carolinecunningham

####warning: only can be run locally & may depend on external code. this is just a place to store this

############### boxplot 1: APOBEC ####################
 apobec_ints = {}


 apobec = ["BLAC_apobec", "stomach_apobec", "breast_apobec", "cervix_apobec", "colonfin_apobec", "pancreas_apobec",
           "glioblast_apobec", "HNCarcinoma_apobec", "pancreatic_apobec", "liver_apobec", "lung_apobec", "glioma_apobec",
           "prostate_apobec", "skin_apobec", "thyroid_apobec"]

carolinecunningham

import matplotlib as mpl
mpl.use('TkAgg')
import matplotlib.pyplot as plt

def graph_logo(ref, alt):

    str = ""

    for num, char in enumerate(ref):
        if char != alt[num]:

carolinecunningham

from itertools import cycle
from flask import *
import multiprocessing
import json
import requests
import urllib
from requests.packages.urllib3.exceptions import InsecureRequestWarning
requests.packages.urllib3.disable_warnings(InsecureRequestWarning)

def mp_ensembl_worker(raw_mutations_chunk):

carolinecunningham

import requests
import json
import csv
import glob

# MUTAGENE_URL = "https://www.ncbi.nlm.nih.gov/research/mutagene"
#MUTAGENE_URL = "https://dev.ncbi.nlm.nih.gov/research/mutagene"
MUTAGENE_URL_M = "http://mwebdev2/research/mutagene"
# MUTAGENE_URL = "http://localhost:5000"
MUTAGENE_URL = "https://www.ncbi.nlm.nih.gov/research/mutagene"