Launch error caused by a deprecated library(Bio.Alphbet)

[cyclinbox]

I installed PhyloSuite by pip install PhyloSuite and launched it by command PhyloSuite, but the launching has failed and I got the Error message like this:

Traceback (most recent call last):
  File "C:\Users\zhang\anaconda3\lib\runpy.py", line 197, in _run_module_as_main
    return _run_code(code, main_globals, None,
  File "C:\Users\zhang\anaconda3\lib\runpy.py", line 87, in _run_code
    exec(code, run_globals)
  File "C:\Users\zhang\anaconda3\Scripts\PhyloSuite.exe\__main__.py", line 4, in <module>
  File "C:\Users\zhang\anaconda3\lib\site-packages\PhyloSuite\PhyloSuite.py", line 20, in <module>
    from src.main import MyMainWindow
  File "C:\Users\zhang\anaconda3\lib\site-packages\PhyloSuite\src\main.py", line 23, in <module>
    from src.Lg_displaySettings import DisplaySettings
  File "C:\Users\zhang\anaconda3\lib\site-packages\PhyloSuite\src\Lg_displaySettings.py", line 18, in <module>
    from src.handleGB import ArrayManager
  File "C:\Users\zhang\anaconda3\lib\site-packages\PhyloSuite\src\handleGB.py", line 12, in <module>
    from Bio.Alphabet import generic_dna
  File "C:\Users\zhang\anaconda3\lib\site-packages\Bio\Alphabet\__init__.py", line 20, in <module>
    raise ImportError(
ImportError: Bio.Alphabet has been removed from Biopython. In many cases, the alphabet can simply be ignored and removed from scripts. In a few cases, you may need to specify the ``molecule_type`` as an annotation on a SeqRecord for your script to work correctly. Please see https://biopython.org/wiki/Alphabet for more information.

It looks like PhyloSuite uses an old version of Bio.Alphabet API in the Biopython library, but in the latest version of Biopython this API is deprecated. I wonder how to fix this error, thanks!

Addtional information:

Python version: 3.9.7
Biopython version: 1.79
OS: Windows 11 x64 (NT 10.0.22621.1992)

[cyclinbox]

Update: I fixed this problem by uninstall the latest version of Biopython and reinstall Biopython 1.77 (lower than 1.77 should work as well but I didn't try)

pip uninstall Biopython
pip install Biopython==1.77

Besides, I also tried Biopython 1.78 and got the same error message as before. So any Biopython version > 1.77 cannot work while version <= 1.77 can work.

[dongzhang0725]

for installation, refer to here: http://phylosuite.jushengwu.com/dongzhang0725.github.io/installation/#2-Install-using-pip

Wanyu.Zhang @.***> 于2023年8月9日周三 11:10写道：

I installed PhyloSuite by pip install PhyloSuite and launched it by command PhyloSuite, but the launching has failed and I got the Error message like this:

Traceback (most recent call last): File "C:\Users\zhang\anaconda3\lib\runpy.py", line 197, in _run_module_as_main return run_code(code, main_globals, None, File "C:\Users\zhang\anaconda3\lib\runpy.py", line 87, in run_code exec(code, run_globals) File "C:\Users\zhang\anaconda3\Scripts\PhyloSuite.exe_main.py", line 4, in File "C:\Users\zhang\anaconda3\lib\site-packages\PhyloSuite\PhyloSuite.py", line 20, in from src.main import MyMainWindow File "C:\Users\zhang\anaconda3\lib\site-packages\PhyloSuite\src\main.py", line 23, in from src.Lg_displaySettings import DisplaySettings File "C:\Users\zhang\anaconda3\lib\site-packages\PhyloSuite\src\Lg_displaySettings.py", line 18, in from src.handleGB import ArrayManager File "C:\Users\zhang\anaconda3\lib\site-packages\PhyloSuite\src\handleGB.py", line 12, in from Bio.Alphabet import generic_dna File "C:\Users\zhang\anaconda3\lib\site-packages\Bio\Alphabet_init.py", line 20, in raise ImportError( ImportError: Bio.Alphabet has been removed from Biopython. In many cases, the alphabet can simply be ignored and removed from scripts. In a few cases, you may need to specify the molecule_type as an annotation on a SeqRecord for your script to work correctly. Please see https://biopython.org/wiki/Alphabet for more information.

It looks like PhyloSuite uses an old version of Bio.Alphabet API in the Biopython library, but in the latest version of Biopython this API is deprecated. I wonder how to fix this error, thanks!

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[dongzhang0725]

@cyclinbox Yes, you are right, as recorded in the installation page, if you use python 3.6, pip install PhyloSuite will work, and Biopython v1.77 will be selected to install.

Dong