Instance variables in Python? Keep getting an assignment error

Question

Hi I am trying to write a simple program that calculates the base content of each base in DNA. I keep getting an assignment error 'no_c referenced before assignment' or 'no_c not defined" in my current configuration and I can't figure out how to solve the issue.

#!/usr/bin/python

#computing the atgc content of a DNA string 


class Base_counter(object):
    def __init__(self, DNA):
        self.DNA = DNA
        no_c = 0
        no_a = 0
        no_g= 0
        no_t= 0

    def c_counter(self):
        for base in self.DNA:   
            if base == 'c':
                no_c = no_c + 1 
        return no_c

    def g_counter(self):
        for base in self.DNA:   
            if base == 'g':
                no_g+=1 
        return no_g

    def a_counter(self):
        for base in self.DNA:   
            if base == 'a':
                no_a+=1 
        return no_a

    def t_counter(self):
        for base in self.DNA:   
            if base == 't':
                no_a+=1 
        return no_t

    def gc_percentage(self):
        return no_c + no_g / len(self.DNA)

    def at_percentage(self):
        return no_a + no_t / len(self.DNA)

    def g_percentage(self):
        return no_g / len(self.DNA)

    def a_percentage(self):
        return no_a / len(self.DNA)

    def t_percentage(self):
        return no_t / len(self.DNA)

    def c_percentage(self):
        return no_c / len(self.DNA)     

def main():
    dna= 'gcgctat'
    analyzer = Base_counter(dna)

    print analyzer.no_c
    print analyzer.c_counter()
    #print analyzer.c_percentage()

if __name__ == '__main__':
    main()

Please try to tag your questions so that they help people later searching for stuff, rather than describing the settings in which you happened to encounter the problem. This question, for example, has nothing to do with bioinformatics or dna sequencing. — Ami Tavory
– Ami Tavory, Commented Mar 31, 2016 at 6:24

Ami Tavory · Accepted Answer · 2016-03-31 06:22:45Z

2

Consider your code

def __init__(self, DNA):
    self.DNA = DNA
    no_c = 0
    no_a = 0
    no_g= 0
    no_t= 0

Only the line

    self.DNA = DNA

creates a member for this object. The other lines create mappings that are local to this function. Consequently, when later calls try to access no_c, the interpreter does not connect it to what you presumably meant here.

I'm guessing that you want to replace every occurrence of no_c with self.no_c.

answered Mar 31, 2016 at 6:22

Ami Tavory

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Comments

Steve Barnes · Accepted Answer · 2016-03-31 18:19:45Z

0

try this:

    def c_counter(self):
        for base in self.DNA:   
            if base == 'c':
                self.no_c = self.no_c + 1 
        return self.no_c

Specifically, access all fields of the object with the self keyword.

edited Mar 31, 2016 at 18:19

Steve Barnes

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answered Mar 31, 2016 at 6:31

yerlilbilgin

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Comments

Steve Barnes · Accepted Answer · 2016-03-31 18:25:59Z

0

Just put self. before all of the no_ values in the class to make them members of each class instance object.

Thus:

class Base_counter(object):
    def __init__(self, DNA):
        self.DNA = DNA
        self.no_c = 0
        self.no_a = 0
        self.no_g= 0
        self.no_t= 0

    def c_counter(self):
        for base in self.DNA:   
            if base == 'c':
                self.no_c += 1 
        return self.no_c

etc.

This is needed so that the instance of a specific class has it's own storage for the values and can reference it.

edited Mar 31, 2016 at 18:25

answered Mar 31, 2016 at 6:22

Steve Barnes

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