def getAlignmentScore(matrix, tour):
""" Returns the total score for this solution """
global fragments, memo
alignmentList = []
for i in range(len(tour) - 1):
alignmentList.append((int(tour[i]), int(tour[i + 1])))
offset = 0
for pair in alignmentList:
if pair[0] == pair[1] == 0:
print("Error, error, error!")
break
if pair in memo:
offset += memo[pair]
else:
theOverlap, addToOffset = overlap(fragments[pair[0]],
fragments[pair[1]])
offset += addToOffset
memo[pair] = addToOffset
# Return the length of the overall alignment
# Offset tells us where the last thing lines up against the whole sequence
# The full length of the aligned fragments is the offset plus the length of
# the last fragment
return offset + len(fragments[tour[-1]])
def getAlignmentScore(matrix, tour):
""" Returns the total score for this solution """
global fragments, memo
alignmentList = []
for i in range( len(tour)-1 ):
alignmentList.append( ( int(tour[i]), int(tour[i+1])) )
offset = 0
for pair in alignmentList:
if pair[0] == pair[1] == 0:
print("Error, error, error!")
break
if pair in memo:
offset += memo[pair]
else:
theOverlap, addToOffset = overlap(fragments[pair[0]], fragments[pair[1]])
offset += addToOffset
memo[pair] = addToOffset
# Return the length of the overall alignment
# Offset tells us where the last thing lines up against the whole sequence
# The full length of the aligned fragments is the offset plus the length of
# the last fragment
return offset + len(fragments[ tour[-1] ])
def writeAlignmentCSV( fileToWriteTo, fragments, alignments ):
offset = 0
csvFile = open(fileToWriteTo, "w")
for pair in alignments:
if pair[0] == pair[1] == 0:
break
csvFile.write( (" ,"*offset) )
for letter in fragments[pair[0]]:
csvFile.write( letter + "," )
csvFile.write("\n")
theOverlap, addToOffset = overlap(fragments[pair[0]], fragments[pair[1]])
#print("Overlap between",fragments[pair[0]], "and", fragments[pair[1]], " was", theOverlap)
offset += addToOffset
def writeAlignmentCSV(fileToWriteTo, fragments, alignments):
offset = 0
csvFile = open(fileToWriteTo, "w")
for pair in alignments:
if pair[0] == pair[1] == 0:
break
csvFile.write((" ," * offset))
for letter in fragments[pair[0]]:
csvFile.write(letter + ",")
csvFile.write("\n")
theOverlap, addToOffset = overlap(fragments[pair[0]],
fragments[pair[1]])
#print("Overlap between",fragments[pair[0]], "and", fragments[pair[1]], " was", theOverlap)
offset += addToOffset
def printAlignments( listOfFragments, alignmentList ):
offset = 0
for pair in alignmentList:
if pair[0] == pair[1] == 0:
break
print( (" "*offset), listOfFragments[pair[0]], sep="" )
theOverlap, addToOffset = overlap(listOfFragments[pair[0]], listOfFragments[pair[1]])
#print("Overlap between",listOfFragments[pair[0]], "and", listOfFragments[pair[1]], " was", theOverlap)
offset += addToOffset
# Count the base pairs:
count = 0
for fragment in listOfFragments:
count += len(fragment)
print("\n\nNumber of base pairs is",count)
print("Expected length of the final sequence is",count,"/ (4*5) = ",count/(4*5))
print("Actual length of the sequence is a bit more than",offset)
def printAlignments(listOfFragments, alignmentList):
offset = 0
for pair in alignmentList:
if pair[0] == pair[1] == 0:
break
print((" " * offset), listOfFragments[pair[0]], sep="")
theOverlap, addToOffset = overlap(listOfFragments[pair[0]],
listOfFragments[pair[1]])
#print("Overlap between",listOfFragments[pair[0]], "and", listOfFragments[pair[1]], " was", theOverlap)
offset += addToOffset
# Count the base pairs:
count = 0
for fragment in listOfFragments:
count += len(fragment)
print("\n\nNumber of base pairs is", count)
print("Expected length of the final sequence is", count, "/ (4*5) = ",
count / (4 * 5))
print("Actual length of the sequence is a bit more than", offset)
