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script.py
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script.py
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#!/usr/bin/python
import argparse
import sys
import math
class PhysioCal():
def __init__(self):
self.data = []
def fasta_reader(self,inputpath):
fileinput = open(inputpath, "r")
line = fileinput.readline()
header = ''
sequence = ''
while line:
line = line.rstrip('\n')
if '>' in line:
header = line
else:
sequence = sequence + line
line = fileinput.readline()
print(line)
print()
return sequence
fileinput.close()
def nucleotide(self,sequence):
seq=str.upper(sequence)
length = len(seq)
A = seq.count('A')
T = seq.count('T')
G = seq.count('G')
C = seq.count('C')
extinction_C=((A*15.4)+(C*7.2)+(G*11.5)+(T*8.7))*0.9*1000
m_weight = ((A * 313.21) + (T * 304.2) + (G * 329.21) + (C * 289.18)) - 61.96
if length < 14:
temp1 = 4 * (G + C) + 2 * (A + T)
print('Theoratical Basic temp. is:%.1f C' % temp1)
elif length >= 14:
temp2 = 64.9 + 41 * (G + C - 16.4) / (A + T + G + C)
print('Theoratical temp. is:%.1f C' % temp2)
print('Lenngth of sequence is %d bP:' % length)
print('Anhydrous Molecular weight:%.1f daltons' % m_weight)
print('No. of Gaunine in sequence are:%d' % G)
print('No. of Cytocine in sequence are:%d' % C)
print('No. of Adnine in sequence are:%d' % A)
print('No. of Thymine in sequence are:%d' % T)
print('GC content of seq. is:%d' % ((G + C) / length * 100), '%')
print('Extenction Coefficient of sequence is: %d /M /cm' %extinction_C)
'''variable for each IUPAC aminoacid codon'''
f1 = 0;f2 = 0;l1 = 0;l2 = 0;l3 = 0;l4 = 0;l5 = 0;l6 = 0;s1 = 0;s2 = 0;s3 = 0
s4 = 0;s5 = 0;s6 = 0;r1 = 0;r2 = 0;r3 = 0;r4 = 0;r5 = 0;r6 = 0;p1 = 0;p2 = 0
p3 = 0;p4 = 0;v1 = 0;v2 = 0;v3 = 0;v4 = 0;t1 = 0;t2 = 0;t3 = 0;t4 = 0;a1 = 0
a2 = 0;a3 = 0;a4 = 0;g1 = 0;g2 = 0;g3 = 0;g4 = 0;i1 = 0;i2 = 0;i3 = 0
stop1 = 0;stop2 = 0;stop3 = 0;y1 = 0;y2 = 0;h1 = 0;h2 = 0;q1 = 0;q2 = 0;n1 = 0
n2 = 0;k1 = 0;k2 = 0;d1 = 0;d2 = 0;e1 = 0;e2 = 0;c1 = 0;c2 = 0;w1 = 0;m = 0
x=0
size=len(seq)
while (x < size):
if ((x + 3) <= size):
if (seq[x:x + 3] == "TTT"):
f1 = f1 + 1
elif (seq[x:x + 3] == "TTC"):
f2 = f2 + 1
elif (seq[x:x + 3] == "TTA"):
l1 = l1 + 1
elif (seq[x:x + 3] == "TTG"):
l2 = l2 + 1
elif (seq[x:x + 3] == "CTT"):
l3 = l3 + 1
elif (seq[x:x + 3] == "CTC"):
l4 = l4 + 1
elif (seq[x:x + 3] == "CTA"):
l5 = l5 + 1
elif (seq[x:x + 3] == "CTG"):
l6 = l6 + 1
elif (seq[x:x + 3] == "ATT"):
i1 = i1 + 1
elif (seq[x:x + 3] == "ATC"):
i2 = i2 + 1
elif (seq[x:x + 3] == "ATA"):
i3 = i3 + 1
elif (seq[x:x + 3] == "ATG"):
m = m + 1
elif (seq[x:x + 3] == "GTT"):
v1 = v1 + 1
elif (seq[x:x + 3] == "GTC"):
v2 = v2 + 1
elif (seq[x:x + 3] == "GTA"):
v3 = v3 + 1
elif (seq[x:x + 3] == "GTG"):
v4 = v4 + 1
elif (seq[x:x + 3] == "TCT"):
s1 = s1 + 1
elif (seq[x:x + 3] == "TCC"):
s2 = s2 + 1
elif (seq[x:x + 3] == "TCA"):
s3 = s3 + 1
elif (seq[x:x + 3] == "TCG"):
s4 = s4 + 1
elif (seq[x:x + 3] == "CCT"):
p1 = p1 + 1
elif (seq[x:x + 3] == "CCC"):
p2 = p2 + 1
elif (seq[x:x + 3] == "CCA"):
p3 = p3 + 1
elif (seq[x:x + 3] == "CCG"):
p4 = p4 + 1
elif (seq[x:x + 3] == "ACT"):
t1 = t1 + 1
elif (seq[x:x + 3] == "ACC"):
t2 = t2 + 1
elif (seq[x:x + 3] == "ACA"):
t3 = t3 + 1
elif (seq[x:x + 3] == "ACG"):
t4 = t4 + 1
elif (seq[x:x + 3] == "GCT"):
a1 = a1 + 1
elif (seq[x:x + 3] == "GCC"):
a2 = a2 + 1
elif (seq[x:x + 3] == "GCA"):
a3 = a3 + 1
elif (seq[x:x + 3] == "GCG"):
a4 += 1
elif (seq[x:x + 3] == "TAT"):
y1 = y1 + 1
elif (seq[x:x + 3] == "TAC"):
y2 = y2 + 1
elif (seq[x:x + 3] == "TAA"):
stop1 = stop1 + 1
elif (seq[x:x + 3] == "TAG"):
stop2 = stop2 + 1
elif (seq[x:x + 3] == "CAT"):
h1 = h1 + 1
elif (seq[x:x + 3] == "CAC"):
h2 = h2 + 1
elif (seq[x:x + 3] == "CAA"):
q1 = q1 + 1
elif (seq[x:x + 3] == "CAG"):
q2 = q2 + 1
elif (seq[x:x + 3] == "AAT"):
n1 = n1 + 1
elif (seq[x:x + 3] == "AAC"):
n2 = n2 + 1
elif (seq[x:x + 3] == "AAA"):
k1 = k1 + 1
elif (seq[x:x + 3] == "AAG"):
k2 = k2 + 1
elif (seq[x:x + 3] == "GAT"):
d1 = d1 + 1
elif (seq[x:x + 3] == "GAC"):
d2 = d2 + 1
elif (seq[x:x + 3] == "GAA"):
e1 = e1 + 1
elif (seq[x:x + 3] == "GAG"):
e2 = e2 + 1
elif (seq[x:x + 3] == "TGT"):
c1 = c1 + 1
elif (seq[x:x + 3] == "TGC"):
c2 = c2 + 1
elif (seq[x:x + 3] == "TGA"):
stop3 = stop3 + 1
elif (seq[x:x + 3] == "TGG"):
w1 = w1 + 1
elif (seq[x:x + 3] == "CGT"):
r1 = r1 + 1
elif (seq[x:x + 3] == "CGC"):
r2 = r2 + 1
elif (seq[x:x + 3] == "CGA"):
r3 = r3 + 1
elif (seq[x:x + 3] == "CGG"):
r4 = r4 + 1
elif (seq[x:x + 3] == "AGT"):
s5 = s5 + 1
elif (seq[x:x + 3] == "AGC"):
s6 = s6 + 1
elif (seq[x:x + 3] == "AGA"):
r5 = r5 + 1
elif (seq[x:x + 3] == "AGG"):
r6 = r6 + 1
elif (seq[x:x + 3] == "GGT"):
g1 = g1 + 1
elif (seq[x:x + 3] == "GGC"):
g2 = g2 + 1
elif (seq[x:x + 3] == "GGA"):
g3 = g3 + 1
elif (seq[x:x + 3] == "GGG"):
g4 = g4 + 1
x = x + 3
print('Genome Biasness')
print("Ala \t GCG \t %d" % a4)
print("Ala \t GCA \t %d" % a3)
print("Ala \t GCT \t %d" % a1)
print("Ala \t GCC \t %d" % a2)
print("Cys \t TGT \t %d" % c1)
print("Cys \t TGC \t %d" % c2)
print("Asp \t GAT \t %d" % d1)
print("Asp \t GAC \t %d" % d2)
print("Glu \t GAG \t %d" % e2)
print("Glu \t GAA \t %d" % e1)
print("Phe \t TTT \t %d" % f1)
print("Phe \t TTC \t %d" % f2)
print("Gly \t GGG \t %d" % g4)
print("Gly \t GGA \t %d" % g3)
print("Gly \t GGT \t %d" % g1)
print("Gly \t GGC \t %d" % g2)
print("His \t CAT \t %d" % h1)
print("His \t CAC \t %d" % h2)
print("Ile \t ATA \t %d" % i3)
print("Ile \t ATT \t %d" % i1)
print("Ile \t ATC \t %d" % i2)
print("Lys \t AAG \t %d" % k2)
print("Lys \t AAA \t %d" % k1)
print("Leu \t TTG \t %d" % l2)
print("Leu \t TTA \t %d" % l1)
print("Leu \t CTG \t %d" % l6)
print("Leu \t CTA \t %d" % l5)
print("Leu \t CTT \t %d" % l3)
print("Leu \t CTC \t %d" % l4)
print("Met \t ATG \t %d" % m)
print("Asn \t AAT \t %d" % n1)
print("Asn \t AAC \t %d" % n2)
print("Pro \t CCG \t %d" % p4)
print("Pro \t CCA \t %d" % p3)
print("Pro \t CCT \t %d" % p1)
print("Pro \t CCC \t %d" % p2)
print("Glu \t CAG \t %d" % q2)
print("Glu \t CAA \t %d" % q1)
print("Arg \t AGG \t %d" % r6)
print("Arg \t AGA \t %d" % r5)
print("Arg \t CGG \t %d" % r4)
print("Arg \t CGA \t %d" % r3)
print("Arg \t CGT \t %d" % r1)
print("Arg \t CGC \t %d" % r2)
print("Ser \t AGT \t %d" % s5)
print("Ser \t AGC \t %d" % s6)
print("Ser \t TCG \t %d" % s4)
print("Ser \t TCA \t %d" % s3)
print("Ser \t TCT \t %d" % s1)
print("Ser \t TCC \t %d" % s2)
print("Thr \t ACG \t %d" % t4)
print("Thr \t ACA \t %d" % t3)
print("Thr \t ACT \t %d" % t1)
print("Thr \t ACC \t %d" % t2)
print("Val \t GTG \t %d" % v4)
print("Val \t GTA \t %d" % v3)
print("Val \t GTT \t %d" % v1)
print("Val \t GTC \t %d" % v2)
print("Try \t TGG \t %d" % w1)
print("Tyr \t TAT \t %d" % y1)
print("Tyr \t TAC \t %d" % y2)
print("End \t TGA \t %d" % stop3)
print("End \t TAG \t %d" % stop2)
print("End \t TAA \t %d" % stop1)
#protein calculation function
def amino_acid(self,sequence):
length = len(sequence)
'''count individual amino acid'''
G = sequence.count('G') # Glysine
A = sequence.count('A') # Alanine
L = sequence.count('L') # Leucine
M = sequence.count('M') # Methionine
F = sequence.count('F') # Phenylalanine
W = sequence.count('W') # Trypthphan
K = sequence.count('K') # Lysine
Q = sequence.count('Q') # Glutamine
E = sequence.count('E') # Glutamic acid
S = sequence.count('S') # Serine
P = sequence.count('P') # Proline
V = sequence.count('V') # Valine
I = sequence.count('I') # Isoleusine
C = sequence.count('C') # Cystine
Y = sequence.count('Y') # Tyrosine
H = sequence.count('H') # Histidine
R = sequence.count('R') # Argnine
N = sequence.count('N') # Asparagine
D = sequence.count('D') # Aspartic Acid
T = sequence.count('T') # Threonine
'''Hydropthy values calculation'''
a = A * 1.800 # Alanine
l = L * 3.800 # Leucine
m = M * 1.900 # Methionine
f = F * 2.800 # Phenylalanine
v = V * 4.200 # Valine
i = I * 4.500 # Isoleusine
c = C * 2.500 # Cystine
g = G * (-0.400) # Glysine
w = W * (-0.900) # Trypthphan
k = K * (-3.900) # Lysine
q = Q * (-3.500) # Glutamine
e = E * (-3.500) # Glutamic acid
s = S * (-0.800) # Serine
p = P * (-1.600) # Proline
y = Y * (-1.300) # Tyrosine
h = H * (-3.200) # Histidine
r = R * (-4.500) # Argnine
n = N * (-3.500) # Asparagine
d = D * (-3.500) # Aspartic Acid
t = T * (-0.700) # Threonine
total = a + l + m + f + v + i + c + g + w + k + q + e + s + p + y + h + r + n + d + t
'''molecular weight calculation'''
w_a = A * 89.0935 # Alanine
w_l = L * 131.1736 # Leucine
w_m = M * 149.2124 # Methionine
w_f = F * 165.1900 # Phenylalanine
w_v = V * 117.1469 # Valine
w_i = I * 131.1736 # Isoleusine
w_c = C * 121.1590 # Cysteine
w_g = G * 75.0669 # Glysine
w_w = W * 204.2262 # Trypthphan
w_k = K * 146.1882 # Lysine
w_q = Q * 146.1451 # Glutamine
w_e = E * 147.1299 # Glutamic acid
w_s = S * 105.0930 # Serine
w_p = P * 115.1310 # Proline
w_y = Y * 181.1894 # Tyrosine
w_h = H * 155.1552 # Histidine
w_r = R * 174.2017 # Argnine
w_n = N * 132.1184 # Asparagine
w_d = D * 133.1032 # Aspartic Acid
w_t = T * 119.1197 # Threonine
total2 = w_a + w_l + w_m + w_f + w_v + w_i + w_c + w_g + w_w + w_k + w_q + w_e + w_s + w_p + w_y + w_h + w_r + w_n + w_d + w_t
h2o = 18.015
molecular_weight = total2 - h2o * (length - 1)
'''Protein half life calculation'''
# mammalian #Yeast #E.coli
hlife = {
'A': ['4.4 hour', '>20hour', '>10 hour'],
'R': ['1 hour', '2 min', '2 min'],
'N': ['1.4 hour', '3 min', '>10 hour'],
'D': ['1.1 hour', '3 min', '>10 hour'],
'C': ['1.2 hour', '>20 hour', '>10 hour'],
'Q': ['0.8 hour', '10 min', '>10 hour'],
'E': ['1 hour', '30 min', '>10 hour'],
'G': ['30 hour', '>20 hour', '>10 hour'],
'H': ['3.5 hour', '10 min', '>10 hour'],
'I': ['20 hour', '30 min', '>10 hour'],
'L': ['5.5 hour', '3 min', '2 min'],
'K': ['1.3 hour', '3 min', '2 min'],
'M': ['30 hour', '>20 hour', '>10 hour'],
'F': ['1.1 hour', '3 min', '2 min'],
'P': ['>20 hour', '>20 hour', '-'],
'S': ['1.9 hour', '>20 hour', '>10 hour'],
'T': ['7.2 hour', '>20 hour', '>10 hour'],
'W': ['2.8 hour', '3 min', '2 min'],
'Y': ['2.8 hour', '10 min', '2 min'],
'V': ['100 hour', '>20 hour', '>10 hour'],
}
'''Isoelectric point'''
Asp = 'D'
Glu = 'E'
Cys = 'C'
Tyr = 'Y'
His = 'H'
Lys = 'K'
Arg = 'R'
NQ, pH = 0.0, 0.0
QN1, QN2, QN3, QN4, QN5, QP1, QP2, QP3, QP4 = 0, 0, 0, 0, 0, 0, 0, 0, 0
var = 1
while 1:
QN1 = -1 / (1.0 + pow(10, (3.65 - pH)))
QN2 = -sequence.count("D") / (1.0 + pow(10, (3.9 - pH)))
QN3 = -sequence.count("E") / (1.0 + pow(10, (4.07 - pH)))
QN4 = -sequence.count("C") / (1.0 + pow(10, (8.18 - pH)))
QN5 =-sequence.count("Y") / (1.0 + pow(10, (10.46 - pH)))
QP1 = sequence.count("H") / (1.0 + pow(10, (pH - 6.04)))
QP2 = 1 / (1.0 + pow(10, (pH - 8.2)))
QP3 = sequence.count("K") / (1.0 + pow(10, (pH - 10.54)))
QP4 = sequence.count("R") / (1.0 + pow(10, (pH - 12.48)))
NQ = QN1 + QN2 + QN3 + QN4 + QN5 + QP1 + QP2 + QP3 + QP4
if (pH >= 14.0):
# you should never see this message
print("Something is wrong - pH is higher than 14")
break
elif (NQ <= 0):
# if this condition is true we can stop calculate
break
pH += 0.01 # if not increase pH
'''extinction coefficient'''
ext_Trp = 5500
ext_Tyr = 1490
ext_Cys = 125
numb_Tyr = Y
numb_Trp = W
numb_Cys = C / 2
ext_coef = (numb_Tyr * ext_Tyr) + (numb_Trp * ext_Trp) + (int(numb_Cys) * ext_Cys)
absorb = ext_coef / molecular_weight
ext_coef2 = (numb_Tyr * ext_Tyr) + (numb_Trp * ext_Trp)
absorb2 = ext_coef2 / molecular_weight
'''results display'''
print("\t\tAA_composition")
print('Aminoacid \t total number \t %age')
print("Gly (G) \t %d \t\t %.2f" % (G, (G / length) * 100))
print("Ala (A) \t %d \t\t %.2f" % (A, (A / length) * 100))
print("Leu (L) \t %d \t\t %.2f" % (L, (L / length) * 100))
print("Met (M) \t %d \t\t %.2f" % (M, (M / length) * 100))
print("Phe (F) \t %d \t\t %.2f" % (F, (F / length) * 100))
print("Trp (W) \t %d \t\t %.2f" % (W, (W / length) * 100))
print("Lys (K) \t %d \t\t %.2f" % (K, (K / length) * 100))
print("Gln (Q) \t %d \t\t %.2f" % (Q, (Q / length) * 100))
print("Glu (E) \t %d \t\t %.2f" % (E, (E / length) * 100))
print("Ser (S) \t %d \t\t %.2f" % (S, (S / length) * 100))
print("Pro (P) \t %d \t\t %.2f" % (P, (P / length) * 100))
print("Val (V) \t %d \t\t %.2f" % (V, (V / length) * 100))
print("Ile (I) \t %d \t\t %.2f" % (I, (I / length) * 100))
print("Cys (C) \t %d \t\t %.2f" % (C, (C / length) * 100))
print("Tyr (Y) \t %d \t\t %.2f" % (Y, (Y / length) * 100))
print("His (H) \t %d \t\t %.2f" % (H, (H / length) * 100))
print("Arg (R) \t %d \t\t %.2f" % (R, (R / length) * 100))
print("Asn (N) \t %d \t\t %.2f" % (N, (N / length) * 100))
print("Asp (D) \t %d \t\t %.2f" % (D, (D / length) * 100))
print("Thr (T) \t %d \t\t %.2f" % (T, (T / length) * 100))
print()
print("Protein Length is:%d" % length)
print("Total negetively charged residues (Asp + Glu): %d" % (D + E))
print("Total positively charged residues (Arg + Lys): %d" % (R + K))
print("Histidine is considered Nutral because pI=7.37")
print("Total polar uncharged residues: %d" % (S + T + C + P + N + Q))
print("Total nonPolar Aliphatic Residues: %d" % (G + A + V + L + I + M))
print("Total Aromatic residues: %d" % (F + Y + W))
print("Grand Average of Hydrophobicity (GRAVY):%.3f " % (total / length))
print("Molecular Weight of protein: %.2f kDa" % (molecular_weight / 1000))
if (sequence[0] == 'A'):
print('protein half life in Mammalian Yeast and E.coli is:\n ', hlife['A'])
elif (sequence[0] == 'R'):
print('protein half life in Mammalian Yeast and E.coli is:\n ', hlife['R'])
elif (sequence[0] == 'N'):
print('protein half life in Mammalian Yeast and E.coli is:\n ', hlife['N'])
elif (sequence[0] == 'D'):
print('protein half life in Mammalian Yeast and E.coli is:\n ', hlife['D'])
elif (sequence[0] == 'C'):
print('protein half life in Mammalian Yeast and E.coli is:\n ', hlife['C'])
elif (sequence[0] == 'Q'):
print('protein half life in Mammalian Yeast and E.coli is:\n ', hlife['Q'])
elif (sequence[0] == 'E'):
print('protein half life in Mammalian Yeast and E.coli is:\n ', hlife['E'])
elif (sequence[0] == 'G'):
print('protein half life in Mammalian Yeast and E.coli is:\n ', hlife['G'])
elif (sequence[0] == 'H'):
print('protein half life in Mammalian Yeast and E.coli is:\n ', hlife['H'])
elif (sequence[0] == 'I'):
print('protein half life in Mammalian Yeast and E.coli is:\n', hlife['I'])
elif (sequence[0] == 'L'):
print('protein half life in Mammalian Yeast and E.coli is:\n ', hlife['L'])
elif (sequence[0] == 'K'):
print('protein half life in Mammalian Yeast and E.coli is:\n ', hlife['K'])
elif (sequence[0] == 'M'):
print('protein half life in Mammalian Yeast and E.coli is:\n ', hlife['M'])
elif (sequence[0] == 'F'):
print('protein half life in Mammalian Yeast and E.coli is:\n ', hlife['F'])
elif (sequence[0] == 'P'):
print('protein half life in Mammalian Yeast and E.coli is:\n ', hlife['P'])
elif (sequence[0] == 'S'):
print('protein half life in Mammalian Yeast and E.coli is:\n ', hlife['S'])
elif (sequence[0] == 'T'):
print('protein half life in Mammalian Yeast and E.coli is:\n ', hlife['T'])
elif (sequence[0] == 'W'):
print('protein half life in Mammalian Yeast and E.coli is:\n ', hlife['W'])
elif (sequence[0] == 'Y'):
print('protein half life in Mammalian Yeast and E.coli is:\n ', hlife['Y'])
elif (sequence[0] == 'V'):
print('protein half life in Mammalian Yeast and E.coli is:\n ', hlife['V'])
print("Protein isoelectric point=%.2f" % pH)
print('Extinction coefficients are in units of M-1 cm-1, at 280 nm measured in water')
print('assuming all pairs of Cys residues form cystines')
print('\tExt. coefficient: %d' % ext_coef)
print('\tAbs 0.1% (=1g/l):', '%.3f' % absorb)
print('assuming all pairs of Cys residues are reduced')
print('\tExt. coefficient: %d' % ext_coef2)
print('\tAbs 0.1% (=1g/l):', '%.3f' % absorb2)
def about(self):
print( '===============================================================================\n' )
print( '\t\tPhysioCal:A Physical Properties Calculation Script\n' )
print( 'AUTHOR: \t\tUmer Farooq, [email protected]' )
print( 'COPYRIGHTS: \t\tUmer Farooq\n' )
print( '\t\t\tDecember 2017' )
print( '===============================================================================\n' )
def run(args):
obj = PhysioCal()
fin=args.input
seq=obj.fasta_reader(fin)
op=args.operation
obj.about()
if (op == 'N' or op == 'n'):
with open (args.output,"w") as fout:
sys.stdout=fout
obj.nucleotide(seq)
fout.close()
elif (op == 'A' or op == 'a'):
with open (args.output,"w") as fout:
sys.stdout=fout
obj.amino_acid(seq)
fout.close()
def main():
parser=argparse.ArgumentParser(description="PhysioCal: Physical Properties Calculation Script")
parser.add_argument("-in",help="sequence input file", dest="input", type=str, required=True)
parser.add_argument("-out",help="results output file", dest="output", type=str, required=True)
parser.add_argument("-op",help="operation to perform,N for nucleotide, A for protein ", dest="operation", type=str, required=True)
parser.set_defaults(func=run)
args=parser.parse_args()
args.func(args)
if __name__=="__main__":
main()