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moitf2entrez = {}
entrez2motif = {}
# humanTFs_all.csv -> Motif_ID[0],Gene_Symbol[1],Entrez_ID[2]
with open('id_conversion/humanTFs_all.csv','r') as inFile:
    inFile.readline() # Get rid of header
    while 1:
        inLine = inFile.readline()
        if not inLine:
            break
        splitUp = inLine.strip().split(',')

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import GEOparse
import pandas as pd
import matplotlib.pyplot as plt
import numpy
from matplotlib.backends.backend_pdf import PdfPages

gseNums = ['GSE32658']

with PdfPages('GSE_boxplots.pdf') as pdf:
    for gse1 in gseNums:

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# To access a specific probe (row)
exprs.loc['ILMN_2314140']

# Only select LSB samples
samples = []
time = []
for i in metadata['agent']:
    if metadata['agent'][i]=='LSB':
        samples.append(i)
        time.append(int(metadata['time'][i].lstrip('Day')))

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# -*- coding: utf-8 -*-
"""
Created on Sat Mar 24 12:19:38 2018
@author: Fuzzy
"""

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

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#!/usr/bin/env Rscript

suppressMessages(library(WGCNA))
#suppressMessages(library(multicore))
suppressMessages(library(getopt))
suppressMessages(library(parallel))
suppressMessages(library(impute))
suppressMessages(library(survival))

# read command line arguments

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# Loading JSON file
# https://www.safaribooksonline.com/library/view/python-cookbook-3rd/9781449357337/ch06s02.html
# Example:
# import json
#
# # Reading data back
# with open('data.json', 'r') as f:
#      data = json.load(f)

# From Table S13 in Plaisier et al., Cell Systems 2016

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# -*- coding: utf-8 -*-
"""
Created on Sat Apr 07 21:10:33 2018

@author: Fuzzy
"""
import math
import pandas as pd
import numpy as np
import matplotlib.pyplot as plt

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# Loading JSON file
# https://www.safaribooksonline.com/library/view/python-cookbook-3rd/9781449357337/ch06s02.html
# Example:
# import json
#
# # Reading data back
# with open('data.json', 'r') as f:
#      data = json.load(f)

import json

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import json
import pandas as pd
from scipy.stats import pearsonr

# Make a Biotapestry CSV file
def biotapestry(filename, data, regions):
    writeMe = []
    writeMe.append('"# Model Commands",,,,,,,,,,')
    writeMe.append('"# Command Type","Model Name","Parent Model",,,,,,,,')
    writeMe.append('"model","root",,,,,,,,,')