CODEWITHSUNDEEP
pythongetattr
Malonge
Malonge

Reputation: 2040

How to invoke a method with the methods name as a string

I am using Biopython's Restriction class to perform in silico restriction digestions. As I understand it, in order to digest a certain sequence with a certain enzyme, the .catalyze() method must be implemented. 

digestTuple = Restriction.EcoRI.catalyse(this_seq)  # Or whichever enzyme is desired.

Right now I apply a conditional to see which enzyme is being used as input. For Example:

RS = restrictionSite         # From user
amb = IUPACAmbiguousDNA()
this_seq = Seq(sequence, amb) # sequence from user

if RS == 'EcoRI':
    digestTuple = Restriction.EcoRI.catalyse(this_seq)

I apply a conditional for any enzymes that I would foresee myself needing. This takes up a bunch of lines of code and is inefficient. I would like to be able to search for membership in Restrictions set of all possible enzymes, Restriction.AllEnzymes. Something like this:

if RS in Restriction.AllEnzymes:
    digestTuble = Restriction.RS.catalyze(this_seq)

else:
    print('Please type in enzyme name correctly')

This problem is that python doesn't equate:

RS = "EcoRI" 
digestTuple = Restriction.RS.catalyze(this_seq)

with

digestTuple = Restriction.EcoRI.catalyze(this_seq)

As it is trying to use the string name associated with the enzyme and not actually invoking the proper method.

Is there a way to invoke this method using the single conditional that searches all possible enzymes?

Maybe something like this Invoking a method by its name but in python?

The technical wording regarding this question is a little confusing for me, so I probably did not explain the problem accurately. Ill happily answer any clarifying questions.

Thank you

Upvotes: 3

Views: 187

Answers (2)

kindall
kindall

Reputation: 184131

Use getattr(), e.g.:

RS = "EcoRI"
digestTuple = getattr(Restriction, RS).catalyze(this_seq)

Upvotes: 4

f.rodrigues
f.rodrigues

Reputation: 3587

As simple as:

getattr(your_object,"methodname")()

example:

class My_Class:
    def print_hi(self):
        print 'hi'

a = My_Class()

getattr(a,'print_hi')()

output:

hi

In your case:

RS = "EcoRI" 
digestTuple = getattr(Restriction, RS).catalyze(this_seq)

Upvotes: 4

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