cpgtools 2.0.5__py3-none-any.whl

cpgmodule/BED.py

@@ -0,0 +1,441 @@
+#!/usr/bin/env python
+
+#import built-in modules
+import os,sys
+import re
+import string
+import warnings
+import string
+import collections
+import math
+from operator import itemgetter
+from itertools import groupby
+
+
+#import third-party modules
+from bx.bitset import *
+from bx.bitset_builders import *
+from bx.intervals import *
+
+#from itertools import *
+from cpgmodule import ireader
+
+BED12 = '''
+1. chrom - The name of the chromosome (e.g. chr3, chrY, chr2_random) or scaffold (e.g. scaffold10671).
+2. chromStart - The starting position of the feature in the chromosome or scaffold. The first base in a chromosome is numbered 0.
+3. chromEnd - The ending position of the feature in the chromosome or scaffold. 
+4. name - Defines the name of the BED line. 
+5. score.
+6. strand - Defines the strand. Either "." (=no strand) or "+" or "-".	 	 	 	 	 	 	 	 	 
+7. thickStart - The starting position at which the feature is drawn thickly (for example, the start codon in gene displays). 
+8. thickEnd - The ending position at which the feature is drawn thickly (for example the stop codon in gene displays).
+9. itemRgb - An RGB value of the form R,G,B (e.g. 255,0,0). 
+10. blockCount - The number of blocks (exons) in the BED line.
+11. blockSizes - A comma-separated list of the block sizes. 
+12. blockStarts - A comma-separated list of block starts.
+
+Detailed description of BED format: https://genome.ucsc.edu/FAQ/FAQformat.html#format1
+'''
+
+
+__author__ = "Liguo Wang"
+__copyright__ = "Copyleft"
+__credits__ = []
+__license__ = "GPL"
+__version__="0.1.0"
+__maintainer__ = "Liguo Wang"
+__email__ = "wang.liguo@mayo.edu"
+__status__ = "Development"
+
+
+
+class ParseBED:
+	'''
+	Manipulate BED (http://genome.ucsc.edu/FAQ/FAQformat.html) format file.
+	Input BED file must be 12-column (i.e. BED-12).
+	'''
+	
+	def __init__(self,bedFile):
+		'''This is constructor of ParseBED'''
+		self.f=bedFile
+		self.fileName=os.path.basename(bedFile)
+		self.ABS_fileName=bedFile
+
+	def getExons(self,uniquify = True, stranded = True):
+		'''
+		Get all exons (including both coding exons and UTR exons) from BED-12 file.
+		uniquify: if the returned blocks should be uniquify. 
+		'''
+		
+		reblocks = []
+		for l in ireader.reader(self.f):
+			l = l.strip()
+			if l.startswith(('#','track','browser')):continue
+			f = l.split()
+			if len(f) < 12:
+				print ("Standard BED format has 12 columns.\n%s" % (BED), file=sys.stderr)
+				sys.exit(1)
+			chrom = f[0]
+			chrom_start = int(f[1])
+			name = f[4]
+			strand = f[5]
+			cdsStart = int(f[6])
+			cdsEnd = int(f[7])
+			blockCount = int(f[9])
+			blockSizes = [ int(i) for i in f[10].strip(',').split(',') ]
+			blockStarts = [ chrom_start + int(i) for i in f[11].strip(',').split(',') ]
+			for base,offset in zip( blockStarts, blockSizes ):
+				if stranded:
+					reblocks.append((chrom, base, base+offset, strand))
+				else:
+					reblocks.append((chrom, base, base+offset))
+		#self.f.seek(0)
+		if uniquify:
+			return list(set(reblocks))
+		else:
+			return reblocks
+		
+	def getCDSExons(self,uniquify=True, stranded = True):
+		
+		'''
+		Get only CDS exon regions from BED-12 file. Both 5' and 3' UTR parts are removed.
+		uniquify: if the returned blocks should be uniquify. 
+		'''	
+		reblocks = []	
+		for l in ireader.reader(self.f):
+			l = l.strip()
+			if l.startswith(('#','track','browser')):continue
+			f = l.split()
+			if len(f) < 12:
+				print ("\nInput error!\nStandard BED format has 12 columns.\n%s" % (BED12), file=sys.stderr)
+				sys.exit(1)
+
+			chrom = f[0]
+			chrom_start = int(f[1])
+			name = f[4]
+			strand = f[5]
+			cdsStart = int(f[6])
+			cdsEnd = int(f[7])
+			blockCount = int(f[9])
+			blockSizes = [ int(i) for i in f[10].strip(',').split(',') ]
+			blockStarts = [ chrom_start + int(i) for i in f[11].strip(',').split(',') ]
+			cds_exons = []
+			genome_seq_index = []
+			for base,offset in zip( blockStarts, blockSizes ):
+				if (base + offset) < cdsStart: continue
+				if base > cdsEnd: continue
+				exon_start = max( base, cdsStart )
+				exon_end = min( base+offset, cdsEnd ) 
+				if stranded:
+					reblocks.append((chrom,exon_start,exon_end, strand))
+				else:
+					reblocks.append((chrom,exon_start,exon_end))
+		#self.f.seek(0)
+		if uniquify:
+			return list(set(reblocks))
+		else:
+			return reblocks
+
+	def getUTRs(self,utr=35, uniquify=True, stranded = True):
+		'''
+		Get UTR regions from BED-12 file.
+		When utr=35 [default], extract both 5' and 3' UTR.
+		When utr=3, only extract 3' UTR.
+		When utr=5, only extract 5' UTR
+		uniquify: if the returned blocks should be uniquify.
+		'''
+		
+		reblocks = []
+		for l in ireader.reader(self.f):
+			l = l.strip()
+			if l.startswith(('#','track','browser')):continue
+			f = l.split()
+			if len(f) < 12:
+				print ("\nInput error!\nStandard BED format has 12 columns.\n%s" % (BED12), file=sys.stderr)
+				sys.exit(1)
+
+			chrom = f[0]
+			chrom_start = int(f[1])
+			name = f[4]
+			strand = f[5]
+			cdsStart = int(f[6])
+			cdsEnd = int(f[7])
+			blockCount = int(f[9])
+			blockSizes = [ int(i) for i in f[10].strip(',').split(',') ]
+			blockStarts = [ chrom_start + int(i) for i in f[11].strip(',').split(',') ]
+			exon_start = []
+			exon_end = []
+			for base,offset in zip( blockStarts, blockSizes ):
+				exon_start.append(base)
+				exon_end.append(base+offset)
+			if strand == '+':
+				if (utr==35 or utr==5):
+					for st,end in zip(exon_start,exon_end):
+						if st < cdsStart:
+							utr_st = st
+							utr_end = min(end,cdsStart)
+							if stranded:
+								reblocks.append((chrom,utr_st,utr_end,strand))
+							else:
+								reblocks.append((chrom,utr_st,utr_end))				
+				if (utr==35 or utr==3):
+					for st,end in zip(exon_start,exon_end):
+						if end > cdsEnd:
+							utr_st = max(st, cdsEnd)
+							utr_end = end
+							if stranded:
+								reblocks.append((chrom,utr_st,utr_end,strand))
+							else:
+								reblocks.append((chrom,utr_st,utr_end))				
+			if strand == '-':
+				if (utr==35 or utr==3):
+					for st,end in zip(exon_start,exon_end):
+						if st < cdsStart:
+							utr_st = st
+							utr_end = min(end,cdsStart)
+							if stranded:
+								reblocks.append((chrom,utr_st,utr_end,strand))
+							else:
+								reblocks.append((chrom,utr_st,utr_end))				
+				if (utr==35 or utr==5):
+					for st,end in zip(exon_start,exon_end):
+						if end > cdsEnd:
+							utr_st = max(st, cdsEnd)
+							utr_end = end
+							if stranded:
+								reblocks.append((chrom,utr_st,utr_end,strand))
+							else:
+								reblocks.append((chrom,utr_st,utr_end))				
+		#self.f.seek(0)
+		if uniquify:
+			return list(set(reblocks))
+		else:
+			return reblocks
+				
+	def getIntrons(self, itype, uniquify=True, stranded=True):
+		'''
+		Get Intron regions from BED-12 file. 
+		separated bed file, each row represents one intron
+		
+		itype = :
+		* 'all': all introns
+		* 'first': Only return the first intron of each gene. The gene should have at least 1 intron. 
+		* 'internal': return all internal introns. The gene should have at least 3 introns. 
+		* 'last': Return the last intron. The gene should have at least 2 introns. 
+		* 'cds': Return introns within CDS region. 
+		* 'utr': Return introns within UTR regions. 
+		'''
+
+		reblocks=[]
+		for l in ireader.reader(self.f):
+			l = l.strip()
+			if l.startswith(('#','track','browser')):continue
+			f = l.split()
+			chrom = f[0]
+			chrom_start = int(f[1])
+			name = f[4]
+			strand = f[5]
+			cdsStart = int(f[6])
+			cdsEnd = int(f[7])
+			blockCount = int(f[9])
+			if blockCount == 1:continue
+			blockSizes = [ int(i) for i in f[10].strip(',').split(',') ]
+			blockStarts = [ chrom_start + int(i) for i in f[11].strip(',').split(',') ]
+			exon_start = []
+			exon_end = []
+			for base,offset in zip( blockStarts, blockSizes ):
+				exon_start.append(base)
+				exon_end.append(base+offset)
+	   	   
+			intron_start = exon_end[:-1]
+			intron_end=exon_start[1:]
+			
+			intron_list = list(zip(intron_start,intron_end))
+			intron_number = len(intron_list)
+			
+			if itype == 'all':
+				for (st,end) in intron_list:
+					if stranded:
+						reblocks.append((chrom,st,end, strand))
+					else:
+						reblocks.append((chrom,st,end))
+
+			elif itype == 'first':
+				if intron_number == 0:
+					continue
+				if strand == '-':
+					if stranded:
+						reblocks.append((chrom, intron_list[-1][0], intron_list[-1][1], strand))
+					else:
+						reblocks.append((chrom, intron_list[-1][0], intron_list[-1][1]))
+				else:
+					if stranded:
+						reblocks.append((chrom, intron_list[-1][0], intron_list[-1][1], strand))
+					else:
+						reblocks.append((chrom, intron_list[-1][0], intron_list[-1][1]))
+			
+			elif itype == 'last':
+				if intron_number < 2:
+					continue
+				if strand == '-':
+					if stranded:
+						reblocks.append((chrom, intron_list[-1][0], intron_list[-1][1], strand))
+					else:
+						reblocks.append((chrom, intron_list[-1][0], intron_list[-1][1]))
+				else:
+					if stranded:
+						reblocks.append((chrom, intron_list[-1][0], intron_list[-1][1], strand))
+					else:
+						reblocks.append((chrom, intron_list[-1][0], intron_list[-1][1]))			
+			elif itype == 'internal':
+				if intron_number < 3:
+					continue
+				for (st,end) in intron_list[1:-1]:
+					if stranded:
+						reblocks.append((chrom,st,end, strand))
+					else:
+						reblocks.append((chrom,st,end))
+			
+			elif itype == 'cds':
+				for (st,end) in  intron_list:
+					if end < cdsStart: continue
+					if st > cdsEnd: continue
+					if stranded:
+						reblocks.append((chrom,st,end, strand))
+					else:
+						reblocks.append((chrom,st,end))
+			elif itype == 'utr':
+				for (st,end) in  intron_list:
+					if end < cdsStart:
+						if stranded:
+							reblocks.append((chrom,st,end, strand))
+						else:
+							reblocks.append((chrom,st,end))
+					if st > cdsEnd:
+						if stranded:
+							reblocks.append((chrom,st,end, strand))
+						else:
+							reblocks.append((chrom,st,end))
+									
+		#self.f.seek(0)
+		if uniquify:
+			return list(set(reblocks))
+		else:
+			return reblocks
+
+
+	def getIntergenic(self,direction='up', size=2000, uniquify=True, stranded = True):
+		'''get intergenic regions. direction=up or down or both.'''
+		
+		reblocks=[]
+		for l in ireader.reader(self.f):
+			l = l.strip()
+			if l.startswith(('#','track','browser')):continue
+			f = l.split()
+			chrom     = f[0]
+			tx_start  = int( f[1] )
+			tx_end    = int( f[2] )
+			strand    = f[5]
+			if(direction=="up" or direction=="both"):
+				if strand=='-':
+					region_st=tx_end
+					region_end=tx_end +size
+				else:
+					region_st = max(tx_start-size,0)
+					region_end=tx_start
+				reblocks.append((chrom,region_st,region_end, strand))
+			if (direction=="down" or direction=="both"):
+				if strand == '-':
+					region_st = max(0,tx_start-size)
+					region_end = tx_start
+				else:
+					region_st = tx_end
+					region_end = tx_end+size
+				if stranded:
+					reblocks.append((chrom,region_st,region_end, strand))
+				else:
+					reblocks.append((chrom,region_st,region_end))
+		#self.f.seek(0)
+		if uniquify:
+			return list(set(reblocks))
+		else:
+			return reblocks
+
+		
+
+
+
+def unionBed3(lst):
+	'''Take the union of 3 column bed files. return a new list'''
+	bitsets = binned_bitsets_from_list(lst)
+	ret_lst=[]
+	for chrom in bitsets:
+		bits = bitsets[chrom]
+		end = 0
+		while 1:
+			start = bits.next_set( end )
+			if start == bits.size: break
+			end = bits.next_clear( start )
+			ret_lst.append([chrom, start, end])
+	bitsets=dict()
+	return ret_lst
+
+def intersectBed3(lst1,lst2):
+	'''Take the intersection of two bed files (3 column bed files)'''
+	bits1 = binned_bitsets_from_list(lst1)
+	bits2 = binned_bitsets_from_list(lst2)
+
+	bitsets = dict()
+	ret_lst = []
+	for key in bits1:
+		if key in bits2:
+			bits1[key].iand( bits2[key] )
+			bitsets[key] = bits1[key]
+
+	for chrom in bitsets:
+		bits = bitsets[chrom]
+		end = 0
+		while 1:
+			start = bits.next_set( end )
+			if start == bits.size: break
+			end = bits.next_clear( start )
+			ret_lst.append([chrom, start, end])
+	bits1.clear()
+	bits2.clear()
+	bitsets.clear()
+	return ret_lst
+
+def subtractBed3(lst1,lst2):
+	'''subtrack lst2 from lst1'''
+	bitsets1 = binned_bitsets_from_list(lst1)
+	bitsets2 = binned_bitsets_from_list(lst2)
+	
+	ret_lst=[]
+	for chrom in bitsets1:  
+		if chrom not in bitsets1:
+			continue
+		bits1 = bitsets1[chrom]
+		if chrom in bitsets2:
+			bits2 = bitsets2[chrom]
+			bits2.invert()
+			bits1.iand( bits2 )
+		end=0
+		while 1:
+			start = bits1.next_set( end )
+			if start == bits1.size: break
+			end = bits1.next_clear( start )
+			ret_lst.append([chrom,start,end])
+	bitsets1 = dict()
+	bitsets2 = dict()
+	return ret_lst
+
+def tillingBed(chrName,chrSize,stepSize=10000):
+	'''tilling whome genome into small sizes'''
+	#tilling genome
+	for start in xrange(0,chrSize,stepSize):
+		end = start + stepSize
+		if end < chrSize:
+			yield (chrName,start,end)
+		else:
+			yield (chrName,start,chrSize)
+		

cpgmodule/MI.py

@@ -0,0 +1,193 @@
+#!/usr/bin/env python
+'''calculate mutual information of two lists of numbers or symbols'''
+
+import numpy as np
+
+from collections import Counter
+from sklearn.feature_selection import mutual_info_classif
+from sklearn.metrics import mutual_info_score
+
+
+__author__ = "Liguo Wang"
+__copyright__ = ""
+__credits__ = []
+__license__ = "GPLv2"
+__version__ = "1.0.0"
+__maintainer__ = "Liguo Wang"
+__email__ = "Wang.Liguo@mayo.edu"
+__status__ = "Development" #Prototype or Production
+
+
+
+
+def Mutual_information1(x,y):
+	'''
+	x and y are lists of symbols (like 'A','C','G','T').
+	Calculation mutual information based on: MI = H(x) + H(y) - H(x,y)
+	Log2 based, unit is bit
+	'''
+	x = [str(i) for i in x]
+	y = [str(i) for i in y]
+	if len(x) != len(y):
+		return 0
+	xy = [''.join(i) for i in zip(x,y)]
+	
+	x_freq = np.array(list(Counter(x).values()))	#a.items(): [('A', 3), ('C', 2), ('T', 4), ('G', 1)]
+	y_freq = np.array(list(Counter(y).values()))
+	xy_freq = np.array(list(Counter(xy).values()))
+	
+	x_freq = x_freq*1.0/sum(x_freq)
+	y_freq = y_freq*1.0/sum(y_freq)
+	xy_freq = xy_freq*1.0/sum(xy_freq)
+	
+	x_H = -sum([i * np.log2(i) for i in x_freq])
+	y_H = -sum([i * np.log2(i) for i in y_freq])
+	xy_H = -sum([i * np.log2(i) for i in xy_freq])
+	
+	return (x_H,y_H,xy_H, x_H+y_H-xy_H)
+
+def Mutual_information2(x,y):
+	'''
+	x and y are lists of symbols (like 'A','C','G','T'). 
+	Calculate mutual information based on its original definition. 
+	Log2 based, unit is bit
+	'''
+	x = [str(i) for i in x]
+	y = [str(i) for i in y]
+	if len(x) != len(y):
+		return 0
+	xy = [''.join(i) for i in zip(x,y)]
+	
+	px = {}
+	py = {}
+	pxy = {}
+	for i,j in list(Counter(x).items()):
+		px[i] = j*1.0/len(x)
+	for i,j in list(Counter(y).items()):
+		py[i] = j*1.0/len(y)
+	for i,j in list(Counter(xy).items()):
+		pxy[i] = j*1.0/len(xy)
+	#print px
+	#print py
+	#print pxy
+	
+	mi_sum = 0.0
+	tmp = set()
+	for xi, yi in zip(x,y):
+		xyi = xi + yi
+		if xyi in tmp: continue
+		#print "%s::px:%f, py:%f, pxy:%f" % (xyi,px[xi],py[yi],pxy[xyi])
+		mi_sum += (pxy[xyi] * np.log(pxy[xyi] / (px[xi] * py[yi])))
+		tmp.add(xyi)
+	return mi_sum
+
+def PMI(x,y):
+	'''
+	x and y are lists of symbols (like 'A','C','G','T'). 
+	Calculate pointwise mutual information based on its original definition. 
+	Log2 based, unit is bit
+	'''
+	x = [str(i) for i in x]
+	y = [str(i) for i in y]
+	
+	if len(x) != len(y):
+		return 0
+	xy = [''.join(i) for i in zip(x,y)]
+	#print xy
+	#print set(x)
+	#print set(y)
+	px = {}
+	py = {}
+	pxy = {}
+	for i,j in list(Counter(x).items()):
+		px[i] = j*1.0/len(x)
+	for i,j in list(Counter(y).items()):
+		py[i] = j*1.0/len(y)
+	for i,j in list(Counter(xy).items()):
+		pxy[i] = j*1.0/len(xy)
+	#print px
+	#print py
+	#print pxy
+	
+	#print set(x)
+	#print set(y)
+
+	for i in set(x):
+		#if px[i] < 0.05:continue
+		for j in set(y):
+			#if py[j] < 0.05:continue
+			tmp1 = i + j
+			if i + j in pxy:
+				tmp2 = np.log2(pxy[i+j]/(px[i] * py[j]))
+				#tmp2 = -(np.log2(pxy[i+j]/(px[i] * py[j]))) / np.log2(pxy[i+j])
+			else:
+				continue
+			print(tmp1,tmp2)
+	
+def Mutual_expected():
+	'''
+	x and y are lists of symbols (like 'A','C','G','T').
+	Calculation mutual information based on: MI = H(x) + H(y) - H(x,y)
+	Log2 based, unit is bit
+	'''
+	x_freq = [0.25]*4
+	y_freq = [0.25]*4
+	xy_freq= [0.0625]*16
+	
+	x_H = -sum([i * np.log2(i) for i in x_freq])
+	y_H = -sum([i * np.log2(i) for i in y_freq])
+	xy_H = -sum([i * np.log2(i) for i in xy_freq])
+	
+	return (x_H,y_H,xy_H, x_H+y_H-xy_H)
+
+	
+if __name__=='__main__':
+	x=['G', 'T', 'C', 'A', 'T', 'T', 'A', 'C', 'T', 'A']
+	y=['A', 'C', 'A', 'C', 'A', 'A', 'G', 'A', 'G', 'A']
+	z=['A', 'C', 'A', 'T', 'A', 'A', 'T', 'A', 'G', 'T']
+	
+	
+	X_0 = (0, 0, 1, 1, 0, 1, 1, 2, 2, 2)
+	X_1 = (3, 4, 5, 5, 3, 2, 2, 6, 6, 1)
+	X_2 = [7, 2, 1, 3, 2, 8, 9, 1, 2, 0]
+	
+	C8 = ['T', 'A', 'A', 'A', 'T', 'T', 'G', 'C', 'T', 'A', 'A', 'A', 'A', 'T', 'T', 'T', 'A', 'T', 'T', 'A', 'G', 'A', 'C', 'A', 'G', 'G', 'G', 'G', 'T', 'A', 'T', 'T', 'A', 'G', 'C', 'T', 'T', 'T', 'A', 'T', 'G', 'G', 'A', 'C', 'T', 'C', 'C', 'C', 'C', 'T', 'G', 'A', 'T', 'A', 'T', 'A', 'A', 'T', 'C', 'C', 'T', 'G', 'A', 'C', 'G', 'T', 'T', 'C', 'T', 'T', 'A', 'T', 'A', 'A', 'A', 'A', 'T', 'G', 'A', 'A', 'T', 'G', 'A', 'C', 'T', 'A', 'C', 'A', 'A', 'C', 'C', 'A', 'A', 'A', 'C', 'C', 'T', 'T', 'T', 'A', 'A', 'A', 'G', 'A', 'C', 'T', 'A', 'C', 'T', 'T', 'T', 'T', 'T', 'T', 'G', 'A', 'A', 'T', 'A', 'G', 'G', 'A', 'A', 'A', 'T', 'A', 'G', 'G', 'C', 'C', 'T', 'C', 'G', 'A', 'T', 'T', 'G', 'T', 'T', 'C', 'G', 'G', 'C', 'T', 'T', 'G', 'A', 'G', 'T', 'A', 'T', 'T', 'T', 'A', 'T', 'A', 'C', 'C', 'C', 'C', 'T', 'T', 'T', 'A', 'C', 'C', 'A', 'A', 'C', 'T', 'C', 'A', 'C', 'T', 'T', 'T', 'T', 'A', 'G', 'T', 'A', 'G', 'T', 'C', 'A', 'T', 'C', 'A', 'C', 'C', 'C', 'T', 'T']
+	C9 = ['T', 'T', 'G', 'A', 'C', 'T', 'A', 'C', 'G', 'C', 'G', 'G', 'G', 'G', 'G', 'T', 'C', 'G', 'T', 'A', 'G', 'G', 'T', 'G', 'C', 'T', 'T', 'C', 'G', 'T', 'G', 'G', 'C', 'T', 'C', 'A', 'T', 'T', 'C', 'A', 'T', 'A', 'A', 'C', 'C', 'G', 'T', 'G', 'C', 'C', 'T', 'C', 'G', 'C', 'T', 'T', 'C', 'C', 'T', 'A', 'T', 'C', 'G', 'A', 'C', 'T', 'C', 'T', 'T', 'C', 'A', 'T', 'G', 'A', 'A', 'G', 'T', 'C', 'T', 'T', 'T', 'C', 'A', 'T', 'T', 'T', 'T', 'T', 'G', 'A', 'A', 'C', 'T', 'G', 'C', 'C', 'T', 'C', 'C', 'A', 'G', 'G', 'G', 'G', 'G', 'A', 'G', 'A', 'G', 'T', 'T', 'C', 'T', 'A', 'C', 'G', 'G', 'T', 'G', 'C', 'C', 'G', 'A', 'A', 'G', 'A', 'G', 'T', 'A', 'C', 'A', 'C', 'C', 'G', 'G', 'C', 'A', 'C', 'G', 'C', 'A', 'A', 'A', 'T', 'G', 'A', 'T', 'T', 'A', 'A', 'G', 'A', 'T', 'G', 'A', 'A', 'A', 'A', 'C', 'A', 'G', 'C', 'C', 'A', 'C', 'C', 'G', 'A', 'C', 'C', 'T', 'T', 'T', 'C', 'C', 'T', 'T', 'A', 'A', 'C', 'T', 'A', 'G', 'A', 'G', 'C', 'T', 'A', 'T', 'C', 'A', 'T', 'G']
+	
+	#AR motif pos-5 and pos-11
+	C5 =  ['C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'G', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'G', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'T', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'T', 'C', 'C', 'C', 'C', 'T', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C']
+	C11 = ['G', 'G', 'G', 'G', 'G', 'G', 'G', 'G', 'G', 'G', 'G', 'G', 'G', 'G', 'G', 'G', 'G', 'G', 'G', 'G', 'G', 'G', 'G', 'G', 'G', 'G', 'G', 'G', 'G', 'G', 'G', 'G', 'G', 'G', 'G', 'G', 'G', 'G', 'G', 'G', 'G', 'G', 'G', 'G', 'G', 'G', 'G', 'G', 'G', 'G', 'G', 'G', 'G', 'G', 'G', 'G', 'G', 'G', 'G', 'G', 'G', 'G', 'G', 'G', 'G', 'G', 'G', 'G', 'G', 'G', 'G', 'G', 'G', 'G', 'C', 'G', 'G', 'G', 'G', 'G', 'G', 'G', 'G', 'G', 'G', 'G', 'A', 'T', 'G', 'G', 'G', 'G', 'G', 'G', 'G', 'G', 'G', 'G', 'G', 'G', 'G', 'G', 'G', 'G', 'A', 'G', 'G', 'G', 'G', 'G', 'A', 'G', 'G', 'G', 'G', 'G', 'G', 'G', 'G', 'G', 'G', 'G', 'G', 'G', 'G', 'G', 'G', 'G', 'G', 'G', 'G', 'G', 'G', 'G', 'G', 'G', 'G', 'G', 'G', 'G', 'G', 'G', 'G', 'G', 'G', 'G', 'G', 'G', 'G', 'G', 'G', 'G', 'G', 'G', 'G', 'G', 'G', 'G', 'G', 'G', 'G', 'G', 'G', 'G', 'G', 'G', 'G', 'G', 'G', 'G', 'G', 'G', 'G', 'G', 'G', 'G', 'G', 'G', 'G', 'G', 'G', 'G', 'G', 'G', 'G', 'G', 'G', 'A', 'G', 'G', 'G', 'G', 'G']
+	#PMI(C5,C11)
+
+
+	#https://en.wikipedia.org/wiki/Pointwise_mutual_information example
+	x=[0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,1,1,1]
+	y=[0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,0,0,0,1]
+	z=[1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,0,0,0,0]
+	PMI(x,z)
+	#print (Mutual_information1(x,z))
+	print (Mutual_information2(x,z))
+	print (mutual_info_score(x,z))
+	print (mutual_info_score(y,z))
+	
+	#C1 = ['A','C','G','T']
+	#C2 = ['A','C','G','T']
+	#a=Mutual_information2(x,y)
+	#b=Mutual_information2(x,z)
+	#print(a)
+	#print(b)	
+	
+	
+	#b=Mutual_information2(C1,C2)
+	#print(b)
+
+'''
+from sklearn.feature_selection import mutual_info_classif
+from sklearn.metrics import mutual_info_score
+a = np.array([1, 1, 1, 0, 0, 1, 0, 0, 0, 1])
+b = np.array([1, 1, 1, 0, 0, 1, 0, 0, 0, 1])
+
+print(stats.entropy([0.5,0.5])) # entropy of 0.69, expressed in nats
+print(mutual_info_classif(a.reshape(-1,1), b, discrete_features = True)) # mutual information of 0.69, expressed in nats
+print(mutual_info_score(a,b)) # information gain of 0.69, expressed in nats
+'''

cpgmodule/_version.py

@@ -0,0 +1 @@
+__version__ = "2.0.5"