I installed Biopython, but I am unable to get the computer to recognize the modules. For example, I create a text file in Komodo like this:
from Bio.Alphabet import IUPAC
from Bio import Seq
my_prot=Seq.Seq("AGTACACTGGT",IUPAC.protein)
and run it in terminal and receive:
Traceback (most recent call last):
File "bio.py", line 1, in <module>
from Bio.Alphabet import IUPAC
ImportError: No module named Bio.Alphabet
For the record, I can't get modules to import in interactive mode either. The documentation states that I can append the module search path by exporting to an environmental variable called PYTHONPATH (like with PATH), but when I type 'env' into the terminal, I see no environmental variable of the sort. I'm a biologist--not a computer scientist or programmer. Please bear with my naiveté if this sounds like nonsense.
You must find in which directory situated the module that you needs (Bio) and then add the path to the directory to PYTHONPATH.
$ export PYTHONPATH=/usr/local/bio-python/
Instead of /usr/local/bio-python/ you must specify the path that you've found.
To find the module you must use something like:
$ find / -name \*Bio\*
That is just an example. Of course it would be better if you could give some additional information (e.g. where you've installed the module and so on).
Press the start button, right click on my computer, select properties, go to advanced, click environment variables. Then find your path variable, and edit it by adding a semicolon, then your path. For example, if my path variable at the moment is "C:\Program Files\Java\jdk1.7.0_02\bin", I can change it to "C:\Program Files\Java\jdk1.7.0_02\bin;(PUT PATH HERE)"
Related
How do I change initial path directory in Jupyter lab, when i want to get a file via "~/"?
Have tried to generate config, and then change some parameters but only got confused.
You can change file directory like that.
import shutil
File= r'C:\Users\ivan\Desktop\Somewhereidonotknow\example.csv'
Whereyou_want= r'C:\Users\ivan\Desktop\example.csv'
shutil.move(File, Whereyou_want)
You should be using the %cd magic command to change the working directory. And then to set up using tab completion, you'd start by typing ./ before hitting tab at the place where you want to choose your CSV file.
In the demonstration set-up for the screenshot below I made a test directory in the root (home) location and made two CSV files in there.
Using %cd test first I am then able to use tab completion to get the option to select one of the two CSV files:
I probably should have included running pwd to 'print the working directoryafter I ran the%cd test` command to demonstrate things more fully.
Before I executed the command %cd test, the tab-completion was showing the root (home directory) when I tried for tab completion.
The tilde symbol (~) always means the HOME directory on the system. It won't change. So you were always specifying to start in HOME in your example in your post, no matter what the current working directory is in the notebook's active namespace. You want to use relative paths for when the working directory has been adjusted.
There are more complex settings you can take advantage of using inside the notebook in conjunction with the %cd magic.
For example, this post and answer shows how you can use the %boookmark magic to set assign a directory to a bookmark setting and then you can more easily switch around to various directories using %cd.
Background: I have a .py script which uses c.10 libraries/dependencies (e.g., pandas numpy json) and the script also relies on a .ini file, which it looks for in the same dir as it is located.I want to add this .py file to Windows Scheduler, but before I can, I must make the file executable.
Issue: I used PyInstaller to create an executable file. I also added -- onefile and -w when creating the .exe file. My issue is that when I attempt to run the main.exe (either by double-clicking or through cmd) I get the following Unhandled exception in script -
Help: I am trying to understand how this is happening, especially as my understanding of PyInstaller is that it would create an executable file, which would inc. everything the script needs to run (Note: I have double checked that the .py contains import pandas etc.
Can someone explain to me how I would troubleshoot this and/or if there are any key steps I may have obviously missed, which might be causing this?
Try using this commandline for compiling your python file, pyinstaller.exe --onefile --noconsole --hidden-import pandas {Your_FILE_NAME}.py
I have a myFunction.pyd file which I have tested to make sure that modules defined internally are accessible.
I then created a wheel file myFunction-1.0-py3-none-any.whl
Finally using cmd prompt I installed the wheel file. I can then also see the following location:
C:\Program Files\Python38\Lib\site-packages\myFunction-1.0.dist-info
However, when I do the following import myFunction as mf it gives error ModuleNotFoundError: No module named 'myFunction'
Only thing I can think of is I didn't do anything with the pyd file that I had generated. Do I need to also move that file to some location?
This is kind of embarassing because of how simple and common this problem is but I feel I've checked everything.
WSGI file is located at: /var/www/igfakes/server.wsgi
Apache is complaining that I can't import the module of my project, so I decided to start up a Python shell and see if it's any different - nope.
All the proof is in the following screenshot, I'll walk you through it.
First, see I cannot import my project
Then I import sys and check the path
Note /var/www in the path
Leave python
Check the directory, then confirm my project is in that same directory
My project is exactly where I'm specifying. Any idea what's going on?
I've followed a few different tutorials, all with the same instructions, like this one.
I tried to install tensorflow and finally got there.
I got an error:
ImportError: libcudnn.Version: cannot open shared object file: No such
file or directory
while I was installing but I could handle it. I think it works fine in terminal.
However, the problem is when I tried to import tensorflow in sublime text, it spits the same error.
ImportError: libcudnn.so.6: cannot open shared object file: No such
file or directory
Cause I changed the build system path to /home/username/.conda/envs/tensorflow/bin, I can't understand why I get this error here.
Is there anyone who can help me?
As it is working from terminal I think everything like cuda, cudnn and GPU drivers are setup properly and the export path is added to the .bashrc (~/.bashrc) file. That's why running from terminal works. As adding the export information to only .bashrc file will make it work on terminal but won't help for other programs like sublime.
So, I suggest, you take the export information from .bashrc file and add it to /etc/environment file. You need to log out from current user and login again so environment variables changes take place. The export information on .bashrc file should look something like this.
export PATH=/usr/local/cuda-8.0/bin${PATH:+:${PATH}}
export LD_LIBRARY_PATH=/usr/local/cuda-8.0/lib64\${LD_LIBRARY_PATH:+:${LD_LIBRARY_PATH}}