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three_point_test_cross.py
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three_point_test_cross.py
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#!/usr/bin/env python
import os
import sys
import math
import numpy
import random
basetype = 'abc'
if len(sys.argv) > 1:
basetype = sys.argv[1].strip()
basetype2 = basetype[0]+basetype[2]+basetype[1]
basetype3 = basetype[1]+basetype[0]+basetype[2]
def invertType(genotype):
newtype = ''
for i in range(3):
if genotype[i] == '+':
newtype += basetype[i]
else:
newtype += '+'
return newtype
def flipGene(genotype, gene):
newlist = list(genotype)
for i in range(3):
if basetype[i] == gene:
if genotype[i] == '+':
newlist[i] = basetype[i]
else:
newlist[i] = '+'
newtype = ""
for i in newlist:
newtype += i
return newtype
"""
afile = "bbq-gene_order_answers.txt"
qfile = "bbq-gene_order_questions.txt"
if not os.path.exists(afile):
open(afile, 'a').close()
f = open(afile, "r")
qcount = len(f.readlines()) + 1
f.close()
"""
qcount = 1
#gene order
print("selecting gene order")
geneorder = random.choice([basetype, basetype2, basetype3])
print(geneorder)
print("determine gene distances")
a = numpy.random.poisson(lam=12, size=7)
a.sort()
distances = [a[0], a[-1]]
random.shuffle(distances)
print(distances)
print("------------")
answerString = ("%d. %s - %d - %s - %d - %s"
%(qcount, geneorder[0],distances[0],geneorder[1],distances[1],geneorder[2]))
print(answerString)
print("------------")
print("determine double crossovers")
doublecross = distances[0]*distances[1]/100.
print("doublecross", doublecross*10, 'per 1000')
print("determine progeny size")
gcd1 = math.gcd(distances[0], 100)
gcd2 = math.gcd(distances[1], 100)
gcdfinal = math.gcd(gcd1, gcd2)
print("Final GCD", gcdfinal)
progenybase = 100/gcdfinal
minprogeny = 900/progenybase
maxprogeny = 6000/progenybase
progs = numpy.arange(minprogeny, maxprogeny+1, 1, dtype=numpy.float64)*progenybase
#print(progs)
numpy.random.shuffle(progs)
#print(progs)
bases = progs * distances[0] * distances[1] / 1e4
#print(bases)
devs = (bases - numpy.around(bases, 0))**2
#print(devs)
argmin = numpy.argmin(devs)
progeny = int(progs[argmin])
print(("total progeny: %d\n"%(progeny)))
print("determine parental type")
types = ['+++', '++'+basetype[2], '+'+basetype[1]+'+', '+'+basetype[1]+basetype[2]]
parental = random.choice(types)
print(parental, invertType(parental))
typemap1 = {}
print("determine double type")
doubletype = flipGene(parental, geneorder[1])
doublecount = int(round(doublecross*progeny/100.))
print(doubletype, invertType(doubletype), doublecount)
typemap1[doubletype] = doublecount
print("determine first flip")
firsttype = flipGene(parental, geneorder[0])
firstcount = int(round(distances[0]*progeny/100.)) - doublecount
print(firsttype, invertType(firsttype), firstcount)
typemap1[firsttype] = firstcount
print("determine second flip")
secondtype = flipGene(parental, geneorder[2])
secondcount = int(round(distances[1]*progeny/100.)) - doublecount
print(secondtype, invertType(secondtype), secondcount)
typemap1[secondtype] = secondcount
print("determine parental type count")
parentcount = progeny - doublecount - firstcount - secondcount
print(parental, invertType(parental), parentcount)
typemap1[parental] = parentcount
print("\n\ngenerate table")
typemap = {}
for t in types:
n = invertType(t)
#rand = random.gauss(0.5, 0.01)
try:
count = typemap1[t]
except KeyError:
count = typemap1[n]
tcount = 0
ncount = 0
for i in range(count):
if random.random() > 0.5:
tcount += 1
else:
ncount += 1
sys.stderr.write(".")
#typemap[t] = int(rand * count)
#typemap[n] = count - typemap[t]
typemap[t] = tcount
typemap[n] = ncount
sys.stderr.write("\n")
alltypes = list(typemap.keys())
alltypes.sort()
questionString = "\nQuestion %d:\n"%(qcount)
for t in alltypes:
questionString += ("%s\t%s\t%s\t%d\n"%(t[0], t[1], t[2], typemap[t]))
questionString += "\t\t\t-----\n"
questionString += "\t\tTOTAL\t%d\n\n"%(progeny)
print(questionString)
"""
f = open(afile, "a")
f.write(answerString+"\n")
f.close()
f = open(qfile, "a")
f.write(questionString)
f.close()
"""