consensus_sequence_easy.py

#!/usr/bin/env python

import os
import sys
import copy
import random

dna = ['A', 'C', 'G', 'T',]

"""
num_sequence = 3 #fixed for easy
num_diff_sequence = 1 #fixed for easy / max 3
random_diff_sequence = False
sequence_length = 6
separate = 3
"""

"""
num_sequence = 5 #fixed for easy
num_diff_sequence = 3 #fixed for easy / max 3
random_diff_sequence = True
sequence_length = 12
separate = 3
"""

num_sequence = 9 #fixed for easy
num_diff_sequence = 3 #fixed for easy / max 3
random_diff_sequence = False
sequence_length = 9
separate = 3




#==========================
def colorNucleotide(nt):
	adenine = ' bgcolor="#e6ffe6"' #green
	cytosine = ' bgcolor="#e6f3ff"' #blue
	thymine = ' bgcolor="#ffe6e6"' #red
	guanine = ' bgcolor="#f2f2f2"' #black
	uracil = ' bgcolor="#f3e6ff"' #purple
	if nt == 'A':
		return adenine
	elif nt == 'C':
		return cytosine
	elif nt == 'G':
		return guanine
	elif nt == 'T':
		return thymine
	elif nt == 'U':
		return thymine
	return ''

#==========================
def makeSequences():
	sequence_list = []
	for j in range(num_sequence):
		sequence_list.append('')
	consensus = ''
	
	for i in range(sequence_length):
		other_dna = copy.copy(dna)
		random.shuffle(other_dna)
		letter = other_dna.pop()
		consensus += letter
		indices = list(range(num_sequence))
		random.shuffle(indices)
		if random_diff_sequence is True:
			diff_sequence_indices = indices[:random.randint(0,num_diff_sequence)]
		else:
			diff_sequence_indices = indices[:num_diff_sequence]
		for j in range(num_sequence):
			if j in diff_sequence_indices:
				sequence_list[j] += other_dna.pop()
			else:
				sequence_list[j] += letter

	return consensus, sequence_list

#==========================
def makeSequencesSafe():
	not_good = True
	i = 0
	while not_good is True:
		i += 1
		#print("trying sequences {0}".format(i))
		consensus, sequence_list = makeSequences()
		not_good = False
		for s in sequence_list:
			if s == consensus:
				not_good = True
	return consensus, sequence_list

#==========================
def scoreSequences(seq1, seq2):
	min_length = min(len(seq1), len(seq2))
	score = 0
	for i in range(min_length):
		if seq1[i] == seq2[i]:
			score += 1
	return score

#==========================
def makeHtmlRow(seq):
	htmlrow = ""
	htmlrow += "<tr>"
	for i in range(len(seq)):
		if i > 0 and i % separate == 0:
			htmlrow += "<td>&nbsp;,&nbsp;</td> "
		nt = seq[i]
		htmlrow += "<td {1}>&nbsp;{0}&nbsp;</td> ".format(nt, colorNucleotide(nt))
	return htmlrow

#==========================
def makeHtmlTable(sequence_list):
	table = ""
	table += '<table style="border-collapse: collapse; border: 1px solid silver;"> '
	table += "<tr> "
	for j in range(num_sequence):
		table += makeHtmlRow(sequence_list[j])
	table += '</tr></table> '
	return table

#==========================
def printSequence(seq, consensus=None):
	if consensus is not None:
		score = scoreSequences(seq, consensus)
		sys.stderr.write('{0:02d} '.format(score))
	for i in range(len(seq)):
		if i > 0 and i % separate == 0:
			sys.stderr.write(', ')
		sys.stderr.write(seq[i] + " ")
	sys.stderr.write('\n')

#==========================
def insertCommas(my_str):
	new_str = ''
	for i in range(0, len(my_str), separate):
		new_str += my_str[i:i+separate] + ','
	return new_str[:-1]


# FIB TAB question text TAB answer text TAB answer two text

#==========================
#==========================
def makeCompleteQuestion():
	consensus, sequence_list = makeSequencesSafe()

	#for j in range(num_sequence):
	#	printSequence(sequence_list[j], consensus)
	#printSequence(consensus, consensus)

	table = makeHtmlTable(sequence_list)
	question = "What is the consensus sequence for the table above? "
	question += "<br/> <i> you may include a comma every {0} letters, but ".format(separate)
	question += "do not include any extra commas or spaces in your answer. </i>"


	bbquestion = 'FIB\t'
	bbquestion += table + ' <br/> '
	bbquestion += question + '\t'
	bbquestion += consensus + '\t'	
	bbquestion += insertCommas(consensus)

	#============================
	print("blank 1. "+question)
	print("A. {0}".format(consensus))
	print("B. {0}".format(insertCommas(consensus)))
	print('')
	return bbquestion


#==========================
#==========================
if __name__ == '__main__':
	duplicates = 199
	outfile = 'bbq-' + os.path.splitext(os.path.basename(__file__))[0] + '-questions.txt'
	print('writing to file: '+outfile)
	f = open(outfile, 'w')
	for i in range(duplicates):
		complete_question = makeCompleteQuestion()
		f.write(complete_question)
		f.write('\n')
	f.close()
	
#==========================
#==========================
#==========================
#==========================