#Benjamin Leibowicz
#Biophysics 101
#Assignment 3

# Exercise 1

p53segraw = """cggagcagctcactattcacccgatgagaggggaggagagagagagaaaatgtcctttag
gccggttcctcttacttggcagagggaggctgctattctccgcctgcatttctttttctg
gattacttagttatggcctttgcaaaggcaggggtatttgttttgatgcaaacctcaatc
cctccccttctttgaatggtgtgccccaccccccgggtcgcctgcaacctaggcggacgc
taccatggcgtagacagggagggaaagaagtgtgcagaaggcaagcccggaggcactttc
aagaatgagcatatctcatcttcccggagaaaaaaaaaaaagaatggtacgtctgagaat
gaaattttgaaagagtgcaatgatgggtcgtttgataatttgtcgggaaaaacaatctac
ctgttatctagctttgggctaggccattccagttccagacgcaggctgaacgtcgtgaag
cggaaggggcgggcccgcaggcgtccgtgtggtcctccgtgcagccctcggcccgagccg
gttcttcctggtaggaggcggaactcgaattcatttctcccgctgccccatctcttagct
cgcggttgtttcattccgcagtttcttcccatgcacctgccgcgtaccggccactttgtg
ccgtacttacgtcatctttttcctaaatcgaggtggcatttacacacagcgccagtgcac
acagcaagtgcacaggaagatgagttttggcccctaaccgctccgtgatgcctaccaagt
cacagacccttttcatcgtcccagaaacgtttcatcacgtctcttcccagtcgattcccg
accccacctttattttgatctccataaccattttgcctgttggagaacttcatatagaat
ggaatcaggatgggcgctgtggctcacgcctgcactttggctcacgcctgcactttggga
ggccgaggcgggcggattacttgaggataggagttccagaccagcgtggccaacgtggtg"""

p53seg = ""

rawlength = len(p53segraw)

numC = 0
numG = 0
numT = 0
numA = 0

# We could use the count method to obtain the number of occurences of
# each nucleotide but Python had difficulty getting the length of the
# original string correct. It seemed to be adding an extra mystery
# character to each line. The following method doubles by solving this
# problem.

for i in range(0,rawlength):
	if p53segraw[i]=='a':
		p53seg = p53seg + 'a'
		numA = numA + 1
	elif p53segraw[i]=='t':
		p53seg = p53seg + 't'
		numT = numT + 1
	elif p53segraw[i]=='c':
		p53seg = p53seg + 'c'
		numC = numC + 1
	elif p53segraw[i]=='g':
		p53seg = p53seg + 'g'
		numG = numG + 1

length = len(p53seg)

GCcontent = (float(numC + numG)/float(length))*100

print 'The GC content of p53seg is ',GCcontent, '%.'

# Exercise 2

rc = p53seg[::-1]

reversecomplement = ""

for i in range(0,length):
	if rc[i]=='a':
		reversecomplement = reversecomplement + 't'
	elif rc[i]=='t':
		reversecomplement = reversecomplement + 'a'
	elif rc[i]=='c':
		reversecomplement = reversecomplement + 'g'
	elif rc[i]=='g':
		reversecomplement = reversecomplement + 'c'	

print '\nThe reverse complement of p53seg is:\n', reversecomplement

# Exercise 3

standard = { 'ttt': 'F', 'tct': 'S', 'tat': 'Y', 'tgt': 'C',
		'ttc': 'F', 'tcc': 'S', 'tac': 'Y', 'tgc': 'C',
		'tta': 'L', 'tca': 'S', 'taa': '*', 'tga': '*',
		'ttg': 'L', 'tcg': 'S', 'tag': '*', 'tgg': 'W',
		'ctt': 'L', 'cct': 'P', 'cat': 'H', 'cgt': 'R',
		'ctc': 'L', 'ccc': 'P', 'cac': 'H', 'cgc': 'R',
		'cta': 'L', 'cca': 'P', 'caa': 'Q', 'cga': 'R',
		'ctg': 'L', 'ccg': 'P', 'cag': 'Q', 'cgg': 'R',
 		'att': 'I', 'act': 'T', 'aat': 'N', 'agt': 'S',
 		'atc': 'I', 'acc': 'T', 'aac': 'N', 'agc': 'S',
                'ata': 'I', 'aca': 'T', 'aaa': 'K', 'aga': 'R',
  		'atg': 'M', 'acg': 'T', 'aag': 'K', 'agg': 'R',
		'gtt': 'V', 'gct': 'A', 'gat': 'D', 'ggt': 'G',
		'gtc': 'V', 'gcc': 'A', 'gac': 'D', 'ggc': 'G',
		'gta': 'V', 'gca': 'A', 'gaa': 'E', 'gga': 'G',
		'gtg': 'V', 'gcg': 'A', 'gag': 'E', 'ggg': 'G'}		

# Translate the DNA sequence into a protein sequence in all 6 frames.
		
j = 0
proteinsequenceplus1 = ""

while j<1020:
	codon = p53seg[j:j+3]
	proteinsequenceplus1 = proteinsequenceplus1 + standard[codon]
	j = j+3

print '\nThe protein sequence in the +1 frame is:\n', proteinsequenceplus1

k = 1
proteinsequenceplus2 = ""

while k<1017:
	codon = p53seg[k:k+3]
	proteinsequenceplus2 = proteinsequenceplus2 + standard[codon]
	k = k+3

print '\nThe protein sequence in the +2 frame is:\n', proteinsequenceplus2

l = 2
proteinsequenceplus3 = ""

while l<1017:
	codon = p53seg[l:l+3]
	proteinsequenceplus3 = proteinsequenceplus3 + standard[codon]
	l = l+3

print '\nThe protein sequence in the +3 frame is:\n', proteinsequenceplus3

r = 0
proteinsequenceminus1 = ""

while r<1020:
	codon = reversecomplement[r:r+3]
	proteinsequenceminus1 = proteinsequenceminus1 + standard[codon]
	r = r+3

print '\nThe protein sequence in the -1 frame is:\n', proteinsequenceminus1

s = 1
proteinsequenceminus2 = ""

while s<1017:
	codon = reversecomplement[s:s+3]
	proteinsequenceminus2 = proteinsequenceminus2 + standard[codon]
	s = s+3

print '\nThe protein sequence in the -2 frame is:\n', proteinsequenceminus2

t = 2
proteinsequenceminus3 = ""

while t<1017:
	codon = reversecomplement[t:t+3]
	proteinsequenceminus3 = proteinsequenceminus3 + standard[codon]
	t = t+3

print '\nThe protein sequence in the -3 frame is:\n', proteinsequenceminus3

# Exercise 4

p53segmut = p53seg
import random

for z in range(1,13):
	rand = random.randint(0,length)
	chance = random.randint(1,4)
	if chance==1:
		p53segmut = p53segmut[0:rand] + 'a' + p53segmut[rand+1:length]
	elif chance==2:
		p53segmut = p53segmut[0:rand] + 't' + p53segmut[rand+1:length]
	elif chance==3:
		p53segmut = p53segmut[0:rand] + 'g' + p53segmut[rand+1:length]
	elif chance==4:
		p53segmut = p53segmut[0:rand] + 'c' + p53segmut[rand+1:length]		

m = 0
proteinsequencemut = ""

while m<1020:
	codon = p53segmut[m:m+3]
	proteinsequencemut = proteinsequencemut + standard[codon]
	m = m+3

print '\nThe mutated protein sequence in the +1 frame is:\n', proteinsequencemut

for c in range(0,len(proteinsequenceplus1)):
        if proteinsequenceplus1[c]!=proteinsequencemut[c]:
                print "\nNormal codon:", proteinsequenceplus1[c], "Mutation changes to:", proteinsequencemut[c], "."