Global and local alignments

global_local_alignment

##########################
# Author : Pratik Anand  #
##########################

from tabulate import tabulate
import copy
IS_LOCAL_ALIGNMENT = False
USE_BLOSUM = False
match = 1
mismatch = -1
MIN = -1000


def printTable( rowHeader, columnHeader, table ) :
	new_table = copy.deepcopy(table)
	for indx,innerRow in enumerate(new_table):
		innerRow.insert( 0, rowHeader[indx])
	print tabulate( new_table, headers=columnHeader, tablefmt="grid" )



def sequence_align( strA, strB, charSet= None,blosum = None) :
	print strA + " vS " + strB
	strA = "0" + strA
	strB = "0" + strB
	megaL = []
	for i in range(len(strB)):
		innerL = [0 for x in range(len(strA))]   # list assignment evil
		megaL.append(innerL)

	for i in range( len(strB) ) :
		for j in range( len(strA) ) :
			
			if i==0 and j==0 :
				megaL[i][j] = 0
				continue
			
			indx_i = -1
			indx_j = -1
			if USE_BLOSUM is True :
				listCharSet = list(charSet)
				for indx,string in enumerate(listCharSet) :
					if string == strB[i] :
						indx_i = indx
					if string == strA[j]:
						indx_j = indx

			local_matched = (match if strB[i] == strA[j] else mismatch) if USE_BLOSUM is False else (blosum[indx_i][indx_j] if blosum[indx_i][indx_j] != "?" else MIN )
			
			

			megaL[i][j] = max(  ( megaL[i-1][j-1] if (i-1) >=0 and (j-1) >=0 else MIN ) + local_matched,
								( megaL[i-1][j] if (i-1) >=0 else MIN ) + mismatch,
								( megaL[i][j-1] if (j-1) >=0 else MIN  ) + mismatch,
								  0 if IS_LOCAL_ALIGNMENT is True else MIN
							  )
	#print-sandra
	for i in range( len(strB) ) :
		for j in range( len(strA) ) :
			print str(megaL[i][j]) + "	",

		print "\n"

	printTable(strB, list(strA), megaL)



if __name__ == '__main__' :

	s1 = "TACGGGTAT"
	s2 = "GGACGTACG"

	sequence_align(s1, s2)