def globalAlignment(seq1, seq2, matchScore, misMatchScore, gapScore): matchScore = int(matchScore) misMatchScore = int(misMatchScore) gapScore = int(gapScore) #File input file1 = open(fileA, 'r') file2 = open(fileB, 'r') readLines1 = file1.readlines() readLines2 = file2.readlines() linesA = utils.getArraysFromFile(readLines1) linesB = utils.getArraysFromFile(readLines2) '''Returns the optimal alignment of all sequences located in a fafsta file. ie if there are four sequences on one file and 5 on the other, this will find the alignments of all 20 combinations. This an array containing each of the sequences, the score, and the percent correct.''' ret = utils.initialize2DArray(len(linesA)*len(linesB), 5, 0) retIndex = 0 idInfo1 = utils.getSequenceInfo(readLines1) idInfo2 = utils.getSequenceInfo(readLines2) for i in range(0, len(linesA)): for j in range(0, len(linesB)): info = getAlignment(linesA[i], linesB[j], matchScore, misMatchScore, gapScore) #alignments ret[retIndex][0] = info[0] ret[retIndex][1] = info[1] #score ret[retIndex][2] = info[2] #percent correct ret[retIndex][3] = idInfo1[i] ret[retIndex][4] = idInfo2[j] retIndex += 1 file1.close() file2.close() return ret
def getAlignment(horzChars, vertChars, matchScore, misMatchScore, gapScore):
scores = utils.initialize2DArray(len(horzChars)+1, len(vertChars)+1, 0)
pointers = utils.initialize2DArray(len(horzChars)+1, len(vertChars)+1, [-float('inf'),-float('inf')])
dirs = utils.initialize2DArray(len(horzChars)+1, len(vertChars)+1, -float('inf'))
#print scores
#sets the initial gap scores
for i in range(0, len(horzChars)+1):
scores[i][0] = i*gapScore
for i in range(1, len(vertChars)+1):
scores[0][i] = i*gapScore
for i in range(1, len(horzChars)+1):
for j in range(1, len(vertChars)+1):
if horzChars[i-1] == vertChars[j-1]:
scores[i][j] = utils.maxVal(scores[i-1][j-1]+matchScore, scores[i-1][j]+gapScore, scores[i][j-1]+gapScore)
direc = utils.maxForPointer(scores[i-1][j-1]+matchScore, scores[i-1][j]+gapScore, scores[i][j-1]+gapScore)
else:
scores[i][j] = utils.maxVal(scores[i-1][j-1]+misMatchScore, scores[i-1][j]+gapScore, scores[i][j-1]+gapScore)
direc = utils.maxForPointer(scores[i-1][j-1]+misMatchScore, scores[i-1][j]+gapScore, scores[i][j-1]+gapScore)
if direc == 0:
pointers[i][j] = [i-1,j-1]
dirs[i][j] = direc
elif direc == 1:
pointers[i][j] = [i-1,j]
dirs[i][j] = direc
else:
pointers[i][j] = [i, j-1]
dirs[i][j] = direc
maxScore = scores[len(horzChars)][len(vertChars)]
pt = [len(horzChars),len(vertChars)]
#traceback
horzOut = []
vertOut = []
oldPt = pt
while(pt[0]!= -float('inf') or pt[1]!= -float('inf')):
if dirs[pt[0]][pt[1]] == 0:
horzOut.insert(0, horzChars[pt[0]-1])
vertOut.insert(0, vertChars[pt[1]-1])
elif dirs[pt[0]][pt[1]] == 1:
vertOut.insert(0, '-');
horzOut.insert(0, horzChars[pt[0]-1])
elif dirs[pt[0]][pt[1]] == 2:
horzOut.insert(0, '-');
vertOut.insert(0, vertChars[pt[1]-1])
oldPt = pt
pt = pointers[pt[0]][pt[1]]
#printing indels on edge
pt = oldPt
if pt[0]!=0 or pt[1]!=0:
#in vertical column
if pt[1]!=0:
numIndels = scores[0][pt[1]]/(gapScore)
for i in range(0, numIndels):
horzOut.insert(0, '-')
while(pt[1]!=0):
vertOut.insert(0, vertChars[pt[1]-1])
pt[1] = pt[1]-1;
elif pt[0] != 0:
numIndels = scores[pt[0]][0]/(gapScore)
for i in range(0, numIndels):
vertOut.insert(0, '-');
while(pt[0]!=0):
horzOut.insert(0, horzChars[pt[0]-1])
pt[0] = pt[0]-1;
print "Score: " + str(maxScore)
#utils.printArray(horzOut)
#utils.printArray(vertOut)
#print '\n'
return maxScore