douglaslab / cadnano2 Goto Github PK

When exporting oligos as csv, file gets saved as .csv.txt.


Using latest github version, v2.3.0

Microsoft Windows [Version 10.0.19045.3930]
(c) Microsoft Corporation. All rights reserved.

C:\Users\kwons\OneDrive\document\cadnano2>python main.py
python: can't open file 'C:\Users\kwons\OneDrive\document\cadnano2\main.py': [Errno 2] No such file or directory

C:\Users\kwons\OneDrive\document\cadnano2>

Hello, I am having trouble installing cadnano2 at mac OS

When I ran the code: python3 main.py
The output is

Traceback (most recent call last):
File "/Users/jeonghoonkim/cadnano2/./views/documentwindow.py", line 139, in moveEvent
self.settings.beginGroup("MainWindow")
AttributeError: 'DocumentWindow' object has no attribute 'settings'
zsh: abort python3 main.py

What should I do with this issue?

I edited the staples meanually and when I was almost about to be done on an m13 origami, I noticed that no changes were saved. I remember I continuously hit "ctrl+s" and the save button. Moreover, I tried saving manually by "save as" function as well. That does not work as well. Not to mention, without saving it is almost impossible to work. Please help.

Your sincerely,
Swarup Dey

'pip' is not recognized as an internal or external command,
operable program or batch file.

How to resolve this?

Process: Python [33798]
Path: /usr/local/Cellar/python/3.7.7/Frameworks/Python.framework/Versions/3.7/Resources/Python.app/Contents/MacOS/Python
Identifier: org.python.python
Version: 3.7.7 (3.7.7)
Code Type: X86-64 (Native)
Parent Process: zsh [33731]
Responsible: Terminal [27213]
User ID: 501

Date/Time: 2020-06-19 09:02:23.121 -0400
OS Version: Mac OS X 10.15.5 (19F101)
Report Version: 12
Bridge OS Version: 4.5 (17P5300)
Anonymous UUID: 4D04EE7F-6A6A-48B2-65C1-BE46576CBEFA

Sleep/Wake UUID: E571E43E-D6BC-45A3-AF97-0F54708095C8

Time Awake Since Boot: 69000 seconds
Time Since Wake: 5600 seconds

**System Integrity Protection: enabled

Crashed Thread: 0 Dispatch queue: com.apple.main-thread

Exception Type: EXC_BAD_ACCESS (SIGSEGV)
Exception Codes: EXC_I386_GPFLT
Exception Note: EXC_CORPSE_NOTIFY

Termination Signal: Segmentation fault: 11
Termination Reason: Namespace SIGNAL, Code 0xb
Terminating Process: exc handler [33798]**

I tried uninstalling and reinstalling everything as well. My .bash_profile is identical to what is listed on the site. The application will launch and run for maybe a few minutes and then crash.

I am trying to install cadnano and followed instruction step by step. After I am done, I tried to run Cadnano2 by use the Terminal window to launch Cadnano2 using the following command: "python main.py", but it returned an error:

TypeError: setPixelSize(self, int): argument 1 has unexpected type 'float'

And it won't open cadnano2.

What shall I do?

The mac version crashes frequently - every 5mins or so. The python just crashes. How to solve this?

Traceback (most recent call last):
File "./views/pathview/strand/endpointitem.py", line 223, in mouseMoveEvent
if idx != self._moveIdx: # did we actually move?
AttributeError: 'EndpointItem' object has no attribute '_moveIdx'
Abort trap: 6

Hello ,
I have trouble using cadnano2 in ubuntu where it shows the following error when clicking onto honeycomb lattice option.Although firstly it was fine.The error occured today.

Traceback (most recent call last):
File "/home/nikita/virtualenvs/cn24x/lib/python3.10/site-packages/cadnano2/views/sliceview/slicerootitem.py", line 33, in partAddedSlot
partItem = PartItem(modelPart, parent=self)
File "/home/nikita/virtualenvs/cn24x/lib/python3.10/site-packages/cadnano2/views/sliceview/partitem.py", line 51, in init
self._setLattice([], modelPart.generatorFullLattice())
File "/home/nikita/virtualenvs/cn24x/lib/python3.10/site-packages/cadnano2/model/parts/part.py", line 696, in generatorFullLattice
return product(list(range(self._maxRow)), list(range(self._maxCol)))
TypeError: 'str' object cannot be interpreted as an integer
Aborted (core dumped)

I´m getting this error when I try to run cadnano2. Tried reinstalling pyqt6 but it did not fix this issue. Not sure if it is related or not.

Please how do I add autobreak plugin to Cadnano2. I am currently a Masters Student in CSU, Ohio

Read and replicated the exact readme instructions, tried running the cadnano2 command and while cmd opens for a split second it closes immediately after. Not sure if I'm on an incorrect path.

C:\Users\rvlhu\OneDrive\Documents\GitHub\cadnano2>python main.py
python: can't open file 'C:\Users\rvlhu\OneDrive\Documents\GitHub\cadnano2\main.py': [Errno 2] No such file or directory

C:\Users\rvlhu\OneDrive\Documents\GitHub\cadnano2>python cadnano2\main.py
Traceback (most recent call last):
File "C:\Users\rvlhu\OneDrive\Documents\GitHub\cadnano2\cadnano2\main.py", line 13, in
from . import cadnano
ImportError: attempted relative import with no known parent package

Hi Douglas lab folks --

I am not certain if what I was trying to do was legit, but this behavior has reproduced 3 times. In the pencil tool when one clicks and drags a scaffold 3' end the program crashes with the following message. I was trying to join to broken ends of the scaffold

C:\Users\ostap bender\Documents\GitHub\cadnano2>python main.py
Plugin loaded, has access to cadnano: <module 'cadnano' from '.\cadnano.py'>
Traceback (most recent call last):
File ".\views\pathview\strand\endpointitem.py", line 195, in mousePressEvent
getattr(self, toolMethodName)(modifiers, event, self.idx())
File ".\views\pathview\strand\endpointitem.py", line 314, in pencilToolMousePress
tempXover.updateBase(vhi, mStrand, idx)
File ".\views\pathview\tools\penciltool.py", line 624, in updateBase
self._node5.updateForFloatFromStrand(virtualHelixItem, strand5p, idx)
File ".\views\pathview\tools\penciltool.py", line 360, in updateForFloatFromStrand
self.updatePositionAndAppearance()
File ".\views\pathview\tools\penciltool.py", line 535, in updatePositionAndAppearance
self._updateLabel(isLeft)
File ".\views\pathview\tools\penciltool.py", line 462, in _updateLabel
num = self._partnerVirtualHelix.number()
File ".\views\pathview\virtualhelixitem.py", line 132, in number
return self._modelVirtualHelix.number()
AttributeError: 'NoneType' object has no attribute 'number'

Cheers!
Andrey Revyakin

I got this after following the installation steps.

When adding the seq on the 5' end, no sequence appears along the 3' strand for some distance. So, my sequence file has a lot of question marks. Although, adding another break and thus, another seq to fill this 'empty' part of scaffold strand did help generate an atomic structure but the structure was hollowed along that 'empty' region indicating that Cando didn't consider the seq I had added on the second occasion.

\Documents\GitHub\cadnano2\cadnano2>python main.py
Traceback (most recent call last):
File "main.py", line 13, in
from . import cadnano
ImportError: cannot import name 'cadnano' from 'main' (main.py)

Any solutions? Thanks!

It crashes when I use autobreak function albeit it can be avoided by changing the values in the autobreak dialog box in small increments. Either way, cadnano is acting very glitchy:(

The double prime in the following script before source is not proper, which gave the error of not finding “source.

cat <<END >> ~/.zprofile
alias cn240=“source ~/virtualenvs/cn240/bin/activate && cadnano2"
END

Maybe like this:

cat <<END >> ~/.zprofile
alias cn240="source ~/virtualenvs/cn240/bin/activate && cadnano2"
END

Source: http://douglaslab.org/tutorials/files/Install-Cadnano-macOS-v4.pdf

Thansk.

Hi, I'm currently having an issue opening cadnano2 on macOS. I used the instructions in the README to install cadnano2. I have attempted installation on both Intel and Apple Silicon Macs and in both cases get the same error:

The output is:

Traceback (most recent call last):
File "Users//virtualenvs/cn240/lib/python3.9/site-packages/cadnano2/views/documentwindow.py", line 139, in moveEvent
self.settings.beginGroup("MainWindow")
Attribute error: 'DocumentWindow' object has no attribute 'settings'
zsh abort cadnano2

I appreciate you keeping cadnano on life support. It is a fantastic piece of software :).
Any ideas/feedback are welcome to try to get this working on my end, or if you have any insights. Do let me know if you need some more information to help troubleshoot.

Originally posted by @scikat in #16 (comment)

The error appears when exporting a design with an error (for example staple loops in my case).
full error message:

Traceback (most recent call last):
  File "/Users/[username]/opt/anaconda3/envs/cadnano/lib/python3.6/site-packages/cadnano2/controllers/documentcontroller.py", line 425, in actionExportStaplesSlot
    from ui.dialogs.ui_warning import Ui_Warning
ModuleNotFoundError: No module named 'ui'
zsh: abort      cadnano2

commenting out this part in documentcontroller.py will bypass the problem.

I suppose this part of the code is to call a warning dialogue box, but somehow the ./ui module cannot be found.

system: macOS 12.5.1
cadnano2 2.4.4
pyqt6 6.2.3
pyqt6-qt6 6.2.3
pyqt6-sip 13.2.1
python 3.6.13

same issue on another PC with python 3.10, same installed cadnano2 via pip.

Hello,

I have followed the installation instructions on Windows 10 domain computers but I always end up with the same problem

C:\Users\USER\cadnano2\cadnano2>python main.py
Traceback (most recent call last):
File "C:\Users\USER\cadnano2\cadnano2\main.py", line 13, in
from . import cadnano
ImportError: attempted relative import with no known parent package

Python is installed to c:. What can be the cause of this problem?

Best regards
Marko

On following the installation instructions, the following is the first output on running main.py:

Traceback (most recent call last):
File "C:\Users\XXXXX\Documents\GitHub\cadnano2\cadnano2\main.py", line 18, in
cadnano.initAppWithGui()
File "C:\Users\XXXXX\Documents\GitHub\cadnano2\cadnano2.\cadnano.py", line 43, in initAppWithGui
from .cadnanoqt import CadnanoQt
ImportError: attempted relative import with no known parent package

These relative imports don't seem to work properly, I changed them to just "import X" but progressively making these changes works only until the following:

C:\Users\XXXXX\Documents\GitHub\cadnano2\cadnano2>python main.py
Traceback (most recent call last):
File "C:\Users\XXXXX\Documents\GitHub\cadnano2\cadnano2\main.py", line 18, in
cadnano.initAppWithGui()
File "C:\Users\XXXXX\Documents\GitHub\cadnano2\cadnano2.\cadnano.py", line 43, in initAppWithGui
from cadnanoqt import CadnanoQt
File "C:\Users\XXXXX\Documents\GitHub\cadnano2\cadnano2.\cadnanoqt.py", line 8, in
util.qtWrapImport('QtWidgets', globals(), ['QApplication'])
File "C:\Users\XXXXX\Documents\GitHub\cadnano2\cadnano2.\util.py", line 101, in qtWrapImport
return qtWrapImport(name, globaldict, fromlist)
File "C:\Users\XXXXX\Documents\GitHub\cadnano2\cadnano2.\util.py", line 109, in qtWrapImportFromDummy
imports = import(modName, globaldict, locals(), fromlist, 0)
ModuleNotFoundError: No module named 'dummyqt.QtWidgets'

Python version is 3.10.7, PyQt is 6.5.2, OS is Windows 11 Enterprise.

caDNAno quits unexpectedly when saving a file. Initial saving was successful, but subsequent saving led the program to crush.

Traceback (most recent call last):
File "c:\virtualenvs\cn24x\lib\site-packages\cadnano2\controllers\documentcontroller.py", line 765, in writeDocumentToFile
with open(filename, 'w') as f:
PermissionError: [Errno 13] Permission denied: 'C'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "c:\virtualenvs\cn24x\lib\site-packages\cadnano2\controllers\documentcontroller.py", line 323, in actionSaveSlot
self.writeDocumentToFile()
File "c:\virtualenvs\cn24x\lib\site-packages\cadnano2\controllers\documentcontroller.py", line 769, in writeDocumentToFile
flags = Qt.Dialog | Qt.MSWindowsFixedSizeDialogHint | Qt.WindowType.Sheet
AttributeError: type object 'Qt' has no attribute 'Dialog'

When starting caDNAno2 in an elevated command prompt (run as administrator), saving a file after the initial save creates a file named C in C:\Windows\System32

I am running v2.4.3 in Windows environment.

Hi there,
Sorry to bother you but I am still having this issue. Although #29 , "fixed" it. I am still getting this issue when exporting my staples. My staples and scaffold are supposed to be looped as I am designing a circular ring structure.

Regards,

Hi,

When I entered the command "python main.py", I keep getting this error.

Traceback (most recent call last):
File "C:\Users\Rebekah Adams\Documents\GitHub\cadnano2\cadnano2\main.py", line 12, in
from . import cadnano
ImportError: attempted relative import with no known parent package.

Looking forward to your response.

i met the problem:
main.py:11: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html
import pkg_resources # part of setuptools
Traceback (most recent call last):
File "main.py", line 13, in
from . import cadnano
ImportError: cannot import name 'cadnano' from 'main' (main.py)

I am not able to launch codnano2 using terminal window, it is showing that "no such file or directory" .

Hi, big fan of the transition to pyqt6 and the distribution as a package!

Closing the application with the red "X" button, terminates the window, but does not finish the job in terminal.
It also does not produce any error messages in terminal.
Ctrl + C does not kill the terminal job either. (force quit the blanck Python3.8 App-Icon from the dock, or close terminal window)

Working on Mac Big Sur 10.4, Python 3.8, PyQt6 6.2.2

Hellos!
I am trying to install CaDNAno2 using the Terminal-directed instructions on the website. I am on step 5 and am running into an error (attached screenshot shows the error). My computer is a macOS Monterey 12.3 with that pretentious M1 Max chip that seems to hate everything sometimes. Any help would be great!
Thanks!

Divita

I've read README but I get this error!
Can you help me with this issue please?

Had some trouble with cadnano2, the command python main.py is not working, can anyone indicate me what I might have done wrong? Thank you!

On startup the following messages are printed to stdout. (before the welcome message).

QPainter::begin: Paint device returned engine == 0, type: 2
QPainter::translate: Painter not active
QPainter::rotate: Painter not active
QPainter::begin: Paint device returned engine == 0, type: 2
QPainter::translate: Painter not active
QPainter::rotate: Painter not active


Thank you for using Cadnano2.

We invite you to support the project by citing this reference:
...

Working on Mac Big Sur 10.4, Python 3.8, PyQt6 6.2.2

The "save" function throws an error, although "save as" works without any of the write permission issues:

Using latest github version 2.3.0

Whenever I work on a file and save the changes made, Cadnano doesn't save the file and instead, renames it as 'C' and under the Cadnano directory I can see this 'C' file which is not of json type rather, just file type.

Hello, I am getting a trouble running cadnano2. I have installed it referring README, using a virtual environment on WSL.

cadnano2 : version 2.4.10
PyQt6 : version 6.5.1
sip : version 6.7.9

(cn24x) user@PC:~$ cadnano2
Traceback (most recent call last):
File "/home/user/.local/bin/cadnano2", line 5, in
from cadnano2.main import main
File "/home/user/.local/lib/python3.10/site-packages/cadnano2/main.py", line 18, in
cadnano.initAppWithGui()
File "/home/user/.local/lib/python3.10/site-packages/cadnano2/cadnano.py", line 43, in initAppWithGui
from .cadnanoqt import CadnanoQt
File "/home/user/.local/lib/python3.10/site-packages/cadnano2/cadnanoqt.py", line 8, in
util.qtWrapImport('QtWidgets', globals(), ['QApplication'])
File "/home/user/.local/lib/python3.10/site-packages/cadnano2/util.py", line 104, in qtWrapImport
assert(False) # Have not found a suitable qt framework
AssertionError

When open the cadnano2 after installed. It showed below. Where is wrong. Thankyou.
D:\Users\淑文\Documents\GitHub\cadnano2>python main.py
This application failed to start because it could not find or load the Qt platform plugin "windows"
in "".

Reinstalling the application may fix this problem.

System version: windows 11 22H2 22621.819
Cadnano version: 2.4.8

It's great if you consider to fix this bug in next update.

Thanks for your contribution.

C:\Python310\python.exe: can't open file 'C:\Users\Saurabh\Documents\GitHub\cadnano2\main.py': [Errno 2] No such file or directory

details:
C:\Users\Saurabh\Documents\GitHub\cadnano2>dir
Volume in drive C is OS
Volume Serial Number is 8A2A-F7F4

Directory of C:\Users\Saurabh\Documents\GitHub\cadnano2

05/01/2022 08:26 PM

C:\Users\Saurabh\Documents\GitHub\cadnano2>python main.py
python: can't open file 'C:\Users\Saurabh\Documents\GitHub\cadnano2\main.py': [Errno 2] No such file or directory

C:\Users\Saurabh\Documents\GitHub\cadnano2>pyqt5
'pyqt5' is not recognized as an internal or external command,
operable program or batch file.

C:\Users\Saurabh\Documents\GitHub\cadnano2>pip install PyQt5
Requirement already satisfied: PyQt5 in c:\python310\lib\site-packages (5.15.6)
Requirement already satisfied: PyQt5-sip<13,>=12.8 in c:\python310\lib\site-packages (from PyQt5) (12.10.1)
Requirement already satisfied: PyQt5-Qt5>=5.15.2 in c:\python310\lib\site-packages (from PyQt5) (5.15.2)

C:\Users\Saurabh\Documents\GitHub\cadnano2>pip install networkx
Requirement already satisfied: networkx in c:\python310\lib\site-packages (2.8)

C:\Users\Saurabh\Documents\GitHub\cadnano2>python main.py
python: can't open file 'C:\Users\Saurabh\Documents\GitHub\cadnano2\main.py': [Errno 2] No such file or directory

C:\Users\Saurabh\Documents\GitHub\cadnano2>py main.py
C:\Python310\python.exe: can't open file 'C:\Users\Saurabh\Documents\GitHub\cadnano2\main.py': [Errno 2] No such file or directory

Is the latest version of Cadnano2 still only available for Maya2015? I tried to load the plugin in Maya 2015 following the tutorial from 2018, but I didn't get it loaded successfully

Dear Shawn,

I'm training my left-hander colleague who uses opposite click button configuration, and I found cadnano2 always crushes when the user tries to move mouse with right button holding on path panel, with ctrl key (attempting to pan the panel and holding opposite mouse button by mistake). It's great if you consider to fix this bug in next update.

System: Windows 10
Cadnano version: 2.4.7

Yusuke

Hello

I am wondering where are the plugins? Like autobreak. I installed the cadnano2 package through into virtual server following the mac doc.

Upon using the add sequence tool, the sequence is found missing in certain parts of the nanostructure. I have tried with each of the sequences provided but to no avail.

I cannot seem to upgrade to 2.4.4 on Windows. Despite downloading the latest build and following the instructions in README, I am stuck on 2.4.3 (without the drag-and-drop function and missing the Break Tool icon).

(cn24x) C:\Windows\System32>pip install cadnano2
Collecting cadnano2
Using cached cadnano2-2.4.3-py3-none-any.whl (644 kB)
Collecting PyQt6
Using cached PyQt6-6.2.3-cp36-abi3-win_amd64.whl (6.2 MB)
Collecting PyQt6-sip<14,>=13.2
Using cached PyQt6_sip-13.2.1-cp39-cp39-win_amd64.whl (71 kB)
Collecting PyQt6-Qt6>=6.2.3
Using cached PyQt6_Qt6-6.2.3-py3-none-win_amd64.whl (44.3 MB)
Installing collected packages: PyQt6-sip, PyQt6-Qt6, PyQt6, cadnano2
Successfully installed PyQt6-6.2.3 PyQt6-Qt6-6.2.3 PyQt6-sip-13.2.1 cadnano2-2.4.3

Traceback (most recent call last):
File "C:\Users\Rosa Anna\Downloads\cadnano2.\views\pathview\strand\stranditem.py", line 166, in strandHasNewOligoSlot
self._xover3pEnd._updateColor(strand)
File "C:\Users\Rosa Anna\Downloads\cadnano2.\views\pathview\strand\xoveritem.py", line 458, in _updateColor
vhi5 = self._node5.virtualHelixItem()
AttributeError: 'NoneType' object has no attribute 'virtualHelixItem'

Hi, I have a trouble in installing step 6.
I followed each steps and at step 6, I typed "python main.py" and this happened.

I don't know how to solve this problem. Any comments and helps will be grateful.
Thank you!