Isaure_benchmark.py
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import time
import subprocess
import os
import os.path
from math import sqrt, ceil
import numpy as np
import matplotlib.pyplot as plt
log_path = "test.log"
log = open(log_path, 'a')
def run_test(cmd, log):
log.write(time.asctime(time.localtime(time.time())) + " : Run process \"" + cmd + "\"\n")
log.flush()
process = subprocess.Popen(cmd.split(' ') ,shell=False,stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
# Poll process.stdout to show stdout live
while process.poll() is None:
output = process.stdout.readline()
if output:
log.write(output.decode())
log.flush()
rc = process.poll()
def create_command(name):
#cmd = ("python3 /mnt/c/Users/natha/Documents/IBISC/biorseo2/biorseo/biorseo.py -i " +
cmd = ("python3 /local/local/BiorseoNath/biorseo.py -i " +
"/local/local/BiorseoNath/data/fasta/" +
name + ".fa " +
"-O results/ " +
"--contacts " +
"--patternmatch " +
"--func F --MFE -v " +
"--biorseo-dir /local/local/BiorseoNath " +
"--modules-path /local/local/BiorseoNath/data/modules/ISAURE/Motifs_derniere_version ")
return cmd
# ================== Code from Louis Beckey Benchark.py ==============================
def dbn_to_basepairs(structure):
parenthesis = []
brackets = []
braces = []
rafters = []
basepairs = []
As = []
Bs = []
for i, c in enumerate(structure):
if c == '(':
parenthesis.append(i)
if c == '[':
brackets.append(i)
if c == '{':
braces.append(i)
if c == '<':
rafters.append(i)
if c == 'A':
As.append(i)
if c == 'B':
Bs.append(i)
if c == '.':
continue
if c == ')':
basepairs.append((i, parenthesis.pop()))
if c == ']':
basepairs.append((i, brackets.pop()))
if c == '}':
basepairs.append((i, braces.pop()))
if c == '>':
basepairs.append((i, rafters.pop()))
if c == 'a':
basepairs.append((i, As.pop()))
if c == 'b':
basepairs.append((i, Bs.pop()))
return basepairs
def compare_two_contacts(true_ctc, prediction):
tp = 0
fp = 0
tn = 0
fn = 0
for i in range(len(true_ctc)):
if true_ctc[i] == '*' and prediction[i] == '*':
tp += 1
elif true_ctc[i] == '.' and prediction[i] == '.':
tn += 1
elif true_ctc[i] == '.' and prediction[i] == '*':
fp += 1
elif true_ctc[i] == '*' and prediction[i] == '.':
fn += 1
"""if ((tp + fp) * (tp + fn) * (tn + fp) * (tn + fn) == 0):
print(str(tp) + " " + str(tn) + " " + str(fp) + " " + str(fn) + "\n")
print(true_ctc)
print(prediction)"""
return [tp, tn, fp, fn]
def compare_two_structures(true2d, prediction):
true_basepairs = dbn_to_basepairs(true2d)
pred_basepairs = dbn_to_basepairs(prediction)
tp = 0
fp = 0
tn = 0
fn = 0
for bp in true_basepairs:
if bp in pred_basepairs:
tp += 1
else:
fn += 1
for bp in pred_basepairs:
if bp not in true_basepairs:
fp += 1
tn = len(true2d) * (len(true2d) - 1) * 0.5 - fp - fn - tp
return [tp, tn, fp, fn]
def mattews_corr_coeff(tp, tn, fp, fn):
if ((tp + fp) * (tp + fn) * (tn + fp) * (tn + fn) == 0):
print("warning: division by zero! no contact in the prediction")
#print("tp: " + str(tp) + " fp: " + str(fp) + " tn: " + str(tn) + " fn: " + str(fn))
return -1
elif (tp + fp == 0):
print("We have an issue : no positives detected ! (linear structure)")
return (tp * tn - fp * fn) / sqrt((tp + fp) * (tp + fn) * (tn + fp) * (tn + fn))
def f1_score(tp, tn, fp, fn):
return 2 * tp / (2 * tp + fp + fn)
def specificity(tp, tn, fp, fn):
return tn / (tn + fp)
# ================== Code from Louis Beckey Benchark.py ==============================
def write_mcc_in_file_E(sequence_id, true_contacts, true_structure):
read_prd = open("results/test_" + sequence_id + ".json_pmE_MEA", "r")
write = open("results/test_" + sequence_id + ".mcc_E_MEA", "w")
max_mcc_str = -1;
max_mcc_ctc = -1;
title_exp = ">test_" + sequence_id + ": "
write.write(title_exp)
contacts_exp = true_contacts
structure_exp = true_structure
write.write("structure 2d attendue:\n" + structure_exp + "\n")
write.write("contacts attendus:\n" + contacts_exp + "\n" + len(structure_exp) * "-")
title_prd = read_prd.readline()
structure_prd = read_prd.readline()
sequence_prd = structure_prd
while structure_prd:
structure_prd = read_prd.readline()
if (len(structure_prd) != 0):
write.write("\nstructure 2d predite:\n" + structure_prd[:len(sequence_prd)] + "\n")
mcc_tab = compare_two_structures(structure_exp, structure_prd[:len(sequence_prd)])
mcc_str = mattews_corr_coeff(mcc_tab[0], mcc_tab[1], mcc_tab[2], mcc_tab[3])
if (max_mcc_str < mcc_str):
max_mcc_str = mcc_str
write.write("mcc: " + str(mcc_str) + "\n")
contacts_prd = read_prd.readline()
write.write("\ncontacts predits:\n" + contacts_prd)
if (len(contacts_prd) == len(contacts_exp)):
mcc_tab = compare_two_contacts(contacts_exp, contacts_prd)
mcc_ctc = mattews_corr_coeff(mcc_tab[0], mcc_tab[1], mcc_tab[2], mcc_tab[3])
if (max_mcc_ctc < mcc_ctc):
max_mcc_ctc = mcc_ctc
write.write("mcc: " + str(mcc_ctc) + "\n\n")
else:
write.write("mcc: no expected contacts sequence or not same length between expected and predicted\n\n")
write.write("max mcc 2D:" + str(max_mcc_str))
write.write("max mcc ctc:" + str(max_mcc_ctc))
read_prd.close()
write.close()
return [max_mcc_ctc, max_mcc_str]
def write_mcc_in_file_F(sequence_id, true_contacts, true_structure):
read_prd = open("results/test_" + sequence_id + ".json_pmF_MFE", "r")
write = open("results/test_" + sequence_id + ".mcc_F_MFE", "w")
max_mcc_str = -1;
max_mcc_ctc = -1;
title_exp = ">test_" + sequence_id + ": "
write.write(title_exp)
contacts_exp = true_contacts
structure_exp = true_structure
write.write("structure 2d attendue:\n" + structure_exp + "\n")
write.write("contacts attendus:\n" + contacts_exp + "\n" + len(structure_exp) * "-")
title_prd = read_prd.readline()
structure_prd = read_prd.readline()
sequence_prd = structure_prd
while structure_prd:
structure_prd = read_prd.readline()
if (len(structure_prd) != 0):
write.write("\nstructure 2d predite:\n" + structure_prd[:len(sequence_prd)] + "\n")
mcc_tab = compare_two_structures(structure_exp, structure_prd[:len(sequence_prd)])
mcc_str = mattews_corr_coeff(mcc_tab[0], mcc_tab[1], mcc_tab[2], mcc_tab[3])
if (max_mcc_str < mcc_str):
max_mcc_str = mcc_str
write.write("mcc: " + str(mcc_str) + "\n")
contacts_prd = read_prd.readline()
write.write("\ncontacts predits:\n" + contacts_prd)
if (len(contacts_prd) == len(contacts_exp)):
mcc_tab = compare_two_contacts(contacts_exp, contacts_prd)
mcc_ctc = mattews_corr_coeff(mcc_tab[0], mcc_tab[1], mcc_tab[2], mcc_tab[3])
if (max_mcc_ctc < mcc_ctc):
max_mcc_ctc = mcc_ctc
write.write("mcc: " + str(mcc_ctc) + "\n\n")
else:
write.write("mcc: no expected contacts sequence or not same length between expected and predicted\n\n")
write.write("max mcc 2D:" + str(max_mcc_str))
write.write("max mcc ctc:" + str(max_mcc_ctc))
read_prd.close()
write.close()
return [max_mcc_ctc, max_mcc_str]
def set_axis_style(ax, labels):
ax.xaxis.set_tick_params(direction='out')
ax.xaxis.set_ticks_position('bottom')
ax.set_xticks(np.arange(1, len(labels) + 1))
ax.set_xticklabels(labels)
ax.set_xlim(0.25, len(labels) + 0.75)
ax.set_xlabel('Sample name')
def visualization(list_struct2d, list_contacts, function, color, lines_color):
np_struct2d = np.array(list_struct2d)
np_contacts = np.array(list_contacts)
data_to_plot = [np_struct2d, np_contacts]
fig = plt.figure()
ax = fig.add_axes([0, 0, 1, 1])
labels = ['structure 2D', 'contacts']
ax.set_xticks(np.arange(1, len(labels) + 1))
ax.set_xticklabels(labels)
ax.set_xlabel(function)
ax.set_ylabel('MCC')
violins = ax.violinplot(data_to_plot, showmedians=True)
for partname in ('cbars', 'cmins', 'cmaxes', 'cmedians'):
vp = violins[partname]
vp.set_edgecolor(lines_color)
vp.set_linewidth(1)
for v in violins['bodies']:
v.set_facecolor(color)
plt.savefig('visualisation' + function + '.png', bbox_inches='tight')
#cmd = ("cppsrc/Scripts/create")
#cmd0 = ("cppsrc/Scripts/addDelimiter")
#cmd1 = ("cppsrc/Scripts/countPattern")
#cmd2 = ("cppsrc/Scripts/deletePdb")
myfile = open("data/modules/ISAURE/Motifs_version_initiale/benchmark.txt", "r")
name = myfile.readline()
contacts = myfile.readline()
seq = myfile.readline()
structure2d = myfile.readline()
list_struct2d_E = []
list_contacts_E = []
list_struct2d_F = []
list_contacts_F = []
count = 0
while seq:
name = name[6:].strip()
print(name)
"""
run_test(cmd2 + " " + name + ".fa", log)
print(cmd2 + " " + name + ".fa")
"""
cmd3 = create_command(name)
os.system(cmd3)
"""file_path = "results/test_" + name + ".json_pmE_MEA"
if os.path.isfile(file_path):
tabE = write_mcc_in_file_E(name, contacts, structure2d)
list_contacts_E.append(tabE[0])
list_struct2d_E.append(tabE[1])"""
file_path = "results/test_" + name + ".json_pmF_MFE"
if os.path.isfile(file_path):
tabF = write_mcc_in_file_F(name, contacts, structure2d)
list_contacts_F.append(tabF[0])
list_struct2d_F.append(tabF[1])
count = count + 1
name = myfile.readline()
contacts = myfile.readline()
seq = myfile.readline()
structure2d = myfile.readline()
"""visualization(list_struct2d_E, list_contacts_E, 'E', 'red', '#900C3F')"""
visualization(list_struct2d_F, list_contacts_F, 'F', 'blue', '#0900FF')
print("count: " + str(count) + "\n")
myfile.close()