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SNPcall.pyx
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SNPcall.pyx
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#!/usr/bin/python
import random
def rebuild(pos, calls):
"""function for rebuilding a SNPcall object given its own values. necessary to make SNPcall objects pickle-able"""
sc = SNPcall(pos, calls)
return(sc)
cdef class SNPcall(object):
"""custom class for storing SNP nodes for IntervalTree; stores individual sample calls as a list, and a coordinate"""
cdef public:
int position
list calls
def __init__(self, pos, samps):
"""constructor for SNPcall"""
self.position = int(pos)
self.calls = list(samps)
# def __lt__(self, other):
# return(self.position < other.position)
def __richcmp__(self, other, op):
"""special method defining comparison rules for SNPcall objects"""
if op == 2:#Py_EQ
return(self.position == other.position)
elif op == 3:#Py_NE
return(not self.position == other.position)
elif op == 0:
return(self.position < other.position)
elif op == 1:
return(self.position <= other.position)
elif op == 4:
return(self.position > other.position)
elif op == 5:
return(self.position >= other.position)
else:
assert False
#trying to make it pickle-able
@staticmethod
def rebuild(pos, calls):
sc = SNPcall(pos, calls)
return(sc)
def __reduce__(self):
return(rebuild, (self.position, self.calls))
##############################################################################
#TODO:try to speed this up. 32% of runtime currently
def FGT(self, other, rule):
"""method for comparing a SNPcall object (self) with another SNPcall object to run four-gamete test. Returns: boolean"""
#print("Four gamete test for",self.position,"and",other.position)
cdef list gametes = [0,0,0,0] #00, 01, 10, 11
cdef list hets = list()
cdef int gamete
#TODO: This line takes a long time. 21% of total runtime
valid =set([0, 1, 2])
#cdef list genotypes = [[gt, other.calls[i]] for i, gt in enumerate(self.calls) if gt and other.calls[i] in valid]
cdef list genotypes = [[x,other.calls[i]] for i,x in enumerate(self.calls) if set([x, other.calls[i]]).issubset(valid)]
#print("geno is:",genotypes)
for geno in genotypes:
#print(geno)
gamete = self.hapCheck(geno)
if gamete <= 3: #9 is designated 'missing data' placeholder
gametes[gamete] = 1
else:
if 1 in geno:
if rule == 1:
if geno[0] == 1:
geno[0] = random.choice([0,2])
if geno[1] == 1:
geno[1] = random.choice([0,2])
#print(geno)
gametes[self.hapCheck(geno)] = 1
elif rule == 2:
possible1 = list()
possible2 = list()
if geno[0] == 1:
possible1 = [0,2]
else:
possible1 = [geno[0]]
if geno[1] == 1:
possible2 = [0,2]
else:
possible2 = [geno[1]]
for i in possible1:
for j in possible2:
gametes[self.hapCheck([i,j])] = 1
elif rule == 3:
hets.append(geno)
#print("found gametes:",gametes)
if sum(gametes) == 4:
return(False) #return False if not compatible
elif hets:
if not self.optimisticFGT(gametes, hets):
return(False) #return false if not compatible
else:
return(True)
else:
return(True)
############################################################################
@staticmethod
#TODO: Optimize; currently 11% of runtime after 2X speedup
def hapCheck(geno):
"""finds gametes from a genotype"""
#print(geno)
if geno[0] == 0:
if geno[1] == 0:
return(0)
elif geno[1] ==2:
return(1)
else:
return(9)
elif geno[0] == 2:
if geno[1] == 0:
return(2)
elif geno[1] ==2:
return(3)
else:
return(9)
else:
return(9)
def optimisticFGT(self, seen, hets):
""" Function returns True if any genotype comparison in a provided set of heterozygotes passes the four-gamete test"""
cdef list possibilities = list()
cdef list locals = list()
cdef possible1 = list()
cdef possible2 = list()
for het in hets:
locals = list()
possible1 = list()
possible2 = list()
if het[0] == 1:
possible1 = [0,2]
else:
possible1 = [het[0]]
if het[1] == 1:
possible2 = [2,0]
else:
possible2 = [het[1]]
for i in possible1:
for j in possible2:
copy = seen[:] #deep copy
copy[self.hapCheck([i,j])] = 1
locals.append(copy)
possibilities = locals[:]
#print(possibilities)
for opt in possibilities:
#print(opt)
if sum(opt) != 4: #if ANY possibilities
return True #return False if not compatible
return(False)