Das deutsche Python-Forum

Code: Alles auswählen

for i in xrange(len(text)-2):
    print text[i:i+2]

Code: Alles auswählen

string ="attagctt"
wert = 0

for i in range(len(string)-1):
	paar = string[i:i+2]
	
	if paar == 'ag':
		wert += 1.2
	elif paar == 'at':
		wert += 1.5
	elif paar == 'ct':
		wert += 2.3
	elif paar == 'gc':
		wert += 1.8
	elif paar == 'ta':
		wert += 2.4
	elif paar == 'tt':
		wert += 0.2

print 'Summe: ', wert

Code: Alles auswählen

werte = {
  'ag' : 1.2,
  'at' : 1.5,
 # ...
}
if paar in werte:
  wert += werte[paar]

Code: Alles auswählen

for x in range(10**7): pass

Code: Alles auswählen

# Tm Berechnung

from math import*


sequenz=raw_input("Please enter your sequenz!")
string=sequenz

t=sequenz.count("t")
a=sequenz.count("a")
g=sequenz.count("g")
c=sequenz.count("c")

# Basis < 13 Nukleotide
# Tm=2°C (A+T) + 4°C (G+C)

def methode01():
    global t,a,g,c
    Tm01=(2*(a+t))+(4*(g+c))
    print Tm01


# Basis > 13 Nukleotide
# Tm=64.9+41*(G+C-16.4)/(A+T+G+C)

def methode02():
    global t,a,g,c
    Tm02=64.9+41*(g+c-16.4)/(a+t+g+c)
    print Tm02


# Salzkonezntration 14-70 N
# Tm=81,5°C + 16,6 * (log[M+]) + 0,41 * (%G+C) -(500/N)

def methode03():
    global t,a,g,c
    M=raw_input("Please enter the salt conc in mol/L without unit!")
    GC=(float(g)+float(c))/(float(t)+float(a)+float(g)+float(c))*100 # auf und abrunden!?
    N=t+a+g+c
    Tm03=81.5+16.6*(log10(float(M)))+0.41*float(GC)-(500.0/float(N))
    print Tm03

# Nearest Neighbour Methode

def methode04():

    global string

    kalium=input("Please enter the M Kalium in mol/L")
    magnesium=input("Please enter the M Magnesium in mol/L")
    enden=input("Wieviel überhängende Enden?")
    primer=input("Please enter your primer concentration in mol/L")

    ### Enthalpie H

    # Wärmemenge, die bei konst Temperatur, Druck und Volumen aufgenommen oder abgeben wird.
    # Berechnet aus Enthalpie der Reaktionsproukte minus der Enthalpie der Reaktanten.
    # Einheit kcal/mol

    werte = {"aa":-9.1 , "ac":-6.5 , "ag":-7.8 , "at":-8.6 ,
            "ca":-5.8 , "cc":-11.0 , "cg":-11.9 , "ct":-7.8 ,
            "ga":-5.6 , "gc":-11.1 , "gg":-11.0 , "gt":-6.5 ,
            "ta":-6.0 , "tc":-5.6 , "tg":-5.8 , "tt":-9.1}
    wertH=0
    
    for i in xrange(len(string)-1):
        paar = string[i:i+2]
        if paar in werte:
                wertH +=werte[paar]

    enthalpie_he = (-5000 * enden) / 1000          # in kcal/mol

    gesamt_enthalpie_h_kcalmol = wertH + (enthalpie_he)  

    enthalpie_h = gesamt_enthalpie_h_kcalmol * 1000     # Ergebnis in cal/mol
   


    ### Freie Energie G
    
    werte = {"aa":-1.55 , "ac":-1.40 , "ag":-1.45 , "at":-1.25 ,
            "ca":-1.15 , "cc":-2.30 , "cg":-3.05 , "ct":-1.45 ,
            "ga":-1.15 , "gc":-2.70 , "gg":-2.30 , "gt":-1.40 ,
            "ta":-0.85 , "tc":-1.15 , "tg":-1.15 , "tt":-1.55}
            
    wertG=0
            
    for i in xrange(len(string)-1):
        paar = string[i:i+2]
        if paar in werte:
                wertG +=werte[paar]

    freie_energie_ge = enden * -1000 / 1000          # in kcal/mol

    gesamt_freie_energie_g_kcalmol = wertG + (freie_energie_ge) + 2.2   

    g = gesamt_freie_energie_g_kcalmol * 1000      # Ergebnis in cal/mol

    ### Salzkonzentration

    s =(kalium)+4*(magnesium)**0.5         # Ergebnis

    ### Tm Formel

    upper = 298.2 * (enthalpie_h)
    lower = enthalpie_h - (g) + 1.99 * (298.2)* log(4*10**-7)
    l = 1.0 + 0.7 * (s)
    salz = s / l
    ls =log10(salz)

    tm = (upper/lower) + 16.6 * ls - 269.3

    return tm

Code: Alles auswählen

class Sequence(object):
    def __init__(self, data):
        self.data = data
        self.a = data.count('a')
        self.c = data.count('c')
        self.g = data.count('g')
        self.t = data.count('t')
    
    def __len__(self):
        return len(self.data)
    
    def __getitem__(self, key):
        return self.data[key]
    
    def pair_sum(self, weights):
        return sum(weights.get(self[i:i+2], 0) for i in xrange(len(self)))


def test():
    sequence = Sequence('gattaca')
    print len(sequence)     # -> 7
    print sequence.a, sequence.c, sequence.g, sequence.t    # -> 3 1 1 2
    
    weights = {"aa": -9.1, "ac": -6.5, "ag": -7.8, "at": -8.6,
               "ca": -5.8, "cc": -11.0, "cg": -11.9, "ct": -7.8,
               "ga": -5.6, "gc": -11.1, "gg": -11.0, "gt": -6.5,
               "ta": -6.0, "tc": -5.6, "tg": -5.8, "tt": -9.1}
    print sequence.pair_sum(weights)    # -> -41.6