from pandas import read_csv
import pandas as pd
import subprocess as sp
import numpy as np
import os
from alignment import commons
__author__ = 'peeyush'
import alignment.commons as paths
Path = paths.path()
basepath = Path.basepath
path_to_seq = "/further_analysis/seq4motif/"
path_to_genome = "/ps/imt/f/reference_genomes/homo_sapiens/GRCh37/Sequence/WholeGenomeFasta/"
path_to_program = "/home/sahu/meme/bin"
program = "meme-chip"
motif_db_base = "/home/sahu/Documents/motif_databases"
class MotifAnalysis:
def __init__(self,
name,
dataframe,
background=None,
seqlength=50,
method='meme'):
self.name = name
self.dataframe = dataframe
self.background = background
self.seqlength = seqlength
self.path2folder = ''
self.method = method
__author__ = 'peeyush'
import gc, os
import pysam
from overlap_analysis import differential_binding
import pandas as pd
from alignment import commons
import math
import datetime
import dateutil.relativedelta
import dateutil
import sys
import multiprocessing
Path = commons.path()
basepath = Path.basepath
def color():
cnames = {
'aliceblue': '#F0F8FF',
'aquamarine': '#7FFFD4',
'blueviolet': '#8A2BE2',
'brown': '#A52A2A',
'cadetblue': '#5F9EA0',
'chartreuse': '#7FFF00',
'chocolate': '#D2691E',
'coral': '#FF7F50',
'cornflowerblue': '#6495ED',
'cornsilk': '#FFF8DC',
'crimson': '#DC143C',