#!/usr/bin/python

from __future__ import division
from Bio.Phylo.PAML import codeml
import sys
import os
import shutil
import time
from math import sqrt
from rpy2 import robjects

r = robjects.r
len = len(glob.glob1(".","*.out"))

def compare_models(m1_lnl, m2_lnl, df):
    likelihood = 2*(abs(m2_lnl-m1_lnl))
    p = 1 - robjects.r.pchisq(likelihood, df)[0]
    return p


results = codeml.read(sys.argv[1])
nssites = results.get("NSsites")
m1 = nssites.get(1)
m1_lnl = m1.get("lnL")
nssites = results.get("NSsites")
m2 = nssites.get(2)
m2_lnl = m2.get("lnL")
nssites = results.get("NSsites")
m7 = nssites.get(7)
m7_lnl = m7.get("lnL")
nssites = results.get("NSsites")
m8 = nssites.get(8)
m8_lnl = m8.get("lnL")
m2_p_pos = compare_models(m1_lnl,m2_lnl,2)
m8_p_pos = compare_models(m7_lnl,m8_lnl,2)

r.assign('m2_p_pos', m2_p_pos)
r.assign('m8_p_pos', m8_p_pos)
r.assign('len', len)


paM2 = robjects.r('p.adjust(m2_p_pos, "BH", len)')
paM8 = robjects.r('p.adjust(m8_p_pos, "BH", len)')


print 'M1vM2_pajust-value {} {}'.format(sys.argv[1], paM2[0])
print 'M7vM8_pajust-value {} {}'.format(sys.argv[1], paM8[0])


#!/usr/bin/python

from __future__ import division
from Bio.Phylo.PAML import codeml
import sys
import os
import shutil
import time
import glob
from math import sqrt
from rpy2 import robjects

r = robjects.r
len = len(glob.glob1(".","*.out"))

def compare_models(m1_lnl, m2_lnl, df):
    likelihood = 2*(abs(m2_lnl-m1_lnl))
    p = 1 - robjects.r.pchisq(likelihood, df)[0]
    return p


results = codeml.read(sys.argv[1])
nssites = results.get("NSsites")
m1 = nssites.get(1)
m1_lnl = m1.get("lnL")
nssites = results.get("NSsites")
m2 = nssites.get(2)
m2_lnl = m2.get("lnL")
nssites = results.get("NSsites")
m7 = nssites.get(7)
m7_lnl = m7.get("lnL")
nssites = results.get("NSsites")
m8 = nssites.get(8)
m8_lnl = m8.get("lnL")
m2_p_pos = compare_models(m1_lnl,m2_lnl,2)
m8_p_pos = compare_models(m7_lnl,m8_lnl,2)

r.assign('m2_p_pos', m2_p_pos)
r.assign('m8_p_pos', m8_p_pos)
r.assign('len', len)


paM2 = robjects.r('p.adjust(m2_p_pos, "BH", len)')
paM8 = robjects.r('p.adjust(m8_p_pos, "BH", len)')


print 'M1vM2_pajust-value {} {}'.format(sys.argv[1], paM2[0])
print 'M7vM8_pajust-value {} {}'.format(sys.argv[1], paM8[0])


Update autoPAMLresults.py