Question

def __init__(self,emps=str(""),l=[">"]):
    self.str=emps
    self.bl=l


def fromFile(self,seqfile):
    opf=open(seqfile,'r')                                       
    s=opf.read()                                              
    opf.close()                                                    
    lisst=s.split(">")                                             
    if s[0]==">":
        lisst.pop(0)                                                    
    nlist=[]
    for x in lisst:
        splitenter=x.split('\n')                                        
        splitenter.pop(0)                                               
        splitenter.pop()                                                
        splitstring="".join(splitenter)                                 
        nlist.append(splitstring)                                       
    nstr=">".join(nlist)                                                
    nstr=nstr.split()
    nstr="".join(nstr)
    for i in nstr:
        self.bl.append(i)
    self.str=nstr
    return nstr

def getSequence(self):
    print self.str
    print self.bl
    return self.str

def GpCratio(self):
    pgenes=[]
    nGC=[]
    for x in range(len(self.lb)):                                   
        if x==">":
            pgenes.append(x)                                           
    for i in range(len(pgenes)):                                        
        if i!=len(pgenes)-1:                                            
            c=krebscyclus[pgenes[i]:pgenes[i+1]].count('c')+0.000       
            g=krebscyclus[pgenes[i]:pgenes[i+1]].count('g')+0.000                                          
            ratio=(c+g)/(len(range(pgenes[i]+1,pgenes[i+1])))
            nGC.append(ratio)                                           
    return nGC  

---

s = Sequence()
s.fromFile('D:\Documents\Bioinformatics\sequenceB.txt')
print 'Sequence:\n', s.getSequence(), '\n'
print "G+C ratio:\n", s.GpCratio(), '\n'

---

I dont understand why it gives the error:

in GpCratio     for x in range(len(self.lb)): AttributeError: Sequence instance has no attribute 'lb'. 

When i print the list in def getSequence it prints the correct DNA sequenced list, but i can not use the list for searching for nucleotides. My university only allows me to input 1 file and not making use of other arguments in definitions, but “self”
btw, it is a class, but it refuses me to post it then.. class called Sequence

---

Answer 1

Looks like a typo. You define self.bl in your __init__() routine, then try to access self.lb.

(Also, emps=str("") is redundant – emps="" works just as well.)

But even if you correct that typo, the loop won’t work:

for x in range(len(self.bl)):   # This iterates over a list like [0, 1, 2, 3, ...]
    if x==">":                  # This condition will never be True
        pgenes.append(x) 

You probably need to do something like

pgenes=[]
for x in self.bl:
    if x==">":                  # Shouldn't this be != ?
        pgenes.append(x) 

which can also be written as a list comprehension:

pgenes = [x for x in self.bl if x==">"]

In Python, you hardly ever need len(x) or for n in range(...); you rather iterate directly over the sequence/iterable.

Since your program is incomplete and lacking sample data, I can’t run it here to find all its other deficiencies. Perhaps the following can point you in the right direction. Assuming a string that contains the characters ATCG and >:

>>> gene = ">ATGAATCCGGTAATTGGCATACTGTAG>ATGATAGGAGGCTAG"
>>> pgene = ''.join(x for x in gene if x!=">")
>>> pgene
'ATGAATCCGGTAATTGGCATACTGTAGATGATAGGAGGCTAG'
>>> ratio = float(pgene.count("G") + pgene.count("C")) / (pgene.count("A") + pgene.count("T"))
>>> ratio
0.75

If, however, you don’t want to look at the entire string but at separate genes (where > is the separator), use something like this:

>>> gene = ">ATGAATCCGGTAATTGGCATACTGTAG>ATGATAGGAGGCTAG"
>>> genes = [g for g in gene.split(">") if g !=""]
>>> genes
['ATGAATCCGGTAATTGGCATACTGTAG', 'ATGATAGGAGGCTAG']
>>> nGC = [float(g.count("G")+g.count("C"))/(g.count("A")+g.count("T")) for g in genes]
>>> nGC
[0.6875, 0.875]

However, if you want to calculate GC content, then of course you don’t want (G+C)/(A+T) but (G+C)/(A+T+G+C) –> nGC = [float(g.count("G")+g.count("C"))/len(g)].