# -*- coding: utf-8 -*-
# callCodeML
# Verson: 2.0
# Date: 2021.11.15
# This is used to call Codeml to calculate the positive selection of gene in Branch-Sites Model.(Require codon sequence)
# Usage: python3 callCodeml.py seqDir treeFile
# Refactoring code and running logic to support multiprocess
import re
import sys
import os
from scipy.stats import chi2
import time
def help_info():
print("This script is used to call codeML.\nUsage: python3 callCodeml.py Dir treeFile\n")
def getArgs():
global workDir
global tree_file
global dir_path
start_time = time.strftime('%Y%m%d-%H%M%S') # to keep the working dircitory name
workDir = f"{os.getcwd()}/WorkingDir_{start_time}"
args = sys.argv[1:]
if len(args) == 0:
help_info()
if os.path.isdir(args[0]) is True:
dir_path = os.path.abspath(args[0]) # path of seqences
seqs = os.listdir(dir_path)
seqs = [x for x in seqs if not str(x).startswith('.') ] # remove hided files
tree_file = os.path.abspath(args[1])
print(f"The drictory is: {dir_path}\nThe treeFile is: {tree_file}")
#os.chdir(os.path.abspath(args[0]))
return (dir_path, seqs, tree_file)
else:
help_info()
def create_dir(name):
try:
os.mkdir(f'{workDir}/')
except:pass
try:
os.mkdir(f'{workDir}/{name}')
except:pass
try:
os.mkdir(f'{workDir}/{name}/null')
os.mkdir(f'{workDir}/{name}/alte')
except:pass
def creat_ctl(name, tree_file):
ctl_null = f'''
seqfile = {dir_path}/{name}
treefile = {tree_file}
outfile = {workDir}/{name}/null/{name}_null.res
noisy = 9
verbose = 0
runmode = 0
seqtype = 1
CodonFreq = 2
clock = 0
aaDist = 0
model = 0
NSsites = 0
icode = 0
Mgene = 0
fix_kappa = 0
kappa = 2
fix_omega = 0
omega = 1
fix_alpha = 1
alpha = .0
Malpha = 0
ncatG = 3
getSE = 0
RateAncestor = 0
fix_blength = 0
method = 0
Small_Diff = .45e-6
cleandata = 1
'''
ctl_alte = ctl_null.replace(f'{workDir}/{name}/null/{name}_null.res', f'{workDir}/{name}/alte/{name}_alte.res')\
.replace('model = 0', 'model = 2')
with open(f'{workDir}/{name}/null/null_profile.ctl', 'w') as f:
f.write(ctl_null)
with open(f'{workDir}/{name}/alte/alte_profile.ctl', 'w') as f:
f.write(ctl_alte)
def run_create(dir_path, seqs, tree_file):
for i in (seqs):
name= i.split('/')[-1]
create_dir(name)
creat_ctl(name, tree_file)
with open(f'{workDir}/codeml.sh', 'w') as f:
f.write('''
#!/bin/bash
list=`ls -1 |grep OG`
count=`ls -1 |grep OG|wc|awk '{print $1}'`
echo "Total number: $count"
dir=`pwd`
echo "Start Now..."
for i in $list
do
{
cd $dir/$i/null
codeml ./null_profile.ctl >log.txt
cd $dir/$i/alte
codeml ./alte_profile.ctl >log.txt
#echo "Finished $i..."
}&
done
wait
''')
print(f"{time.strftime('%Y-%m-%d %H:%M:%S')} Files created.\n")
def run_codeml():
os.chdir(workDir)
os.system('bash codeml.sh')
print(f"\n{time.strftime('%Y-%m-%d %H:%M:%S')} Codeml Done...\n")
def run_stat(name):
def get_res(path):
with open(path, "r") as f:
t = f.read()
kappa = re.findall(r"kappa.+", t)[0].split(' ')[-1].replace('\n', '')
ls = re.findall(r'lnL.+', t)[0].split(' ')
ls=[x for x in ls if x!='']
lnL = ls[4]
np = ls[3].replace("):","")
return([lnL, np, kappa])
path1 = f'{workDir}/{name}/alte/{name}_alte.res'
path2 = f'{workDir}/{name}/null/{name}_null.res'
try:
res_alte = get_res(path1)
res_null = get_res(path2)
lnL0 = float(res_null[0])
lnL1 = float(res_alte[0])
np0 = int(res_null[1])
np1 = int(res_alte[1])
kappa = float(res_alte[2])
lnl = abs(lnL0 - lnL1 )*2
np = abs(np0 - np1)
pvalue = 1 - chi2.cdf(lnl, np)
#if pvalue <= 0.05:
with open(f'{workDir}/result.tsv', 'a') as f:
f.write(f"{name}\t{lnL0}\t{lnL1}\t{np0}\t{np1}\t{kappa}\t{pvalue}\n")
except:
print(f"{time.strftime('%Y-%m-%d %H:%M:%S')} {name} failed to stats.")
def main():
arges = getArgs()
run_create(arges[0], arges[1], arges[2])
run_codeml()
for i in os.listdir(workDir):
run_stat(i)
if __name__ == "__main__":
t0 = time.time()
main()
print(f'Total time used: {time.time() - t0} S\n')
