1.
openfile = open('title.txt','w')
openfile.write('This is sequence file')
openfile.close()


2.
openfile = open('title.txt').readline()
print openfile


3.
openfile = open('ap2.fa')

while 1:
	line = openfile.readline()
	if line != '':
		print line.strip()
	else:
		break


4.
openfile = open('ap2.fa')

result = ''
while 1:
	line = openfile.readline()
	if line != '':
		result = result + line
	else:
		break

writefile = open('seq2.txt','w')
writefile.write(line)
writefile.close()


5.
openfile=open('title.txt').readlines()
print openfile.split(' ')[1]


6.
openfile = open('ap2.fa')

seq = ''
while 1:
	line = openfile.readline()
	if line != '':
		if '>' in line:
			title = line.strip()
		else:
			seq = seq + line.strip()
	else:
		break

print title
print seq


7.
dic1 = {}
while 1:
	codon = raw_input('codon?')
	if codon == 'XXX':
		break
	aa = raw_input('aa?')
	dic1[codon] = aa

codon1 = raw_input('codon?')
print dic1[codon1]


8.
openfile = open('ap2.fa').readlines()

title = openfile[0].strip()

seq = ''
for line in openfile:
	if '>' not in line:
		seq = seq + line.strip()

aa={'TTT':'Phe','TTC':'Phe','TTA':'Leu','TTG':'Leu','CTT':'Leu','CTC':'Leu','CTA':'Leu','CTG':'Leu',\
'TCT':'Ser','TCC':'Ser','TCA':'Ser','TCG':'Ser','AGT':'Ser','AGC':'Ser','TAT':'Tyr','TAC':'Tyr',\
'TAA':'Tyr','TAG':'Tyr','TGT':'Cys','TGC':'Cys','TGA':'Trp','TGG':'Trp','CCT':'Pro','CCC':'Pro',\
'CCA':'Pro','CCG':'Pro','CAT':'His','CAC':'His','CAA':'Gln','CAG':'Gln','CGT':'Arg','CGC':'Arg',\
'CGA':'Arg','CGG':'Arg','AGA':'Arg','AGG':'Arg','ATT':'Ile','ATC':'Ile','ATA':'Ile','ATG':'Met',\
'ACT':'Thr','ACC':'Thr','ACA':'Thr','ACG':'Thr','AAT':'Asn','AAC':'Asn','AAA':'Lys','AAG':'Lys',\
'GTT':'Val','GTC':'Val','GTA':'Val','GTG':'Val','GCT':'Ala','GCC':'Ala','GCA':'Ala','GCG':'Ala',\
'GAT':'Asp','GAC':'Asp','GAA':'Glu','GAG':'Glu','GGT':'Gly','GGC':'Gly','GGA':'Gly','GGG':'Gly'}

aaseq = ''

for i in range(len(seq)/3):
	if 3*i+3 > len(seq):
		break
	aaseq = aaseq+aa[3*i:3*i+3]

print aaseq


9.
openfile = open('ap2.fa').readlines()

title = openfile[0].strip()

seq = ''
for line in openfile:
	if '>' not in line:
		seq = seq + line.strip()

aa={'TTT':'Phe','TTC':'Phe','TTA':'Leu','TTG':'Leu','CTT':'Leu','CTC':'Leu','CTA':'Leu','CTG':'Leu',\
'TCT':'Ser','TCC':'Ser','TCA':'Ser','TCG':'Ser','AGT':'Ser','AGC':'Ser','TAT':'Tyr','TAC':'Tyr',\
'TAA':'Tyr','TAG':'Tyr','TGT':'Cys','TGC':'Cys','TGA':'Trp','TGG':'Trp','CCT':'Pro','CCC':'Pro',\
'CCA':'Pro','CCG':'Pro','CAT':'His','CAC':'His','CAA':'Gln','CAG':'Gln','CGT':'Arg','CGC':'Arg',\
'CGA':'Arg','CGG':'Arg','AGA':'Arg','AGG':'Arg','ATT':'Ile','ATC':'Ile','ATA':'Ile','ATG':'Met',\
'ACT':'Thr','ACC':'Thr','ACA':'Thr','ACG':'Thr','AAT':'Asn','AAC':'Asn','AAA':'Lys','AAG':'Lys',\
'GTT':'Val','GTC':'Val','GTA':'Val','GTG':'Val','GCT':'Ala','GCC':'Ala','GCA':'Ala','GCG':'Ala',\
'GAT':'Asp','GAC':'Asp','GAA':'Glu','GAG':'Glu','GGT':'Gly','GGC':'Gly','GGA':'Gly','GGG':'Gly'}

while 1:
	i = raw_input('Enter the position : ')
	if i == 'XXX':break
	print 'The next 3 amino acids are : ',aa[seq[int(i):int(i)+3]],aa[seq[int(i)+3:int(i)+6]],aa[seq[int(i)+6:int(i)+9]]


10.
openfile = open('/data2/python_study/ap2.fa').readlines()

title = openfile[0].strip()

seq = ''
for line in openfile:
	if '>' not in line:
		seq = seq + line.strip()

aa={'TTT':'Phe','TTC':'Phe','TTA':'Leu','TTG':'Leu','CTT':'Leu','CTC':'Leu','CTA':'Leu','CTG':'Leu',\
'TCT':'Ser','TCC':'Ser','TCA':'Ser','TCG':'Ser','AGT':'Ser','AGC':'Ser','TAT':'Tyr','TAC':'Tyr',\
'TAA':'Tyr','TAG':'Tyr','TGT':'Cys','TGC':'Cys','TGA':'Trp','TGG':'Trp','CCT':'Pro','CCC':'Pro',\
'CCA':'Pro','CCG':'Pro','CAT':'His','CAC':'His','CAA':'Gln','CAG':'Gln','CGT':'Arg','CGC':'Arg',\
'CGA':'Arg','CGG':'Arg','AGA':'Arg','AGG':'Arg','ATT':'Ile','ATC':'Ile','ATA':'Ile','ATG':'Met',\
'ACT':'Thr','ACC':'Thr','ACA':'Thr','ACG':'Thr','AAT':'Asn','AAC':'Asn','AAA':'Lys','AAG':'Lys',\
'GTT':'Val','GTC':'Val','GTA':'Val','GTG':'Val','GCT':'Ala','GCC':'Ala','GCA':'Ala','GCG':'Ala',\
'GAT':'Asp','GAC':'Asp','GAA':'Glu','GAG':'Glu','GGT':'Gly','GGC':'Gly','GGA':'Gly','GGG':'Gly'}

seq_aa = ''
for i in range(len(seq)/3):
	seq_aa = seq_aa + aa[seq[3*i:3*i+3]]
while 1:
	j = raw_input('Enter amino acid code :')
	if j == 'XXX':break
	position_list = []
	for i in range(len(seq_aa)/3):
		if seq_aa[3*i:3*i+3] == j:
			position_list.append(str(i+1))
	print 'The amino acid is found at : ' + ', '.join(position_list)