I fetched a cristal structure of a protein using the function retrieve_pdb_file from Bio.PDB. The default format has changed from PDB to PDBx/mmCif. I want to extract the protein sequence from the header in the cif file. There is supposed to be a simple function in Bio.PDB called MMCIF2Dict to do this but the module is not callable. I also downloaded the cif file manually and put it in the script folder but still the same error. My biopython is up to date. Am I doing something wrong or the module is not well implemented? Thank you for your answers.
from Bio.PDB import *
cifFile = '1bu7.cif'
mmcif = MMCIF2Dict(cifFile)
TypeError: 'module' object is not callable
The module is well implemented. The problem with your code is that you are calling a module instead of a function. In your particular case the module and the function have the same names hence the confusion.
To solve that you need to fix your code as follows:
from Bio.PDB import *
cifFile = '1bu7.cif'
mmcif = MMCIF2Dict.MMCIF2Dict(cifFile)
Try:
from Bio.PDB.MMCIF2Dict import MMCIF2Dict
Instead of :
from Bio.PDB import *
Related
For some reason, I had to change a module name from A.py to 0880ceae-8a46-11eb-bcf6-38f9d349be8e.py. 0880ceae-8a46-11eb-bcf6-38f9d349be8e.py is a uid generated by uuid.uuid1().
After my change, I try to import a class B from the py file by the following two ways, both do not work out.
First solution is to import directly
from 0880ceae-8a46-11eb-bcf6-38f9d349be8e import B
It has an error SyntaxError: invalid token
Second solution is to define a variable before import
uid = '0880ceae-8a46-11eb-bcf6-38f9d349be8e'
from uid import Model_API
And it has en error ModuleNotFoundError: No module named 'uid'
Anyone has a good idea? Thanks.
Here is possible solution to your problem tested using python3:
# Modern approach
import importlib
module = importlib.import_module(".", "0880ceae-8a46-11eb-bcf6-38f9d349be8e")
module.hello()
# Deprecated way
module = __import__("0880ceae-8a46-11eb-bcf6-38f9d349be8e")
module.hello()
Both of the above methods are tested and works.
Here are the rules to keep in mind:
Check your filename should end with .py extension, .py.py will cause ModuleNotFoundError.
Make sure to not include .py extension while using in importlib module.
I am using import DiGraph to import my external file and trying to run the following code:
prediction = DiGraph.remove_duplicates(make_trips(G, source='c1', target=['c2', 'c3']))
but I get NameError: name 'make_trips' is not defined
All the names are how they appear in my external file and it is even identical code besides the prediction =. What am I missing?
*Edit:
Thanks, Gilch, Kartikeya Sharma, and Nishat for the explanations.
Did you mean DiGraph.make_trips?
Importing like that only gives you the one module object; it doesn't dump its contents into the current namespace. (You could use from DiGraph import * for that, but star imports get confusing fast, so they're generally not recommended.)
Now I get NameError: name 'G' is not defined. 'G' is a variable at the top of the file. How should I handle this? Thanks
At the top of the DiGraph file? You can do it the same way. DiGraph.G.
If DiGraph is too much to type, you can do
import DiGraph as dg
instead of import DiGraph. Then you can refer to the DiGraph module as dg instead, e.g.
prediction = dg.remove_duplicates(dg.make_trips(dg.G, source='c1', target=['c2', 'c3']))
you can import your external function like this
from <module> import <function>
So if your make_trip function is inside make_trip.py file then you can import like this
from make_trip import make_trip
I've got a Python script.
I've had several functions in this script which I decided to move to a 'package' folder beside the main script.
In this folder, I created a *.py file where I put all my functions.
I've placed an empty init.py near this file within the 'package' folder.
When starting the code of my main script with:
from package_folder.my_functions import *
the script works well when calling every functions from that file.
But when trying to import it directly:
import package_folder.my_functions
it doesn't seems to work as well as with the above technique.
The cause seems to be the fact that in the file wellmy_functions.py, I have a function that needs an other one, declared previously in that file.
I had this obscure error on that function that needs an other one:
TypeError: 'NoneType' object is not callable
Is this permissible and if not, how to manage this case?
It's generally not a good idea to use from module import *. Wildcard importing leads to namespace pollution; you imported more names than you need and if you accidentally refer to an imported name you may not get the NameError you wanted.
Also, if a future version of the library added additional names, you could end up masking other names, leading to strange bugs still:
Example
from my_mod1 import func1
from my_mod2 import *
If you upgrade my_mod2 and it now includes a my_mod2.func1 it'll replace the my_mod1.func1 import in the 1st line.
I have a vaguely defined function of a class Graph of a module I call gt (it is graph-tool). so i declare g = gt.graph() then want to use g.degree_property_map but do not know how. Therefore I want to see where in code g.degree_property_map or in this case just the function, is defined. How can I find that? I'm working on command line on a vm.
Thanks
For reference the library in question is graph-tool - http://projects.skewed.de/graph-tool/
Also I am currently importing it using from graph_tool.all import * . that is of course somewhat of a problem.
You could use inspect.getsource(gt.Graph.degree_property_map). (You have to import inspect.)
Of course, what you pass into getsource() will change depending on how you imported Graph. So if you used from graphtools.all import *, you'd just need to use inspect.getsource(Graph.degree_property_map).
If you open interactive python (type python and hit ENTER on the command line), you should be able to run the command help(<graph's module name>), then, under the FILE section of the help documentation that is generated, you should see the absolute path to the code you are interested in.
For example, I just ran:
import numpy
help(numpy)
# Returned documentation containing:
# FILE
# /usr/lib/python2.7/dist-packages/numpy/__init__.py
Also,
import my_module # A module I just created that contains the "Line" class
help(my_module)
# Returned documentation containing:
# FILE
# /home/<my user name>/Programming/Python/my_module.py
If it is a normal function (not a builtin, ufunc, etc) you can try using the func_code attribute
For example:
>>> inspect.iscode
<function iscode at 0x02EAEF30>
>>> inspect.iscode.func_code
<code object iscode at 02EB2B60, file "C:\Python27\lib\inspect.py", line 209>
Never mind I just did help(graph_tool) and manually jumped through code. Thanks for the help though!
So my first python program, I downloaded the macholib package from PYPI, then unzipped it and ran installed the setup.py using python install, now I'm trying to run a program where I first import the macholib, then when I try to access methods like Macho, it gives me an error saying macholib module has no attributes called Macho.
My understanding is macholib is a package and not a module or something, hence I cant use the contents of the package.
Please answer, I've wasted too much time on such a simple newbie issue.
running a mac with the latest version of python.
Code:
import sys
import macholib
MachO(DivXInstaller.dmg)
I tried macholib.MachO(DivXInstaller.dmg) and macholib.MachO.MachO(DivXInstaller.dmg)
Error for python test.py
Traceback (most recent call last):
File "test.py", line 3, in <module>
MachO(DivXInstaller.dmg)
NameError: name 'MachO' is not defined
You have this line in your code:
MachO(DivXInstaller.dmg)
However, the name MachO is not defined anywhere. So Python tells you this with the error
NameError: name 'MachO' is not defined
If you want to use the MachO module under the name MachO, you have to import it:
from macholib import MachO
This you have not done, which is the cause of your error. All you did was
import macholib
which gives you the name "macholib" that you can use. However, macholib contains mostly submodules which you can not access like that, so that is not particularly useful. If you don't want to pollute the namespace, you can import MachO as
import machlibo.MachO
Which gives you access to the MachO module as macholib.MachO
You haven't defined DivXInstaller.dmg either, so that's going to be your next error. I recommend that you go through a Python tutorial before you start programming in it.
An import statement defines a namespace. Hence, in order to use something defined in the module or package, you need to qualify it. In this case, the module itself is macholib.MachO but you need to dig deeper, to the actual class MachO which, slightly confusingly, has the same name, so you need to import macholib.MachO and use macholib.MachO.MachO (note that when I try to do this I get an error "DistributionNotFound: altgraph", however).
Note further that it takes a filename as an argument, which is a string. Moreover, you are actually creating an instance of a class, so you probably mean
mlib = macholib.MachO.MachO("DivXInstaller.dmg")
where now mlib is actually the object you need to manipulate with further calls...
Alternately you can do from macholib import MachO or even from macholib.MachO import MachO so you could use MachO.MachO(...) or MachO(...) directly.
This is so simple if you understand Python Packages vs. Modules and import vs. from import:
A Python module is simply a Python source file.
A Python package is simply a directory of Python module(s).
1- import:
import package1.package2.module1
To access module1 classes, functions or variables you should use the whole namespace: package1.package2.modlue1.class1
You cannot import a class or function this way: (wrong)
import package1.package2.class1
2- from ... import
Instead use "from" to import a single class, function or variable of a module:
from package1.package2.module1 import class1
no need to address the whole namespace: class1.method1() works now
Note that you cannot import a method of a class this way
Example:
datetime is a class of module datetime that has a method called utcnow(), to access utcnow() one could:
import datetime
datetime.datetime.utcnow()
Or
from datetime import datetime
datetime.utcnow()