Python OOP init - python

class Sequence:
TranscriptionTable = {
"A":"U",
"T":"A",
"C":"G",
"G":"C"
}
def __init__(self, seqstring):
self.seqstring = seqstring.upper()
def transcription(self):
tt = ""
for x in self.seqstring:
if x in 'ATGC':
tt += self.TranscriptionTable[x]
return tt
DangerousVirus = Sequence('atggagagccttgttcttggtgtcaa')
print(DangerousVirus.transcription())
Hi,
I just want some clarification as to how data flows through a class. For instance, is the data in () in DangerousVirus = Sequence('atggagagccttgttcttggtgtcaa') self or seqstring?
I'm confused as to how init can have 2 variables when theres only 1 in the (). Wouldnt that mean that only self contains the sequence and seqstring is empty?
Thanks for the help! (:

self is a reference to a Sequence which is being initialized. The data string is passed as seqstring. You can see this by adding a line to print it:
print(seqstring)

The __init__ method does indeed take two arguments, but once an instance is created the self argument is "bound" to the instance (__init__ becomes a so called bound method of the instance), so you don't have to specify the instance itself anymore. If you call the unbound __init__ function from the class like this
Sequence.__init__(instance, seqstring)
you indeed have to specify the instance explicitly. The name self is just a convention, it could be anything in the definition. Take a look at the tutorial section on instance methods where this is explained.

As the other answers have said, the self arg gets passed automatically to method calls. So you must include it as the first arg in the method definition, but you must not include it in the method call.
However, there's no need to define a class for this, a simple function is sufficient. And you can use the built-in str.translate method to perform the transcription very efficiently. For large sequences, this is much faster than doing it with a Python loop as in your transcription method, since most of the work is done by compiled code, so it runs as fast as if it were written in C, not Python.
trans_table = str.maketrans('ATCG', 'UAGC')
def transcribe(seq):
seq = seq.upper()
return seq.translate(trans_table)
seq = 'atggagagccttgttcttggtgtcaa'
print(transcribe(seq))
output
UACCUCUCGGAACAAGAACCACAGUU
As mentioned in the docs, any chars that aren't in the translation table will remain unchanged in the output string. Eg,
print('abcdABCD'.translate(trans_table))
output
abcdUBGD

Related

How to reference method without calling it?

How to reference method of class in Python?
In PHP there is so called "callable", pretty much an array with two elements, where first is FQCN or object instance, second is method name e.g.:
$callable = [$this, 'methodName']
or with FQCN
$callable = [\My\Namespaced\Foo::class, 'methodName']
Following is very important for me. It is possible to invoke it later e.g. by:
call_user_func($callable);
How to get same in Python and what is the Pythonic name for it?
In Python, you can get (via the descriptor protocol) something called a bound method.
class A:
def foo(self, x):
print(x)
a = A()
f = a.foo
f(3) # Equivalent to a.foo(3)
f is a bound method, an object very much (it seems) like the array you describe in PHP. The bound method f is little more than an object that contains references to a and A.foo, so that when you call f(...), it basically just calls A.foo(a, ...) for you.

TypeError for a function with a string parameter

I am trying to create a simple function that allows me to return a string reversed. However, when I call the function, the error
TypeError: reverseString() takes 1 positional argument but 2 were given
comes up. I'm more familiar with Java, and was wondering what the problem is and if passing a string parameter is the same in Python.
Class myString()
def reverseString(string):
return string[:,:,-1]
p = myString()
p.reversedString('Eric')
Python requires a special first parameter for methods to which it passes the instance that the method is being called on. You can use pretty much any valid variable name, but it's a Python convention to use self and it will make your code easier for other people to read.
class myString:
def reverseString(self, string):
return string[::-1]
p = myString()
print(p.reverseString('Eric'))
To access instance variables, you would use self.var - you can't just do var like in Java.
Also, as #jonrshape pointed out in the comments, you don't need to wrap functions in a class:
def reverseString(string):
return string[::-1]
print(reverseString('Eric'))

Python 3: Calling a Function from a class, self

I am trying to learn about classes, can someone explain to me why this code is not working. I thought when calling a function from a class, "self" is automatically ommitted, but the interpreter tells me that argument "a" is missing (he thinks self = 10).
#! coding=utf-8
class test:
def __init__(self):
"do something here"
def do(self,a):
return a**2
d = test.do
print(d(10))
Instantiate the class first:
d = test().do
print(d(10)) # prints 100
test.do is an unbound method, test().do is bound. The difference is explained in this thread: Class method differences in Python: bound, unbound and static.
You have to instantiate the class first:
d = test()
then you can call a method:
print(d.do(10))
if you want to use method statically you have to declare it in python
#! coding=utf-8
class test:
def __init__(self):
"do something here"
#staticmethod
def do(a):
return a**2
d = test.do
print(d(10)) #and that's work
Since you haven't instantiated the class (a fancy term for created) you can't be assigning methods to any random variable. Like already said, you must create the object first, whilst making sure the method you call is a part of the class you called or connected to the class in some way (such as creating another class and then communicating that class with the current class). So you should first type d=test() followed by d.do().
Also, remember that in your declaration of the method you crated a parameter so what you done was wrong in itself anyway, because when you declared the do function, you should have put within the brackets the number you wanted to send to the method to calculate its square. So you type test.do(10) and then the 10 is sent by the self reference to the method to be done whatever it is you told it to do.
One more thing: although it isn't a huge deal, it helps if all of your class names begin with a capital letter, as this is usually the 'pythonic' way to do things, and it also makes your code much easier to read, because when you first called the class, somebody could easily mistaken it for an ordinary function
class test:
def __init__(self):
"do something here"
def do(self,a):
return a**2
def __call__(self,a):
return self.do(a)
a = test
test.do(a,10)
#or
a = test().do
a(10)
#or
a = test()
test.do(a,10)
#or
a = test()
print(a(10))

Using the self-parameter in python objects

I've got a question about defining functions and the self-parameter in python.
There is following code.
class Dictionaries(object):
__CSVDescription = ["ID", "States", "FilterTime", "Reaction", "DTC", "ActiveDischarge"]
def __makeDict(Lst):
return dict(zip(Lst, range(len(Lst))))
def getDict(self):
return self.__makeDict(self.__CSVDescription)
CSVDescription = __makeDict(__CSVDescription)
x = Dictionaries()
print x.CSVDescription
print x.getDict()
x.CSVDescription works fine. But print x.getDict() returns an error.
TypeError: __makeDict() takes exactly 1 argument (2 given)
I can add the self-parameter to the __makeDict() method, but then print x.CSVDescription wouldn't work.
How do I use the self-parameter correctly?
In python, the self parameter is implicitly passed to instance methods, unless the method is decorated with #staticmethod.
In this case, __makeDict doesn't need a reference to the object itself, so it can be made a static method so you can omit the self:
#staticmethod
def __makeDict(Lst): # ...
def getDict(self):
return self.__makeDict(self.__CSVDescription)
A solution using #staticmethod won't work here because calling the method from the class body itself doesn't invoke the descriptor protocol (this would also be a problem for normal methods if they were descriptors - but that isn't the case until after the class definition has been compiled). There are four major options here - but most of them could be seen as some level of code obfuscation, and would really need a comment to answer the question "why not just use a staticmethod?".
The first is, as #Marcus suggests, to always call the method from the class, not from an instance. That is, every time you would do self.__makeDict, do self.__class__.__makeDict instead. This will look strange, because it is a strange thing to do - in Python, you almost never need to call a method as Class.method, and the only time you do (in code written before super became available), using self.__class__ would be wrong.
In similar vein, but the other way around, you could make it a staticmethod and invoke the descriptor protocol manually in the class body - do: __makeDict.__get__(None, Dictionaries)(__lst).
Or, you could detect yourself what context its being called from by getting fancy with optional arguments:
def __makeDict(self, Lst=None):
if Lst is None:
Lst = self
...
But, by far the best way is to realise you're working in Python and not Java - put it outside the class.
def _makeDict(Lst):
...
class Dictionaries(object):
def getDict(self):
return _makeDict(self.__CSVDescription)
CSVDescription = _makeDict(__CSVDescription)

"self" inside plain function?

I've got a bunch of functions (outside of any class) where I've set attributes on them, like funcname.fields = 'xxx'. I was hoping I could then access these variables from inside the function with self.fields, but of course it tells me:
global name 'self' is not defined
So... what can I do? Is there some magic variable I can access? Like __this__.fields?
A few people have asked "why?". You will probably disagree with my reasoning, but I have a set of functions that all must share the same signature (accept only one argument). For the most part, this one argument is enough to do the required computation. However, in a few limited cases, some additional information is needed. Rather than forcing every function to accept a long list of mostly unused variables, I've decided to just set them on the function so that they can easily be ignored.
Although, it occurs to me now that you could just use **kwargs as the last argument if you don't care about the additional args. Oh well...
Edit: Actually, some of the functions I didn't write, and would rather not modify to accept the extra args. By "passing in" the additional args as attributes, my code can work both with my custom functions that take advantage of the extra args, and with third party code that don't require the extra args.
Thanks for the speedy answers :)
self isn't a keyword in python, its just a normal variable name. When creating instance methods, you can name the first parameter whatever you want, self is just a convention.
You should almost always prefer passing arguments to functions over setting properties for input, but if you must, you can do so using the actual functions name to access variables within it:
def a:
if a.foo:
#blah
a.foo = false
a()
see python function attributes - uses and abuses for when this comes in handy. :D
def foo():
print(foo.fields)
foo.fields=[1,2,3]
foo()
# [1, 2, 3]
There is nothing wrong with adding attributes to functions. Many memoizers use this to cache results in the function itself.
For example, notice the use of func.cache:
from decorator import decorator
#decorator
def memoize(func, *args, **kw):
# Author: Michele Simoniato
# Source: http://pypi.python.org/pypi/decorator
if not hasattr(func, 'cache'):
func.cache = {}
if kw: # frozenset is used to ensure hashability
key = args, frozenset(kw.iteritems())
else:
key = args
cache = func.cache # attribute added by memoize
if key in cache:
return cache[key]
else:
cache[key] = result = func(*args, **kw)
return result
You can't do that "function accessing its own attributes" correctly for all situations - see for details here how can python function access its own attributes? - but here is a quick demonstration:
>>> def f(): return f.x
...
>>> f.x = 7
>>> f()
7
>>> g = f
>>> g()
7
>>> del f
>>> g()
Traceback (most recent call last):
File "<interactive input>", line 1, in <module>
File "<interactive input>", line 1, in f
NameError: global name 'f' is not defined
Basically most methods directly or indirectly rely on accessing the function object through lookup by name in globals; and if original function name is deleted, this stops working. There are other kludgey ways of accomplishing this, like defining class, or factory - but thanks to your explanation it is clear you don't really need that.
Just do the mentioned keyword catch-all argument, like so:
def fn1(oneArg):
// do the due
def fn2(oneArg, **kw):
if 'option1' in kw:
print 'called with option1=', kw['option1']
//do the rest
fn2(42)
fn2(42, option1='something')
Not sure what you mean in your comment of handling TypeError - that won't arise when using **kw. This approach works very well for some python system functions - check min(), max(), sort(). Recently sorted(dct,key=dct.get,reverse=True) came very handy to me in CodeGolf challenge :)
Example:
>>> def x(): pass
>>> x
<function x at 0x100451050>
>>> x.hello = "World"
>>> x.hello
"World"
You can set attributes on functions, as these are just plain objects, but I actually never saw something like this in real code.
Plus. self is not a keyword, just another variable name, which happens to be the particular instance of the class. self is passed implicitly, but received explicitly.
if you want globally set parameters for a callable 'thing' you could always create a class and implement the __call__ method?
There is no special way, within a function's body, to refer to the function object whose code is executing. Simplest is just to use funcname.field (with funcname being the function's name within the namespace it's in, which you indicate is the case -- it would be harder otherwise).
This isn't something you should do. I can't think of any way to do what you're asking except some walking around on the call stack and some weird introspection -- which isn't something that should happen in production code.
That said, I think this actually does what you asked:
import inspect
_code_to_func = dict()
def enable_function_self(f):
_code_to_func[f.func_code] = f
return f
def get_function_self():
f = inspect.currentframe()
code_obj = f.f_back.f_code
return _code_to_func[code_obj]
#enable_function_self
def foo():
me = get_function_self()
print me
foo()
While I agree with the the rest that this is probably not good design, the question did intrigue me. Here's my first solution, which I may update once I get decorators working. As it stands, it relies pretty heavily on being able to read the stack, which may not be possible in all implementations (something about sys._getframe() not necessarily being present...)
import sys, inspect
def cute():
this = sys.modules[__name__].__dict__.get(inspect.stack()[0][3])
print "My face is..." + this.face
cute.face = "very cute"
cute()
What do you think? :3
You could use the following (hideously ugly) code:
class Generic_Object(object):
pass
def foo(a1, a2, self=Generic_Object()):
self.args=(a1,a2)
print "len(self.args):", len(self.args)
return None
... as you can see it would allow you to use "self" as you described. You can't use an "object()" directly because you can't "monkey patch(*)" values into an object() instance. However, normal subclasses of object (such as the Generic_Object() I've shown here) can be "monkey patched"
If you wanted to always call your function with a reference to some object as the first argument that would be possible. You could put the defaulted argument first, followed by a *args and optional **kwargs parameters (through which any other arguments or dictionaries of options could be passed during calls to this function).
This is, as I said hideously ugly. Please don't ever publish any code like this or share it with anyone in the Python community. I'm only showing it here as a sort of strange educational exercise.
An instance method is like a function in Python. However, it exists within the namespace of a class (thus it must be accessed via an instance ... myobject.foo() for example) and it is called with a reference to "self" (analagous to the "this" pointer in C++) as the first argument. Also there's a method resolution process which causes the interpreter to search the namespace of the instance, then it's class, and then each of the parent classes and so on ... up through the inheritance tree.
An unbound function is called with whatever arguments you pass to it. There can't bee any sort of automatically pre-pended object/instance reference to the argument list. Thus, writing a function with an initial argument named "self" is meaningless. (It's legal because Python doesn't place any special meaning on the name "self." But meaningless because callers to your function would have to manually supply some sort of object reference to the argument list and it's not at all clear what that should be. Just some bizarre "Generic_Object" which then floats around in the global variable space?).
I hope that clarifies things a bit. It sounds like you're suffering from some very fundamental misconceptions about how Python and other object-oriented systems work.
("Monkey patching" is a term used to describe the direct manipulation of an objects attributes -- or "instance variables" by code that is not part of the class hierarchy of which the object is an instance).
As another alternative, you can make the functions into bound class methods like so:
class _FooImpl(object):
a = "Hello "
#classmethod
def foo(cls, param):
return cls.a + param
foo = _FooImpl.foo
# later...
print foo("World") # yes, Hello World
# and if you have to change an attribute:
foo.im_self.a = "Goodbye "
If you want functions to share attribute namespaecs, you just make them part of the same class. If not, give each its own class.
What exactly are you hoping "self" would point to, if the function is defined outside of any class? If your function needs some global information to execute properly, you need to send this information to the function in the form of an argument.
If you want your function to be context aware, you need to declare it within the scope of an object.

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