I am new in the python area but I would like to use biopython to align some DNA sequences. I got a script from internet and I ran it as follows (~ is the short for my home path):
~$ python
Python 3.5.1 (default, Jul 3 2016, 12:57:35)
[GCC 5.4.0 20160609] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> from Bio.Align.Applications import MuscleCommandline
>>> muscle_exe = r"/usr/bin/muscle"
>>> in_file = r"~/SpiderOak Hive/LAB/Lab book/Ery/Seqs/tester.fasta"
>>> out_file = "~/SpiderOak Hive/LAB/Lab book/Ery/Seqs/tester_aligned.fasta"
>>> muscle_cline = MuscleCommandline(muscle_exe, input=in_file, out=out_file)
>>> print(muscle_cline)
/usr/bin/muscle -in "~/SpiderOak Hive/LAB/Lab
book/Ery/Seqs/tester.fasta" -out "~/SpiderOak Hive/LAB/Lab
book/Ery/Seqs/tester_aligned.fasta"
but when lauching the application I got:
>>> muscle_cline()
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/opt/python3.5/lib/python3.5/site-packages/Bio/Application/__init__.py",
line 516, in __call__
stdout_str, stderr_str)
Bio.Application.ApplicationError: Non-zero return code 137 from
'/usr/bin/muscle -in "/home/gigiux/SpiderOak Hive/LAB/Lab
book/Ery/Seqs/tester.fasta" -out "/home/gigiux/SpiderOak Hive/LAB/Lab
book/Ery/Seqs/tester_aligned.fasta"', message 'MUSCLE v3.8.31 by
Robert C. Edgar'
>>>
What would be the issue? I have seen on internet that it might be due to memory problems; in that case is the code OK? and how could I run large alignments?
And also: why should I use = r"path" rather than simply "path"?
Many thanks,
Luigi
Your code seems to be correct, and it works with small alignments. The 137 status code might be related to an "Out Of Memory" kill like in this question. Check the last kernel messages with the command dmesg looking for lines like:
kernel: Out of memory: Kill process 52959 (java) score 164 or sacrifice child
Related
Is there a definitive set of instructions to implement OpenCV trackers with OpenVINO and the now-obsolete NCS2 on a RPi 4b - Buster?
My understanding that the last OpenVINO to support the NCS2 was v2020.3.
I attempted to cross-compile using:
https://github.com/opencv/opencv/wiki/Intel-OpenVINO-backend#raspbian-buster
After installing opencv/opencv-contrib 4.5.5 from source:
$ python3
Python 3.7.3 (default, Oct 31 2022, 14:04:00)
[GCC 8.3.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import cv2
>>> cv2.__version__
'4.5.5'
>>> tracker = cv2.TrackerCSRT_create()
>>>
However, in a test.py script I have:
...
import cv2
net = cv2.dnn.readNetFromCaffe(_weights, _model)
net.setPreferableTarget(cv2.dnn.DNN_TARGET_MYRIAD)
...
detections = net.forward()
I get the error relating to DNN_TARGET_MYRIAD:
cv2.error: OpenCV(4.5.5) /home/pi/opencv/modules/dnn/src/dnn.cpp:1414: error: (-215:Assertion failed) preferableBackend != DNN_BACKEND_OPENCV || preferableTarget == DNN_TARGET_CPU || preferableTarget == DNN_TARGET_OPENCL || preferableTarget == DNN_TARGET_OPENCL_FP16 in function 'setUpNet'
I then used this to install OpenVINO:
https://docs.openvino.ai/latest/openvino_docs_install_guides_installing_openvino_raspbian.html
but using this version of OpenVINO (as the last to support the NCS2):
https://storage.openvinotoolkit.org/repositories/openvino/packages/2020.3/l_openvino_toolkit_runtime...
I exported the paths to the new post cross-compiled opencv_install directory:
$ export PYTHONPATH=/home/pi/Desktop/opencv_install/lib/python2.7/dist-packages/:$PYTHONPATH
$ export PYTHONPATH=/home/pi/Desktop/opencv_install/lib/python3.7/site-packages/:$PYTHONPATH
$ export LD_LIBRARY_PATH=/home/pi/Desktop/opencv_install/lib/:$LD_LIBRARY_PATH
I set up the NCS2 with no errors :
$ sudo usermod -a -G users "$(whoami)"
$ sh /opt/intel/openvino_2020.3/install_dependencies/install_NCS_udev_rules.sh
then:
$ source /opt/intel/openvino_2020.3/bin/setupvars.sh
and then checked:
$ python3
Python 3.7.3 (default, Oct 31 2022, 14:04:00)
[GCC 8.3.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import cv2
>>> cv2.__version__
'4.3.0-openvino-2020.3.0'
>>> tracker = cv2.TrackerCSRT_create()
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
AttributeError: module 'cv2' has no attribute 'TrackerCSRT_create'
>>>
If I open a new terminal and $ source /opt/intel/openvino_2020.3/bin/setupvars.sh
then run a test.py script:
...
import cv2
net = cv2.dnn.readNetFromCaffe(_weights, _model)
net.setPreferableTarget(cv2.dnn.DNN_TARGET_MYRIAD)
...
detections = net.forward()
...
I get a segmentation fault error.
So far I have not edited any of the setup scripts.
Thanks for any help! I'd like to put this NCS2 to work.
Generally, if you are able to run some OpenVINO demo with NCS2 after following this installation guide, then you should be able to use that OpenCV functionality (ensured that you had installed the correct OpenCV).
It's recommended to use the recent OpenVINO and OpenCV version.
As indicated in this OpenVINO System Requirements, the current recommended OpenCV version is 4.5.
While trying to import glob in a python venv environment, it is referring to the system package and not the virtual environment even though pandas module is referring to the virtual environment.
I am using python 3.8 and I created a virtual environment using python venv :
cd trial_3
python3 -m venv trial_3_env
On trying to use glob module (which i haven't yet installed in the environment), I can see that it is not throwing any error, but using the glob module from the system packages.
Please find the screenshot showing the same below:
(trial_3_env) anitta#vinjohn:~/Desktop/Study_Data_Engineering/virtualenv_trial/trial_3$ pip freeze
numpy==1.23.4
pyspark==3.3.0
python-dateutil==2.8.2
pytz==2022.6
six==1.16.0
(trial_3_env) anitta#vinjohn:~/Desktop/Study_Data_Engineering/virtualenv_trial/trial_3$ python3
Python 3.8.10 (default, Jun 22 2022, 20:18:18)
[GCC 9.4.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import glob
>>> glob.__file__
'/usr/lib/python3.8/glob.py'
>>>
I tried checking this behavior with pandas module, but they are working as expected and throw error while importing when I have not preinstalled them in my system.
(trial_3_env) anitta#vinjohn:~/Desktop/Study_Data_Engineering/virtualenv_trial/trial_3$ python3
Python 3.8.10 (default, Jun 22 2022, 20:18:18)
[GCC 9.4.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>>
>>> import pandas
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
ModuleNotFoundError: No module named 'pandas'
>>>
Could someone let me know the cause of globs behavior ? and if such scenario can occur for other modules as well.
Thanks in advance!
#ChrisD and #sinoroc answers helped me. standard libraries of venv python interpreter are referenced from the system python interpreter path itself and venv folder doesn't have any python standard libraries stored inside.
I upgraded OpenCV 4.4.0 from OpenCV 4.2.x with pip command :
pip install --upgrade opencv-python==4.4.0.40
and checked the upgrade completed :
Collecting opencv-python==4.4.0.40
|████████████████████████████████| 33.5 MB 283 kB/s
Requirement already satisfied, skipping upgrade: numpy>=1.17.3 in c:\users\kangs\anaconda3\lib\site-packages (from opencv-python==4.4.0.40) (1.18.5)
Found existing installation: opencv-python 4.3.0.36
Successfully uninstalled opencv-python-4.3.0.36
PS C:\Users\kangs\Documents\TELPA\Source\numberplateRecognition> python
Python 3.8.3 (default, Jul 2 2020, 17:30:36) [MSC v.1916 64 bit (AMD64)] :: Anaconda, Inc. on win32
Type "help", "copyright", "credits" or "license" for more information.
>>> import cv2
>>> cv2.__version__
'4.4.0'
>>> exit()
However, I still get this error message when I run this code :
cv2.dnn.readNet(WEIGHTS, CFG)
Error message :
Traceback (most recent call last):
File "c:\Users\kangs\Documents\TELPA\Source\numberplateRecognition\number_plate_v4c.py", line 54, in <module>
File "c:\Users\kangs\Documents\TELPA\Source\numberplateRecognition\algorithm\detection\yolodetector.py", line 39, in __init__
self.load_dir(dir_path)
File "c:\Users\kangs\Documents\TELPA\Source\numberplateRecognition\algorithm\detection\yolodetector.py", line 50, in load_dir
self.load_files(file_list)
File "c:\Users\kangs\Documents\TELPA\Source\numberplateRecognition\algorithm\detection\yolodetector.py", line 78, in load_files
self.net = cv2.dnn.readNet(WEIGHTS, CFG)
cv2.error: OpenCV(4.2.0) C:\projects\opencv-python\opencv\modules\dnn\src\darknet\darknet_io.cpp:686: error: (-212:Parsing error) Unsupported activation: mish in function 'cv::dnn::darknet::ReadDarknetFromCfgStream'
I found out that the code still linked to the previous library OpenCV 4.2.0.
Can someone please let me know why this happens and how to solve this problem?
I've installed the mortgage package using pip. The command prompt below shows where it's installed.
C:\Users\benja>pip show mortgage
Name: mortgage
Version: 1.0.5
Summary: Mortgage Calculator
Home-page: https://github.com/austinmcconnell/mortgage
Author: Austin McConnell
Author-email: austin.s.mcconnell#gmail.com
License: MIT license
Location: c:\users\benja\appdata\local\programs\python\python36\lib\site-packages
Requires:
Required-by:
I'm able to run Python through the command prompt and successfully import/use the package, like so...
C:\Users\benja>py
Python 3.6.4 (v3.6.4:d48eceb, Dec 19 2017, 06:54:40) [MSC v.1900 64 bit (AMD64)] on win32
Type "help", "copyright", "credits" or "license" for more information.
>>> from mortgage import Loan
>>> Loan(principal=250000, interest=.04, term=30)
<Loan principal=250000, interest=0.04, term=30>
This makes sense because the sys path points to the folder where the package is installed.
C:\Users\benja>py
Python 3.6.4 (v3.6.4:d48eceb, Dec 19 2017, 06:54:40) [MSC v.1900 64 bit (AMD64)] on win32
Type "help", "copyright", "credits" or "license" for more information.
>>> import sys
>>> from pprint import pprint as pp
>>> pp(sys.path)
['',
'C:\\Users\\benja\\AppData\\Local\\Programs\\Python\\Python36\\python36.zip',
'C:\\Users\\benja\\AppData\\Local\\Programs\\Python\\Python36\\DLLs',
'C:\\Users\\benja\\AppData\\Local\\Programs\\Python\\Python36\\lib',
'C:\\Users\\benja\\AppData\\Local\\Programs\\Python\\Python36',
'C:\\Users\\benja\\AppData\\Local\\Programs\\Python\\Python36\\lib\\site-packages',
'C:\\Users\\benja\\AppData\\Local\\Programs\\Python\\Python36\\lib\\site-packages\\win32',
'C:\\Users\\benja\\AppData\\Local\\Programs\\Python\\Python36\\lib\\site-packages\\win32\\lib',
'C:\\Users\\benja\\AppData\\Local\\Programs\\Python\\Python36\\lib\\site-packages\\Pythonwin']
The issue: I've created a module buysellcalculator.py that imports the mortgage package, simliar to what I did in the command prompt above. However, I get an error message when trying to run this module. What am I doing wrong?
C:\Users\benja\OneDrive\Documents\R\Real Estate\PyRM>buysellcalculator.py
Traceback (most recent call last):
File "C:\Users\benja\OneDrive\Documents\R\Real Estate\PyRM\buysellcalculator.py", line 10, in <module>
from mortgage import Loan
ModuleNotFoundError: No module named 'mortgage'
I installed OpenCV 4.1.2 from source with CUDA support. Had no issues. and created a symbolic link from OpenCV’s installation directory to my virtualenv
ln -s /usr/local/lib/python3.6/site-packages/cv2/python3.6/cv2.cpython-36m-aarch64-linux-gnu.so cv2.so
I am having an issue with import cv2
$ python
Python 3.6.9 (default, Nov 7 2019, 10:44:02)
[GCC 8.3.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import cv2
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
ModuleNotFoundError: No module named 'cv2'
>>>
I checked site-packages directory and I can see cv2.so. I am obviously missing something.
The main issue here in my view I am not able to link to my virtualenv, in fact I am able to check my installation and its working
/usr/local/lib/python3.6/site-packages/cv2/python-3.6$ python
Python 3.6.9 (default, Nov 7 2019, 10:44:02)
[GCC 8.3.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import cv2
>>>
Issue solved a very very little mistake
I changed the name from
cv2.cpython-36m-aarch64-linux-gnu.so to cv2.so
I realized it was an issue with one of the folders, this will do the magic:
ln -s /usr/local/lib/python3.6/site-packages/cv2/python-3.6/cv2.so cv2.so
notice its python-3.6 not python3.6 after cv2