"AttributeError: 'ExactPosition' object has no attribute 'position' when using QUEEN(seq='...')" in Colab

[OMTikker]

When running the Example code 1 (Create a QUEEN class object (blunt-ends), dna = QUEEN(seq="CCGGTATGCGTCGA")) in Colab, I now get the "AttributeError". This error has probably occurred between 20-25.12 2023. I have tried with both versions in Colab (queen=1.1.0 and 1.2.0). Interestingly, it works locally in jupyter notebook.

[ponnhide]

Thank you for your report. The issue stems from a recent update in Biopython, where the newest version has removed the location.position parameter. Consequently, this is causing the error in QUEEN that you've encountered.
I am currently working on updating QUEEN to be compatible with the new Biopython version.
I apologize for the inconvenience and appreciate your understanding.

[OMTikker]

Hi!Thanks a lot for the clarification!I could solve the issue for me by using the previous Biopython.All the best in the new year.OliverOn 30. Dec 2023, at 10:19, Hideto Mori ***@***.***> wrote: Thank you for your report. The issue stems from a recent update in Biopython, where the newest version has removed the location.position parameter. Consequently, this is causing the error in QUEEN that you've encountered. I am currently working on updating QUEEN to be compatible with the new Biopython version. I apologize for the inconvenience and appreciate your understanding. —Reply to this email directly, view it on GitHub, or unsubscribe.You are receiving this because you authored the thread.Message ID: ***@***.***>

[yyigitgezer]

Thank you for your report. The issue stems from a recent update in Biopython, where the newest version has removed the location.position parameter. Consequently, this is causing the error in QUEEN that you've encountered. I am currently working on updating QUEEN to be compatible with the new Biopython version. I apologize for the inconvenience and appreciate your understanding.

which version of biopython module should I use to not encounter this problem ?

[ponnhide]

The latest version in the GitHub repository is compatible with the newest BioPython. You can install it from the repository directory. However, please note that the GitHub version is still under development, even on the 'master' branch, so please check for updates periodically. Once the development reaches a certain level, I will update the version on pip. Sorry for the inconvenience.