translocation_problem.py

#!/usr/bin/env python

import os
import sys
import random

def list2string(mylist, spacer=""):
	mystring = spacer.join(mylist)
	return mystring
	mystring = ""
	for letter in mylist:
		mystring += letter + spacer
	return mystring

def list2text(mylist):
	mystring = ""
	if len(mylist) > 2:
		sublist = mylist[:-1]
		for letter in sublist:
			mystring += letter+", "
		mystring += "and "+mylist[-1]
	elif len(mylist) == 2:
		mystring = mylist[0]+" and "+mylist[1]
	return mystring

num2word = {
	1: 'one', 2: 'two', 3: 'three', 4: 'four', 5: 'five',
	6: 'six', 7: 'seven', 8: 'eight', 9: 'nine', 10: 'ten',
	11: 'eleven', 12: 'twelve', 13: 'thirteen', 14: 'fourteen',
	15: 'fifteen', 16: 'sixteen', 17: 'seventeen', 18: 'eighteen', 19: 'nineteen',
	20: 'twenty',
}

def cutChromosome(chromolist, cut):
	chromosome_A = []
	chromosome_B = []
	count = 0
	for item in chromolist:
		count += 1
		if count <= cut:
			chromosome_A.append(item)
		else:
			chromosome_B.append(item)
	return chromosome_A, chromosome_B

def drawChromosomeCut(chromolist, cut):
	mystr = ""
	count = 0
	for item in chromolist:
		count += 1
		mystr += item
		if count == cut:
			mystr += "|"
	return mystr

#====================
def makeQuestion():
	if len(sys.argv) >= 2:
		min_size = int(sys.argv[1])
	else:
		min_size = 5
	if min_size < 4:
		print("Sorry, you must have at least 4 genes for this program")
		sys.exit(1)
	if min_size > 9:
		print("Sorry, you cant have a minimum bigger than 9 genes per chromosome for this program")
		sys.exit(1)

	print(("Minimum chromosome size: %d"%(min_size)))

	charlist = list("ABCDEFGHJKMPQRSTWXYZ")

	chromosome1_size = random.randint(min_size, 10)
	chromosome1 = charlist[:chromosome1_size]

	chromosome2_size = random.randint(min_size, len(charlist)-chromosome1_size-1)
	chromosome2_shift = random.randint(chromosome1_size+1, len(charlist)-chromosome2_size)
	chromosome2 = charlist[chromosome2_shift:chromosome2_shift+chromosome2_size]


	chromosome1_cut = random.randint(2, chromosome1_size-2)
	chromosome2_cut = random.randint(2, chromosome2_size-2)
	#print chromosome1_cut, chromosome2_cut

	print(list2string(chromosome1), chromosome1_cut, chromosome1_size)
	print(list2string(chromosome2), chromosome2_cut, chromosome2_size)
	print(drawChromosomeCut(chromosome1, chromosome1_cut))
	print(drawChromosomeCut(chromosome2, chromosome2_cut))

	chromosome1_A, chromosome1_B = cutChromosome(chromosome1, chromosome1_cut)
	chromosome2_A, chromosome2_B = cutChromosome(chromosome2, chromosome2_cut)

	#this should not happen, but it does
	if len(chromosome1_A) <= 1:
		print("ERROR")
		return None
	if len(chromosome1_B) <= 1:
		print("ERROR")
		return None
	if len(chromosome2_A) <= 1:
		print("ERROR")
		return None
	if len(chromosome2_B) <= 1:
		print("ERROR")
		return None

	choices = []
	choices.append( chromosome1_A + chromosome2_B )
	choices.append( chromosome2_A + chromosome1_B )
	choices.append( chromosome1_A + chromosome2_A[::-1] )
	choices.append( chromosome1_B[::-1] + chromosome2_B )

	#so many wrong answer to choose from, want a short answer
	if len(chromosome1_A) < len(chromosome1_B):
		chromosome_piece1 = chromosome1_A
	else:
		#make sure telomeres are on the left
		chromosome_piece1 = chromosome1_B[::-1]
	if len(chromosome2_A) < len(chromosome2_B):
		chromosome_piece2 = chromosome2_A
	else:
		#make sure telomeres are on the left
		chromosome_piece2 = chromosome2_B[::-1]

	### SPEND A LOT OF TIME TO CREATE A WRONG ANSWER:
	#now merge pieces for a wrong answer
	if random.random() < 0.5:
		if random.random() < 0.5:
			wrong_answer = chromosome_piece1 + chromosome_piece2
		else:
			wrong_answer = chromosome_piece1[::-1] + chromosome_piece2
	else:
		if random.random() < 0.5:
			wrong_answer = chromosome_piece2 + chromosome_piece1
		else:
			wrong_answer = chromosome_piece2[::-1] + chromosome_piece1

	choices.append(wrong_answer)
	#print("\n")



	bar = " <b>|</b> "

	question = ''
	question += ("Two chromosomes with the gene sequences ")
	question += list2string(chromosome1_A, "") + list2string(chromosome1_B, "")
	question += (" and ")
	question += list2string(chromosome2_A, "") + list2string(chromosome2_B, "")
	question += (" undergo a reciprocal translocation after breaks between ")
	question += chromosome1_A[-1] + bar + chromosome1_B[0]
	question += (" and ")
	question += chromosome2_A[-1] + bar + chromosome2_B[0]
	question += (". Which one of the following is <b>NOT</b> a possible product of this translocation?")

	blackboard = "MC\t"
	blackboard += question
	#print(question)


	random.shuffle(choices)
	for i,a in enumerate(choices):
		blackboard += "\t"
		display = (charlist[i] + ". ")
		if random.random() < 0.5:
			display += list2string(a, "")
			blackboard += list2string(a, "")
		else:
			display += list2string(a[::-1], "")
			blackboard += list2string(a[::-1], "")
		print(display)
		if a == wrong_answer:
			correct_letter = charlist[i]
			blackboard += '\tCorrect'
		else:
			blackboard += '\tIncorrect'

	print("Answer: "+correct_letter)
	return blackboard

if __name__ == "__main__":
	outfile = 'bbq-' + os.path.splitext(os.path.basename(__file__))[0] + '-questions.txt'
	print('writing to file: '+outfile)
	f = open(outfile, 'w')	
	duplicates = 89
	for i in range(duplicates):
		blackboard = makeQuestion()
		if blackboard is not None:
			f.write(blackboard+'\n')
		else:
			sys.exit(1)
	f.close()