takes an input Entrez ID and outputs a .sif file

TF_NetworkEntrez.py

# -*- coding: utf-8 -*-
"""
Created on Mon Mar 12 18:16:24 2018

@author: Fuzzy
"""

import json
with open('tfbsDb_plus_and_minus_5000_entrez.json', 'r') as f:
    data = json.load(f)

motif2Id = {}
id2Motif = {}

with open('id_conversion/humanTFs_All.CSV','r') as inFile:
    header = inFile.readline().strip().split(',') #get rid of header, strip gets rid of whitespace, split each in element by comma
    while 1:
        inLine = inFile.readline()
        if not inLine:
            break
        split = inLine.strip().split(',')#create an array with element 0 as key, element 2 as ID
        motif2Id[split[0]] = split[2]#store element 0 as key and element 2 as the string
        #creating Id to motif, mapping one motif to many Ids, create list inside dictonary
        if not split[2] in id2Motif:
            id2Motif[split[2]] = []
        id2Motif[split[2]].append(split[0])
      

# Starting ID list
tfStartId = ['430', '1052', '1053', '1385', '84699', '9586', '1871', '1874', '144455', '79733', '1960', '1997', '2002', '2004', '80712', '2114', '2115', '2120', '51513', '2551', '2623', '2624', '2625', '9421', '3232', '10320', '3659', '3662', '3670', '91464', '3726', '10661', '11278', '128209', '10365', '9314', '1316', '51176', '9935', '23269', '4602', '4774', '4790', '7025', '9480', '5468', '5914', '5916', '3516', '5971', '864', '6257', '4093', '6659', '6660', '6662', '25803', '347853', '30009', '9496', '6929', '6925', '8463', '7022', '29842', '10155', '6935', '132625', '23051', '85416', '7707', '7764', '23528', '201516']
# Create a TFreg -> TFtarg dictionary
geneNetwork = {}
for TFreg in tfStartId:
    if TFreg in id2Motif:
        for motif in id2Motif[TFreg]:
            if motif in data:
                for geneTarg in data[motif]:
                    if geneTarg in tfStartId:
                        if not TFreg in geneNetwork:
                            geneNetwork[TFreg] = []
                        geneNetwork[TFreg].append(geneTarg)

#create .sif file
interact = 'r2t'
writeMe = []
for key in geneNetwork:
    for gene in geneNetwork[key]:
        writeMe.append(key+'\t'+interact+'\t'+gene) 

with open('gene2GeneNetwork.sif','w') as outFile:
    outFile.write('\n'.join(writeMe))