def getPrimerChoices(top_sequence, primer_len):
bottom_sequence = seqlib.complement(top_sequence)
primer_set = []
primer = top_sequence[:primer_len]
primer_set.append(primer) #answer1
answer1 = primer
primer_set.append(seqlib.flip(primer))
primer = bottom_sequence[:primer_len]
primer_set.append(primer)
primer_set.append(seqlib.flip(primer))
primer = top_sequence[-primer_len:]
primer_set.append(primer)
primer_set.append(seqlib.flip(primer))
primer = bottom_sequence[-primer_len:]
primer_set.append(primer) #answer2
primer_set.append(seqlib.flip(primer))
answer2 = seqlib.flip(primer)
answer_set = [answer1, answer2]
for ans in answer_set:
for nt in list('ACGT'):
if not nt in ans:
return False, answer_set
primer_set.sort()
print(primer_set)
print(answer_set)
convert_set = []
for primer in primer_set:
subprimer = primer.replace('T', 'A')
convert_set.append(subprimer)
subprimer = primer.replace('C', 'G')
convert_set.append(subprimer)
if len(list(set(convert_set))) < 16:
print("BAD PRIMERS")
#sys.exit(1)
return False, answer_set
return primer_set, answer_set
def makeChoices(primer_set, answer_set): choices = set() choices.add(tuple(answer_set)) wrong = (answer_set[0], seqlib.flip(answer_set[1])) choices.add(wrong) wrong = (answer_set[1], seqlib.flip(answer_set[0])) choices.add(wrong) wrong = (seqlib.flip(answer_set[0]), seqlib.flip(answer_set[1])) choices.add(wrong) while len(choices) < 6: c1 = random.choice(primer_set) c2 = random.choice(primer_set) if c1 != c2: choices.add((c1, c2)) choices_list = list(choices) print(choices_list) random.shuffle(choices_list) return choices_list
def makeMultipleChoiceQuestion(enzyme_class, question_number=13):
charlist = list("ABCDEFGHJKMPQRSTWXYZ")
name = restrictlib.html_monospace(enzyme_class.__name__)
cut_description = restrictlib.html_monospace(restrictlib.format_enzyme(enzyme_class))
question = "{0}. ".format(question_number)
question += "The restriction enzyme <b>{0}</b> cuts the sequence: {1}. ".format(name, cut_description)
question += "Which one of the following sequences is the "
question += "single-stranded nucleotide overhang region after cleavage? "
#A. 5'-TGCA-3' B. 5'-CTGCA-3' C. 5'-TGCAG-3' D. 5'-ACGT-3'
choices = []
#print(enzyme_class.ovhgseq)
#print(enzyme_class.site)
#print(enzyme_class.elucidate())
shift = (len(enzyme_class.site) - len(enzyme_class.ovhgseq))//2
#print(shift)
answer = ("5'-{0}-3'".format(enzyme_class.ovhgseq))
choices.append(answer)
inverse = ("5'-{0}-3'".format(seqlib.flip(enzyme_class.ovhgseq)))
choices.append(inverse)
expanded1 = ("5'-{0}-3'".format(enzyme_class.site[shift:]))
choices.append(expanded1)
expanded2 = ("5'-{0}-3'".format(enzyme_class.site[:-shift]))
choices.append(expanded2)
expandflip1 = ("5'-{0}-3'".format(seqlib.flip(enzyme_class.site[shift:])))
choices.append(expandflip1)
expandflip2 = ("5'-{0}-3'".format(seqlib.flip(enzyme_class.site[:-shift])))
choices.append(expandflip2)
#print(choices)
choices = list(set(choices))
#print(choices)
if len(choices) > 5:
a = choices.pop()
if a == answer:
choices.pop()
choices.append(answer)
try:
choices.remove("5'--3'")
except ValueError:
pass
#print(choices)
random.shuffle(choices)
#print(choices)
if len(choices) <= 3:
return None
print(question)
for i in range(len(choices)):
ltr = charlist[i]
choice = choices[i]
prefix = ""
if choice == answer:
prefix = "*"
print("{0}{1}. {2}".format(prefix, ltr, choice))
seq = seqlib.makeSequence(seqlen)
answer = seqlib.complement(seq)
#============================
print(
"1. Which one of the following DNA sequences is complimentary to the direction-less DNA sequence {0} ?"
.format(seqlib.html_monospace(seq)))
#============================
choices = []
half = int(seqlen // 2)
#choice 1
choices.append(answer)
#choice 2
choices.append(seqlib.flip(seq))
extra_choices = []
extra_choices.append(answer[:half] + seq[half:])
extra_choices.append(seq[:half] + answer[half:])
extra_choices.append(seqlib.flip(seq[:half]) + seq[half:])
extra_choices.append(seq[:half] + seqlib.flip(seq[half:]))
extra_choices.append(seqlib.flip(answer[:half]) + answer[half:])
extra_choices.append(answer[:half] + seqlib.flip(answer[half:]))
extra_choices.append(answer[:half] + seqlib.flip(seq[half:]))
random.shuffle(extra_choices)
extra_choices = list(set(extra_choices))
random.shuffle(extra_choices)
for i in range(3):
choices.append(extra_choices.pop())
#!/usr/bin/env python
import sys
import seqlib
import random
if __name__ == '__main__':
if len(sys.argv) >= 2:
seqlen = int(sys.argv[1])
else:
seqlen = 7
#============================
seq = seqlib.makeSequence(seqlen)
answer = seqlib.flip(seqlib.complement(seq))
#============================
if random.random() < 0.5:
print("1. Which one of the following sequences is complimentary to the sequence <span style='font-family: monospace;'>5'-%s-3'</span>? Hint: pay attention to the 5' and 3' directions!"%(seq))
else:
print("1. Which one of the following sequences is complimentary to the sequence <span style='font-family: monospace;'>3'-%s-5'</span>? Hint: pay attention to the 5' and 3' directions!"%(seqlib.flip(seq)))
#============================
choices = []
half = int(seqlen//2)
#choice 1
choices.append(seq)
#choice 2
choices.append(seqlib.flip(seq))
#choice 3
#!/usr/bin/env python
import sys
import seqlib
if __name__ == '__main__':
if len(sys.argv) >= 2:
seqlen = int(sys.argv[1])
else:
seqlen = 10
#============================
seq = seqlib.makeSequence(seqlen)
answer = seqlib.transcribe(seqlib.complement(seq))
#============================
print(
"blank 1. What is the RNA sequence to the DNA template strand sequence <span style='font-family: monospace;'>{0}</span>?"
.format(seq))
#============================
print("A. {0}".format(answer))
print("B. {0}".format(seqlib.flip(answer)))
#!/usr/bin/env python
import sys
import seqlib
import random
if __name__ == '__main__':
if len(sys.argv) >= 2:
seqlen = int(sys.argv[1])
else:
seqlen = 7
#============================
seq = seqlib.makeSequence(seqlen)
answer = seqlib.flip(seqlib.complement(seq))
#============================
question = "1. Which one of the following sequences is RNA transcription to the "
if random.random() < 0.5:
dirseq = "5'-{0}-3'".format(seq)
question += "DNA non-template/coding strand sequence {0} ?".format(seqlib.html_monospace(dirseq))
else:
dirseq = "3'-{0}-5'".format(seqlib.flip(seq))
question += "DNA template strand sequence {0} ?".format(seqlib.html_monospace(dirseq))
question += " Hint: pay attention to the 5' and 3' directions!"
print(question)
#============================
choices = []
half = int(seqlen//2)