import die

# Code Means Comp CompCode

# { 'M', "AC", 'K' }, // GT K

# { 'R', "AG", 'Y' }, // CT Y

# { 'W', "AT", 'W' }, // AT W

# { 'S', "CG", 'S' }, // CG S

# { 'Y', "CT", 'R' }, // AG R

# { 'K', "GT", 'M' }, // AC M

# { 'V', "ACG", 'B' }, // CGT B

# { 'H', "ACT", 'D' }, // AGT D

# { 'D', "AGT", 'H' }, // ACT H

# { 'B', "CGT", 'V' }, // ACG V

# { 'X', "GATC", 'X' }, // ACGT X

# { 'N', "GATC", 'N' }, // ACGT N

def MatchLetter(a, b):

if b == 'A' or b == 'C' or b == 'G' or b == 'T':

return a == b

elif b == 'S':

return a == 'C' or a == 'G'

elif b == 'Y':

return a == 'T' or a == 'C'

elif b == 'K':

return a == 'G' or a == 'T'

elif b == 'V':

return a == 'A' or a == 'C' or a == 'G'

elif b == 'H':

return a == 'A' or a == 'C' or a == 'T'

elif b == 'D':

return a == 'A' or a == 'G' or a == 'T'

elif b == 'B':

return a == 'C' or a == 'G' or a == 'T'

elif b == 'X' or b == 'N':

return a == 'G' or a == 'A' or a == 'T' or a == 'C'

elif b == 'R':

return a == 'A' or a == 'G'

elif b == 'M':

return a == 'A' or a == 'C'

elif b == 'H':

return a == 'A' or a == 'C' or a == 'T'

elif b == 'W':

return a == 'A' or a == 'T'

else:

die.Die("Bad letter in primer '%c'" % b)

return 0

def MatchPrefix(Seq, Primer):

L = len(Seq)

PrimerLength = len(Primer)

n = PrimerLength

if L < n:

n = L

Diffs = 0

for i in range(0, n):

if not MatchLetter(Seq[i], Primer[i]):

Diffs += 1

return Diffs

def MatchPos(Seq, Primer):

L = len(Seq)

PrimerLength = len(Primer)

for Pos in range(0, L-PrimerLength):

if MatchPrefix(Seq[Pos:], Primer) == 0:

return Pos

return -1

def Match(Seq, Primer):

L = len(Seq)

PrimerLength = len(Primer)

for Pos in range(0, L-PrimerLength):

if MatchPrefix(Seq[Pos:], Primer) == 0:

return Pos

return -1

def BestMatch(Seq, Primer):

L = len(Seq)

PrimerLength = len(Primer)

BestDiffs = PrimerLength

BestPos = -1

for Pos in range(0, L-PrimerLength+1):

d = MatchPrefix(Seq[Pos:], Primer)

if d < BestDiffs:

BestDiffs = d

BestPos = Pos

return BestPos, BestDiffs