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Commit fcd3b21b by Mustafa Tekpinar
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Removed gemmeAnal.py. Not needed anymore.

parent 8f6e1b64
Showing with 4 additions and 275 deletions
gemmeAnal.py deleted 100644 → 0
# -*- coding: utf-8 -*-
# Copyright (c) 2018-2022: Elodie Laine - Mustafa Tekpinar
# This code is part of the gemme package and governed by its license.
# Please see the LICENSE.txt file included as part of this package.
import sys
import os
import argparse
import re
import math
import subprocess
import shutil
import glob
import pandas as pd
import numpy as np
# Moved to sgemme.py
# def extractQuerySeq(filename):
# """
# # Extract the query sequence from the input alignment
# """
# fIN = open(filename,"r")
# lines = fIN.readlines()
# fIN.close()
# if lines[0][0]!=">":
# raise Exception('bad FASTA format')
# else:
# prot = re.compile("[^A-Z0-9a-z]").split(lines[0][1:])[0]
# fOUT = open(prot+".fasta","w")
# fOUT.write(">"+prot+"\n")
# seq=""
# i = 1
# while lines[i][0]!=">":
# seq = seq + lines[i].strip().strip(".").strip("-")
# fOUT.write(lines[i])
# i = i + 1
# fOUT.close()
# return prot,seq,i-1
# def getNbSeq(filename):
# #TODO: Remove bash dependency and count the sequences within Python!
# """
# # Get the number of sequences in a multi-fasta file
# """
# if filename!='':
# proc=subprocess.Popen("grep -c '^>' "+filename,stdout=subprocess.PIPE,shell=True)
# return int(proc.stdout.read())
# else:
# return 0
# def createPDB(prot,seq):
# """
# If there is not a real PDB file for a given sequence,
# create a fake PDB containing only dummy CA atoms.
# """
# d = {'C': 'CYS', 'D': 'ASP', 'S': 'SER', 'Q': 'GLN', 'K': 'LYS',
# 'I': 'ILE', 'P': 'PRO', 'T': 'THR', 'F': 'PHE', 'N': 'ASN',
# 'G': 'GLY', 'H': 'HIS', 'L': 'LEU', 'R': 'ARG', 'W': 'TRP',
# 'A': 'ALA', 'V': 'VAL', 'E': 'GLU', 'Y': 'TYR', 'M': 'MET'}
# fOUT = open(prot+'.pdb','w')
# i = 1
# for let in seq:
# if(let != '-'):
# fOUT.write('ATOM%7d CA %s A%4d 43.524 70.381 46.465 1.00 0.0\n'%(i,d[let.upper()],i))
# i += 1
# fOUT.close()
# def editConfJET(N):
# """
# # Edit JET configuration file with correct number of Seqs & MSA
# """
# reCode=subprocess.call("sed -i 's/results\t\t5000/results\t\t"+str(N)+"/' default.conf",shell=True)
# return(reCode)
# def minMaxNormalization(data):
# """
# Min-max normalization of a data array.
# """
# return (data - np.min(data)) / (np.max(data) - np.min(data))
# # Run JET to compute TJET values
# def launchJET(prot, retMet, bFile, fFile, pdbfile, chains, n, N, nl):
# """
# Call JET2 and produce prot+"_jet.res" file.
# prot+"_jet.res" will be used in the following steps (in launchPred)
# to calculate independent and epistatic models.
# Ideally, this call to JET2 should be from Dockers or Singularity
# because installing all requirements of JET2 is a pain in the ass!
# Parameters
# ----------
# prot: string ???
# Name of the protein ???
# retMet: string
# Retreival method of multiple sequence alignments file
# It can be 'input', 'local' or 'server'. Default is local.
# bFile: string
# A multiple sequence alignment file obtained with psiblast.
# It is used only if the retMet (explained above) is input.
# fFile: string
# A multiple sequence alignment file obtained with psiblast.
# It is used only if the retMet (explained above) is input.
# pdbfile: string
# a Protein Data Bank file obtained with rcsb.org or any
# computational method like alphafold.
# If it is None, only JET and PC scores are calculated.
# Otherwise, CV and other structural-dynamical features also
# can be calculated.
# chains: list
# A list of chains available in the pdb file.
# Most of the time, it is supposed to be just one!
# n: int
# Number of JET2 iterations.
# N: int
# Default 40000
# nl: int
# Number of lines after > character in the query sequences file.
# It is obtained in extractQuerySeq() function.
# Returns
# -------
# Nothing
# """
# chainID = chains[0]
# #TODO: Remove Bash dependency here. Make the copying process in Python
# subprocess.call("cp $SGEMME_PATH/default.conf .",shell=True)
# if retMet=="input":
# if bFile!='':
# #TODO: I think these two lines must be here as well but I am not sure.
# # print(N)
# # editConfJET(N)
# if(bFile == prot+"_"+chainID+".psiblast"):
# shutil.copy2(bFile, bFile+".orig")
# shutil.copy2(bFile+".orig ", prot+"_"+chainID+".psiblast")
# else:
# shutil.copy2(bFile+" ", prot+"_"+chainID+".psiblast")
# if(pdbfile == None):
# jetcmd = "java -Xmx4096m -cp $JET2_PATH:$JET2_PATH/jet/extLibs/vecmath.jar jet.JET -c default.conf -i "+\
# prot+".pdb -o `pwd` -p J -r input -b "+prot+"_"+chainID+".psiblast -d chain -n "+n+" > "+prot+".out"
# else:
# # jetcmd = "java -Xmx4096m -cp $JET2_PATH:$JET2_PATH/jet/extLibs/vecmath.jar jet.JET -c default.conf -i "+\
# # prot+".pdb -o `pwd` -p AVJ -r input -b "+prot+"_"+chainID+".psiblast -d chain -n "+n+" > "+prot+".out"
# jetcmd = "java -Xmx4096m -cp $JET2_PATH:$JET2_PATH/jet/extLibs/vecmath.jar jet.JET -c default.conf -i "+\
# prot+".pdb -o `pwd` -p AVJCG -r input -f "+prot+"_"+chainID+".psiblast -d chain -n "+n+" -a 5"+" > "+prot+".out"
# #One can also add: -g 'trace,pc,cv,clusters,axs'
# else:
# print(N)
# editConfJET(N)
# if(fFile == prot+"_"+chainID+".fasta"):
# shutil.copy2(fFile, fFile+".orig")
# #I think this subprocess call causes overwriting of the fasta file.
# #subprocess.call("cp "+fFile+" "+prot+"_"+chainID+".fasta",shell=True)
# grpcmd="grep -m "+str(int(N)+1)+" -A "+str(nl)+" '^>' "+fFile+".orig > "+prot+"_"+chainID+".fasta"
# else:
# #subprocess.call("cp "+fFile+" "+prot+"_"+chainID+".fasta",shell=True)
# grpcmd="grep -m "+str(int(N)+1)+" -A "+str(nl)+" '^>' "+fFile+" > "+prot+"_"+chainID+".fasta"
# print("\nRunning:\n"+grpcmd)
# subprocess.call(grpcmd,shell=True)
# if(pdbfile == None):
# jetcmd = "java -Xmx4096m -cp $JET2_PATH:$JET2_PATH/jet/extLibs/vecmath.jar jet.JET -c default.conf -i "+\
# prot+".pdb -o `pwd` -p J -r input -f "+prot+"_"+chainID+".fasta -d chain -n "+n+" > "+prot+".out"
# print("\nRunning command:\n"+jetcmd)
# reCode=subprocess.call(jetcmd,shell=True)
# if os.path.isfile(prot+"/"+prot+"_jet.res"):
# os.rename(prot+"/"+prot+"_jet.res",prot+"_jet.res")
# else:
# # Calculate SC1
# jetcmd = "java -Xmx4096m -cp $JET2_PATH:$JET2_PATH/jet/extLibs/vecmath.jar jet.JET -c default.conf -i "+\
# prot+".pdb -o `pwd` -p AVJCG -r input -f "+prot+"_"+chainID+".fasta -d chain -n "+n+" -a 3"+" > "+prot+".out"
# #One can also add: -g 'trace,pc,cv,clusters,axs'
# print("\nRunning for SC1:\n"+jetcmd)
# reCode=subprocess.call(jetcmd,shell=True)
# if os.path.isfile(prot+"/"+prot+"_jet.res"):
# os.rename(prot+"/"+prot+"_jet.res",prot+"_jet.res")
# dir_name = prot+"/"
# if os.path.isdir(dir_name):
# for f in os.listdir(dir_name):
# f_path = os.path.join(dir_name, f)
# if os.path.isfile(f_path):
# os.remove(f_path)
# os.rmdir(dir_name)
# else:
# if(pdbfile == None):
# jetcmd = "java -Xmx4096m -cp $JET2_PATH:$JET2_PATH/jet/extLibs/vecmath.jar jet.JET -c default.conf -i "+\
# prot+".pdb -o `pwd` -p J -r "+retMet+" -d chain -n "+n+" > "+prot+".out"
# else:
# # jetcmd = "java -Xmx4096m -cp $JET2_PATH:$JET2_PATH/jet/extLibs/vecmath.jar jet.JET -c default.conf -i "+\
# # prot+".pdb -o `pwd` -p AVJ -r "+retMet+" -d chain -n "+n+" > "+prot+".out"
# jetcmd = "java -Xmx4096m -cp $JET2_PATH:$JET2_PATH/jet/extLibs/vecmath.jar jet.JET -c default.conf -i "+\
# prot+".pdb -o `pwd` -p AVJCG -r "+retMet+" -d chain -n "+n+" -a 5"+" > "+prot+".out"
# reCode=subprocess.call(jetcmd,shell=True)
# if os.path.isfile(prot+"/"+prot+"_jet.res"):
# os.rename(prot+"/"+prot+"_jet.res",prot+"_jet.res")
# dir_name = prot+"/"
# if os.path.isdir(dir_name):
# for f in os.listdir(dir_name):
# f_path = os.path.join(dir_name, f)
# if os.path.isfile(f_path):
# os.remove(f_path)
# os.rmdir(dir_name)
# # print("\nRunning:\n"+jetcmd)
# # reCode=subprocess.call(jetcmd,shell=True)
# # if os.path.isfile(prot+"/"+prot+"_jet.res"):
# # os.rename(prot+"/"+prot+"_jet.res",prot+"_jet.res")
# return(reCode)
# # Run Rscript to compute predictions
# def launchPred(prot,inAli,mutFile, normWeightMode, alphabet):
# if mutFile!='':
# rcmd="Rscript --save $SGEMME_PATH/computePred.R "+prot+" "+inAli+" FALSE "+mutFile+" "+normWeightMode+" "+alphabet
# else:
# rcmd="Rscript --save $SGEMME_PATH/computePred.R "+prot+" "+inAli+" TRUE none "+normWeightMode+" "+alphabet
# print("\nRunning: \n"+rcmd)
# reCode=subprocess.call(rcmd,shell=True)
# #Add plots here with gemmemore
# return(reCode)
# # Remove temporary files
# def cleanTheMess(prot,bFile,fFile, chainID):
# if bFile!='':
# if bFile!=prot+"_"+chainID+".psiblast":
# os.remove(prot+"_"+chainID+".psiblast")
# else:
# if os.path.isfile(prot+"/"+prot+"_"+chainID+".psiblast"):
# os.rename(prot+"/"+prot+"_"+chainID+".psiblast",prot+"_"+chainID+".psiblast")
# if fFile!='':
# if fFile!=prot+"_"+chainID+".fasta":
# if os.path.isfile(prot+"_"+chainID+".fasta"):
# os.remove(prot+"_"+chainID+".fasta")
# # if os.path.isfile(prot+"/"+prot+"_jet.res"):
# # os.rename(prot+"/"+prot+"_jet.res",prot+"_jet.res")
# # os.remove(prot+".pdb")
# # Get all files with suffix nwk
# treefiles = glob.glob('*.nwk')
# # Iterate over the list of files and remove individually
# for file in treefiles:
# os.remove(file)
# dir_name = prot+"/"
# if os.path.isdir(dir_name):
# for f in os.listdir(dir_name):
# f_path = os.path.join(dir_name, f)
# if os.path.isfile(f_path):
# os.remove(f_path)
# os.rmdir(dir_name)
sgemme.py
......@@ -14,15 +14,17 @@ import subprocess
import math
import numpy as np
import matplotlib.pylab as plt
import shutil
import glob
from prody import *
from scipy.stats import rankdata
from gemmeAnal import *
#from gemmeAnal import *
import pandas as pd
#############The following part between # signs are moved from gemmeAnal.py to
#############The following part between # signs is moved from gemmeAnal.py to
# make the code more simple.
def extractQuerySeq(filename):
"""
......
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