annotate tools/myTools/bin/SFA_virtscreen.py @ 1:7e5c71b2e71f draft default tip

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#!/usr/bin/env python3
import os
import numpy as np
import pandas as pd
import networkx as nx
import random
import sfa
import csv
from sys import argv
from sklearn.preprocessing import StandardScaler
import itertools
########INPUTS############
fpath =  os.path.join( argv[1])            # location of networkfile
samples=pd.read_csv(argv[2],index_col = 0)          # input samples (normexp initial states)
inits=argv[3]                    #the initial states of interest

phenotypes = pd.read_csv(argv[4],delim_whitespace=True, index_col = False)
initz = phenotypes[phenotypes.isin([inits]).any(axis=1)]['name'].tolist()
samples = samples[initz]

FC_nodes=open(argv[5]).read().strip().split('\n')   # FC set
FC_perts=pd.read_csv(argv[6],delim_whitespace=True,index_col=0,header=0,names=FC_nodes)


class ThreeNodeCascade(sfa.base.Data):
    def __init__(self):
        super().__init__()
        self._abbr = "TNC"
        self._name = "A simple three node cascade"

        signs = {'activates':1, 'inhibits':-1}
        A, n2i, dg = sfa.read_sif(fpath, signs=signs, as_nx=True)
        self._A = A
        self._n2i = n2i
        self._dg = dg
        self._i2n = {idx: name for name, idx in n2i.items()}
        
    # end of def __init__
# end of def class

if __name__ == "__main__":
## initalize parameters from SFA
    data = ThreeNodeCascade()
    algs = sfa.AlgorithmSet()
    alg = algs.create('SP')
    alg.data = data
    alg.params.apply_weight_norm = True
    alg.initialize()
    alg.params.exsol_forbidden=True
    alg.params.alpha=0.9

 
    netnodes= list(data.dg.nodes)    
    
    n = data.dg.number_of_nodes() #the number of nodes
    b = np.zeros((n,))
    
    alllogss=pd.DataFrame()
    for name, item in samples.iteritems():                    #for each simulated initial condition
        logss=pd.DataFrame(index=FC_perts.index,columns=netnodes,copy=True) # create dataframe for the FC perturbations
        enodes=item.index.tolist()                            # get expressed nodes
        for node in enodes:                                     # set initial state to simulated value
            b[data.n2i[node]]=float(str(item.loc[node]))
        for name2,item2 in FC_perts.iterrows():                  # for each FCnode perturbation
            pnode=item2.index.tolist()
            pi = []
            for node in pnode: #if logFC.loc[node].at['logFC']>0: # if the logfc is postive (res > veh)
                if int(item2.loc[node])==-1:          #if the perturbation is 0
                    if node in enodes:
                        b[data.n2i[node]]=float(str(item.loc[node]))-2.5*(float(str(item.loc[node])))        #downregulate the expression. fix to 0
                    else:
                        b[data.n2i[node]]=-2.5    #downregulate the expression. fix to 0
                    pi.append(data.n2i[node])
                if int(item2.loc[node])==1:          #if the perturbation is 1
                    if node in enodes:
                        b[data.n2i[node]]=float(str(item.loc[node]))+2.5*(float(str(item.loc[node]))) #upregulate the expression
                    else:
                        b[data.n2i[node]]=2.5 #upregulate the expression
                    pi.append(data.n2i[node])
            x = alg.compute(b,pi)                                      # Run SFA calculation
            logss.loc[name2,netnodes]=x[0]
        logss=logss.astype(float).round(3)
        alllogss=pd.concat([alllogss,logss],axis=0)
    multi=pd.MultiIndex.from_product([samples.columns.tolist(),FC_perts.index.tolist()],names=['replicate', 'perturbation'])
    alllogss.set_index(multi,inplace=True)
    alllogss.to_csv('pert_logss.txt', sep=' ',float_format='%.3f',chunksize=10000)