and reference probabilities 
     according to the methods chosen to establish the reference state
     Then calculation of the Pobs / Pref ratio
-    """
+    """ 
-    # global idxQueue
+    setproctitle("Compute ratio from csv")
-    # thr_idx = idxQueue.get()
-    # setproctitle(f"Worker {thr_idx+1} : Compute ratio from {fpath}")  
-
     df = pd.read_csv(fpath)
     del df['Unnamed: 0']
     del df['Unnamed: 0.1']
@@ -401,9 +472,8 @@ def compute_ratio_from_csv(fpath, avg_file, qch_file):
     s_tot=sum(sommes)
     for s in sommes:
         pref_avg_list.append(s/s_tot)
-    print(sommes)
+   
-    # return
+    
-    # pbar = tqdm(total=df.shape[0], position=thr_idx, desc="Preparing "+avg_file, leave=False)
     df_bis=df.copy()
     # if method=averaging
     for i in range(df.shape[0]):
@@ -412,14 +482,7 @@ def compute_ratio_from_csv(fpath, avg_file, qch_file):
             df_bis.iloc[i,j]=df.iloc[i,j]/(sum(df.iloc[i, k] for k in range(1, df.shape[1])))
             # ratio between the observed probability and the reference probability
             df_bis.iloc[i,j]=df_bis.iloc[i,j]/pref_avg_list[j-1]
-        # pbar.update(1)
+        
-    # idxQueue.put(thr_idx) # replace the thread index in the queue
-    # setproctitle(f"RNANet statistics.py Worker {thr_idx+1} finished")
-    print(df_bis)
-    
-    # thr_idx = idxQueue.get()
-    # setproctitle(f"Worker {thr_idx+1} : Compute ratio from {fpath}")
-    # pbar = tqdm(total=df.shape[0], position=thr_idx, desc="Preparing "+qch_file, leave=False)
     # if method=quasi-chemical
     df_ter=df.copy()
@@ -430,20 +493,18 @@ def compute_ratio_from_csv(fpath, avg_file, qch_file):
             # calculate the mole fractions of the atom corresponding to the pair in row i
             if atom_count.at[k, 'atom']==df.iloc[i, 0].split('-')[0] or atom_count.at[k, 'atom']==df.iloc[i, 0].split('-')[1]:
                 x.append(atom_count.at[k, 'mole_fraction'])
-                # print(x)
+                
         for j in range(1, df.shape[1]):
             if len(x)==2:
                 df_ter.iloc[i, j]=df.iloc[i,j]/(x[0]*x[1]*sommes[j-1]) # ratio for qchA method (Nijobs(r)/xi*xj*Nobs(r))
             if len(x)==1:
                 df_ter.iloc[i, j]=df.iloc[i,j]/(x[0]*x[0]*sommes[j-1]) 
-        # pbar.update(1)
+    df_bis.to_csv(runDir + '/results/statistical_potential/ratio/all-atoms/' + avg_file)
-    # idxQueue.put(thr_idx) # replace the thread index in the queue
+    df_ter.to_csv(runDir + '/results/statistical_potential/ratio/all-atoms/' + qch_file)
-    # setproctitle(f"RNANet statistics.py Worker {thr_idx+1} finished")
-    print(df_ter)
-    # ajouter ce qui est dans la fct save_into_database ici?
-    df_bis.to_csv(runDir + '/results/statistical_potential/all-atoms/' + avg_file)
-    df_ter.to_csv(runDir + '/results/statistical_potential/all-atoms/' + qch_file)
+    setproctitle("Compute ratio from csv finished")
+    
+@trace_unhandled_exceptions
 def sql_new_table(conn):
     cur = conn.cursor()
     sql = """ CREATE TABLE IF NOT EXISTS all_atoms (
@@ -482,10 +543,11 @@ def sql_new_table(conn):
     conn.execute("pragma journal_mode=wal")
     #conn.close()
-
+@trace_unhandled_exceptions
 def save_into_database():
-    df_avg = pd.read_csv(runDir + '/results/statistical_potential/all-atoms/avg_ratio_pobs_pref.csv')
+    setproctitle("Saving statistical potentials(avg, qch) into database")
-    df_qch = pd.read_csv(runDir + '/results/statistical_potential/all-atoms/qch_ratio_pobs_pref.csv')
+    df_avg = pd.read_csv(runDir + '/results/statistical_potential/ratio/all-atoms/avg_ratio_pobs_pref.csv')
+    df_qch = pd.read_csv(runDir + '/results/statistical_potential/ratio/all-atoms/qch_ratio_pobs_pref.csv')
     ratio_list=[]
     del df_avg['Unnamed: 0']
     del df_qch['Unnamed: 0']
@@ -495,80 +557,57 @@ def save_into_database():
             ratio_list.append([df_avg.iloc[i,0], df_avg.columns[j], df_avg.iloc[i, j], df_qch.iloc[i,j]])
-    with sqlite3.connect(runDir + "/results/Stats.db", timeout=20.0) as conn:
+    with sqlite3.connect(runDir + "/results/Stat_potential.db", timeout=20.0) as conn:
         conn.execute('pragma journal_mode=wal') # Allow multiple other readers to ask things while we execute this writing query
         # We use the REPLACE keyword to get the latest information
         sql_execute(conn, """INSERT OR REPLACE INTO all_atoms (atom_pair, distance_bin, avg_ratio_pobs_pref, qch_ratio_pobs_pref )
                                 VALUES (?, ?, ?, ?);""", 
                     many=True, 
                     data=ratio_list
-                    )  
+                    ) 
-
+    setproctitle("Saving statistical potentials(avg, qch) into database finished") 
-def stat_potential(pair, f, method):
+@trace_unhandled_exceptions
+def stat_potential(f, method):
     df=pd.read_csv(f)
     del df['Unnamed: 0']
     df.set_index('atom_pair_type', inplace=True)
     df=df.T
-    c=df[pair].tolist()
+    setproctitle(f"RNANet statistics.py stat_potential({method})")
-    new=[]
+    for pair in df.columns:
-    for x in c:
+        c=df[pair].tolist()
-        if x!=0.0 and not np.isnan(x):
+        new=[]
-            new.append(-log(x))
+        for x in c:
-            new.append(-log(x))
+            if x!=0.0 and not np.isnan(x):
-        if x==0.0:
+                new.append(-log(x))
-            new.append(0.0)
+                new.append(-log(x))
-            new.append(0.0)
+            if x==0.0:
-        if np.isnan(x):
+                new.append(0.0)
-            new.append(0.0)
+                new.append(0.0)
-            new.append(0.0)
+            if np.isnan(x):
-    abs=[]
+                new.append(0.0)
-    
+                new.append(0.0)
-    for i in range(0, 150, 5):
+        abs=[]
-        abs.append(i)
+        
-        abs.append(i+5)
+        for i in range(0, 150, 5):
-    abs.append(150)
+            abs.append(i)
-    abs.append(300)
+            abs.append(i+5)
-    print(new)
+        abs.append(150)
-    print(abs)
+        abs.append(300)
-
+
-    x=abs
+        x=abs
-    y=new
+        y=new
-    x=np.array(x)
+        x=np.array(x)
-    y=np.array(y)
+        y=np.array(y)
-    plt.plot(x, y)
+        plt.plot(x, y)
-    plt.xlabel('Distance')
+        plt.xlabel('Distance')
-    plt.ylabel("- ln(Pobs/Pref)")
+        plt.ylabel("- ln(Pobs/Pref)")
-    plt.title(f'Statistical potential of {pair} distance ({method} method)')
+        plt.title(f'Statistical potential of {pair} distance ({method} method)')
-    plt.savefig(f"/home/atabot/RNANet/results/statistical_potential/all-atoms/{method}_statistical_pot_{pair}.png")
+        plt.savefig(runDir + f"/results/statistical_potential/figures/all-atoms/{method}_method/{method}_statistical_pot_{pair}.png")
-    plt.close()
+        plt.close()
+
+    setproctitle(f"RNANet statistics.py stat_potential({method}) finished")
-# mettre en option le choix de la méthode?
 if __name__ == "__main__":
-    os.makedirs(runDir + '/results/statistical_potential/all-atoms/', exist_ok=True)
-    # compute_ratio_from_csv('/home/atabot/RNANet/results/geometry/all-atoms/distances_classes/occur_dist_classes.csv', 'avg_ratio_pobs_pref.csv', 'qch_ratio_pobs_pref.csv')
-    # exit(1)
-    with sqlite3.connect(runDir + '/results/Stats.db') as conn:
-        sql_new_table(conn)
-    save_into_database()
-    exit(1)
-
-    # count_occur_atom_dist(runDir + '/results/geometry/all-atoms/distances_classes/', 'occur_dist_classes.csv')
-    # os.makedirs(runDir + '/results/figures/all-atoms/distances/hist/', exist_ok=True)
-    # histo_occur(runDir + '/results/geometry/all-atoms/distances_classes/occur_dist_classes.csv')
-    # exit(1)
-    mole_fraction(runDir + '/results/geometry/all-atoms/atom_count/', 'atom_count.csv')
-    exit(1)
-    # print(measure_from_structure(os.listdir(path_to_3D_data + "rna_only")[0]))
-    if n_unmapped_chains:
-    #     os.makedirs(runDir+"/results/geometry/all-atoms/distances/", exist_ok=True)
-        os.makedirs(runDir+"/results/geometry/all-atoms/distances_classes/", exist_ok=True)
-        os.makedirs(runDir+"/results/geometry/all-atoms/atom_count/", exist_ok=True)
-    #    liste_struct = os.listdir(path_to_3D_data + "rna_only")
-        liste_struct=liste_repres('/home/data/RNA/3D/latest_nr_list_4.0A.csv')[:100]
-        # measure_from_structure(liste_struct[0])
-        # exit(1)
-        #measure_from_structure('5e81_1_2K.cif')
-        #exit(1)
-    # concat_dataframes(runDir + '/results/geometry/Pyle/distances/', 'distances.csv')
\ No newline at end of file
+    print("This file is not supposed to be run directly. Run statistics.py instead.")
--- a/statistics.py
View file @e184384
+++ b/statistics.py
View file @e184384
@@ -38,6 +38,7 @@ LSU_set = ("RF00002", "RF02540", "RF02541", "RF02543", "RF02546")   # From Rfam 
 SSU_set = ("RF00177", "RF02542",  "RF02545", "RF01959", "RF01960")  # From Rfam CLAN 00111
 from geometric_stats import *   # after definition of the variables
+from statistical_potential import *
 @trace_unhandled_exceptions
 def reproduce_wadley_results(carbon=4, show=False, sd_range=(1,4), res=2.0):
@@ -1181,13 +1182,16 @@ def measure_from_structure(f):
         s = parser.get_structure(f, os.path.abspath(path_to_3D_data+ "rna_only/" + f))
     #pyle_measures(name, s, thr_idx)
-    measures_aa(name, s, thr_idx)
+    # measures_aa(name, s, thr_idx)
     if DO_HIRE_RNA_MEASURES:
         measures_hrna(name, s, thr_idx)
         measures_hrna_basepairs(name, s, path_to_3D_data, thr_idx)
     if DO_WADLEY_ANALYSIS:
         measures_pyle(name, s, thr_idx)
-    
+    if DO_STAT_POTENTIAL_MEASURES:
+        # measures_heavy_atoms(name, s, thr_idx)
+        if DO_WADLEY_ANALYSIS:
+            pyle_measures_for_potentials(name, s, thr_idx)
     idxQueue.put(thr_idx) # replace the thread index in the queue
     setproctitle(f"RNANet statistics.py Worker {thr_idx+1} finished")
@@ -1335,10 +1339,11 @@ if __name__ == "__main__":
     REDUNDANT_DIST_MAT = True
     DO_HIRE_RNA_MEASURES = False
     RESCAN_GMM_COMP_NUM = False
+    DO_STAT_POTENTIAL_MEASURES = False
     try:
         opts, _ = getopt.getopt( sys.argv[1:], "r:h", 
                     [ "help", "from-scratch", "wadley", "distance-matrices", "non-redundant", "resolution=", 
-                      "3d-folder=", "seq-folder=", "hire-rna", "rescan-nmodes" ])
+                      "3d-folder=", "seq-folder=", "hire-rna", "rescan-nmodes", "stat-potential" ])
     except getopt.GetoptError as err:
         print(err)
         sys.exit(2)
@@ -1364,6 +1369,7 @@ if __name__ == "__main__":
             print("--wadley\t\t\tReproduce Wadley & al 2007 clustering of pseudotorsions.")
             print("--hire-rna\t\t\tCompute distances between atoms and torsion angles for HiRE-RNA model,\n\t\t\t\t  and plot GMMs on the data.")
             print("--rescan-nmodes\t\t\tDo not assume the number of modes in distances and angles distributions, measure it.")
+            print("--stat-potential\t\t\tCompute statistical potentials based on averaging and quasi-chemical approximation methods.")
             sys.exit()
         elif opt == "--version":
             print("RNANet statistics 1.6 beta")
@@ -1407,7 +1413,14 @@ if __name__ == "__main__":
             RESCAN_GMM_COMP_NUM = True
         elif opt == "--non-redundant":
             REDUNDANT_DIST_MAT = False
-
+        elif opt == "--stat-potential":
+            DO_STAT_POTENTIAL_MEASURES = True
+            os.makedirs(runDir + "/results/geometry/Pyle/distances_i_i+1/", exist_ok=True)
+            os.makedirs(runDir + "/results/geometry/all-atoms/distances_classes/", exist_ok=True)
+            os.makedirs(runDir + "/results/geometry/all-atoms/atom_count/", exist_ok=True)
+            os.makedirs(runDir + "/results/statistical_potential/ratio/Pyle/", exist_ok=True)
+            os.makedirs(runDir + "/results/statistical_potential/ratio/all-atoms/", exist_ok=True)
+            os.makedirs(runDir + "/results/statistical_potential/figures/all-atoms/", exist_ok=True)
     # Load mappings. famlist will contain only families with structures at this resolution threshold.
     print("Loading mappings list...")
@@ -1420,19 +1433,19 @@ if __name__ == "__main__":
                                     WHERE issue = 0 AND resolution <= {res_thr} AND rfam_acc != 'unmappd'
                                     GROUP BY rfam_acc;
                                 """, conn)
-    families.drop(families[families.n_chains == 0].index, inplace=True)
+    # families.drop(families[families.n_chains == 0].index, inplace=True)
-    mappings_list = {}
+    # mappings_list = {}
-    for k in families.rfam_acc:
+    # for k in families.rfam_acc:
-        mappings_list[k] = [ x[0] for x in sql_ask_database(conn,  f"""SELECT chain_id 
+    #     mappings_list[k] = [ x[0] for x in sql_ask_database(conn,  f"""SELECT chain_id 
-                                                                        FROM chain JOIN structure ON chain.structure_id=structure.pdb_id 
+    #                                                                     FROM chain JOIN structure ON chain.structure_id=structure.pdb_id 
-                                                                        WHERE rfam_acc='{k}' AND issue=0 AND resolution <= {res_thr};""") ]
+    #                                                                     WHERE rfam_acc='{k}' AND issue=0 AND resolution <= {res_thr};""") ]
-    famlist = families.rfam_acc.tolist()
+    # famlist = families.rfam_acc.tolist()
-    ignored = families[families.n_chains < 3].rfam_acc.tolist()
+    # ignored = families[families.n_chains < 3].rfam_acc.tolist()
-    famlist.sort(key=family_order)
+    # famlist.sort(key=family_order)
-
+
-    print(f"Found {len(famlist)} families with chains or better.")
+    # print(f"Found {len(famlist)} families with chains or better.")
-    if len(ignored):
+    # if len(ignored):
-        print(f"Idty matrices: Ignoring {len(ignored)} families with only one chain:", " ".join(ignored)+'\n')
+        # print(f"Idty matrices: Ignoring {len(ignored)} families with only one chain:", " ".join(ignored)+'\n')
     if DELETE_OLD_DATA:
         for f in famlist:
@@ -1456,9 +1469,9 @@ if __name__ == "__main__":
     joblist = []
     # Do eta/theta plots
-    if n_unmapped_chains and DO_WADLEY_ANALYSIS:    
+    # if n_unmapped_chains and DO_WADLEY_ANALYSIS:    
-       joblist.append(Job(function=reproduce_wadley_results, args=(1, False, (1,4), res_thr)))
+    #    joblist.append(Job(function=reproduce_wadley_results, args=(1, False, (1,4), res_thr)))
-       joblist.append(Job(function=reproduce_wadley_results, args=(4, False, (1,4), res_thr)))
+    #    joblist.append(Job(function=reproduce_wadley_results, args=(4, False, (1,4), res_thr)))
     # Do distance matrices for each family excl. LSU/SSU (will be processed later)
     if DO_AVG_DISTANCE_MATRIX:  
@@ -1474,23 +1487,23 @@ if __name__ == "__main__":
             joblist.append(Job(function=get_avg_std_distance_matrix, args=(f, res_thr, False, REDUNDANT_DIST_MAT, False)))
     # Do general family statistics
-    joblist.append(Job(function=stats_len)) # Computes figures about chain lengths
+    # joblist.append(Job(function=stats_len)) # Computes figures about chain lengths
-    joblist.append(Job(function=stats_freq)) # updates the database (nucleotide frequencies in families)
+    # joblist.append(Job(function=stats_freq)) # updates the database (nucleotide frequencies in families)
-    for f in famlist:
+    # for f in famlist:
-        joblist.append(Job(function=parallel_stats_pairs, args=(f,))) # updates the database (intra-chain basepair types within a family)
+    #     joblist.append(Job(function=parallel_stats_pairs, args=(f,))) # updates the database (intra-chain basepair types within a family)
-        if f not in ignored:
+    #     if f not in ignored:
-            joblist.append(Job(function=to_id_matrix, args=(f,))) # updates the database (identity matrices of families)
+            # joblist.append(Job(function=to_id_matrix, args=(f,))) # updates the database (identity matrices of families)
     # Do geometric measures
     if n_unmapped_chains:
         os.makedirs(runDir + "/results/geometry/all-atoms/distances/", exist_ok=True)
         structure_list = representatives_from_nrlist(res_thr)
-        for f in structure_list:
+        for f in structure_list[:10]:
             if path.isfile(path_to_3D_data + "datapoints/" + f.split('.')[0]):
                 joblist.append(Job(function=measure_from_structure, args=(f,), how_many_in_parallel=nworkers))   # All-atom distances
-    process_jobs(joblist)
+    # process_jobs(joblist)
     # Now process the memory-heavy tasks family by family
     if DO_AVG_DISTANCE_MATRIX:
@@ -1511,31 +1524,55 @@ if __name__ == "__main__":
     # finish the work after the parallel portions
-    per_chain_stats()   # per chain base frequencies and basepair types
+    # per_chain_stats()   # per chain base frequencies and basepair types
-    seq_idty()          # identity matrices from pre-computed .npy matrices
+    # seq_idty()          # identity matrices from pre-computed .npy matrices
-    stats_pairs()
+    # stats_pairs()
     if n_unmapped_chains:
-        general_stats()
+        # general_stats()
         os.makedirs(runDir+"/results/figures/GMM/", exist_ok=True)
         os.makedirs(runDir+"/results/geometry/json/", exist_ok=True)
-        concat_dataframes(runDir + '/results/geometry/all-atoms/distances/', 'dist_atoms.csv', nworkers)
+        # concat_dataframes(runDir + '/results/geometry/all-atoms/distances/', 'dist_atoms.csv', nworkers)
         if DO_HIRE_RNA_MEASURES:
             concat_dataframes(runDir + '/results/geometry/HiRE-RNA/distances/', 'distances_HiRERNA.csv', nworkers)
             concat_dataframes(runDir + '/results/geometry/HiRE-RNA/angles/', 'angles_HiRERNA.csv', nworkers)
             concat_dataframes(runDir + '/results/geometry/HiRE-RNA/torsions/', 'torsions_HiRERNA.csv', nworkers)
             concat_dataframes(runDir + '/results/geometry/HiRE-RNA/basepairs/', 'basepairs_HiRERNA.csv', nworkers)
-        if DO_WADLEY_ANALYSIS:
+        # if DO_WADLEY_ANALYSIS:
-            concat_dataframes(runDir + '/results/geometry/Pyle/distances/', 'distances_pyle.csv', nworkers)
+        #     concat_dataframes(runDir + '/results/geometry/Pyle/distances/', 'distances_pyle.csv', nworkers)
-            concat_dataframes(runDir + '/results/geometry/Pyle/angles/', 'flat_angles_pyle.csv', nworkers)
+        #     concat_dataframes(runDir + '/results/geometry/Pyle/angles/', 'flat_angles_pyle.csv', nworkers)
+        # if DO_STAT_POTENTIAL_MEASURES:
+            # with sqlite3.connect(runDir + '/results/Stat_potential.db') as conn:
+            #     sql_new_table(conn)
+            # joblist=[]
+            # joblist.append(Job(function=count_occur_atom_dist, args=(runDir + '/results/geometry/all-atoms/distances_classes/', 'occur_dist_classes.csv')))
+            # joblist.append(Job(function=mole_fraction, args=(runDir + '/results/geometry/all-atoms/atom_count/', 'atom_count.csv')))
+            # process_jobs(joblist)
+            # compute_ratio_from_csv(runDir + '/results/geometry/all-atoms/distances_classes/occur_dist_classes.csv', 'avg_ratio_pobs_pref.csv', 'qch_ratio_pobs_pref.csv')
+            # if DO_WADLEY_ANALYSIS:
+            #     concat_dataframes(runDir + '/results/geometry/Pyle/distances_i_i+1/', 'distances.csv', nworkers)
         joblist = []
-        joblist.append(Job(function=gmm_aa_dists, args=(RESCAN_GMM_COMP_NUM,)))
+        # joblist.append(Job(function=gmm_aa_dists, args=(RESCAN_GMM_COMP_NUM,)))
-        joblist.append(Job(function=gmm_aa_torsions, args=(RESCAN_GMM_COMP_NUM, res_thr)))
+        # joblist.append(Job(function=gmm_aa_torsions, args=(RESCAN_GMM_COMP_NUM, res_thr)))
         if DO_HIRE_RNA_MEASURES:
             joblist.append(Job(function=gmm_hrna, args=(RESCAN_GMM_COMP_NUM,)))
             joblist.append(Job(function=gmm_hrna_basepairs, args=(RESCAN_GMM_COMP_NUM,)))
-        if DO_WADLEY_ANALYSIS:
+        # if DO_WADLEY_ANALYSIS:
-            joblist.append(Job(function=gmm_pyle, args=(RESCAN_GMM_COMP_NUM, res_thr)))
+        #     joblist.append(Job(function=gmm_pyle, args=(RESCAN_GMM_COMP_NUM, res_thr)))
-        process_jobs(joblist)
+            
-        merge_jsons(DO_HIRE_RNA_MEASURES)
+        if DO_STAT_POTENTIAL_MEASURES:
+            methods = ['avg', 'qch']
+            os.makedirs(runDir + "/results/statistical_potential/figures/all-atoms/avg_method/", exist_ok=True)
+            os.makedirs(runDir + "/results/statistical_potential/figures/all-atoms/qch_method/", exist_ok=True)
+            # save_into_database()
+            # for method in methods:
+            #     joblist.append(Job(function=stat_potential, args=(runDir + '/results/statistical_potential/ratio/all-atoms/' + method + '_ratio_pobs_pref.csv', method)))
+            if DO_WADLEY_ANALYSIS:
+                os.makedirs(runDir + "/results/statistical_potential/figures/Pyle/", exist_ok=True)
+                os.makedirs(runDir + "/results/statistical_potential/json/Pyle/", exist_ok=True)
+                # joblist.append(Job(function=gmm_pyle_per_type, args=(RESCAN_GMM_COMP_NUM,)))
+                # gmm_pyle_per_type(RESCAN_GMM_COMP_NUM)
+                stat_potential_pyle()
+        # process_jobs(joblist)
+        # merge_jsons(DO_HIRE_RNA_MEASURES)