ImportError: Bio.Alphabet has been removed from Biopython

[NgoTanw]

Unable to run PhyloSuite after installation. I get an error about Bio.Alphabet for both pip install and installation by source.

[ngotanw@RankA ~]$ PhyloSuite
Traceback (most recent call last):
  File "/usr/bin/PhyloSuite", line 33, in <module>
    sys.exit(load_entry_point('PhyloSuite==1.2.2', 'console_scripts', 'PhyloSuite')())
  File "/usr/bin/PhyloSuite", line 25, in importlib_load_entry_point
    return next(matches).load()
  File "/usr/lib/python3.9/importlib/metadata.py", line 77, in load
    module = import_module(match.group('module'))
  File "/usr/lib/python3.9/importlib/__init__.py", line 127, in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
  File "<frozen importlib._bootstrap>", line 1030, in _gcd_import
  File "<frozen importlib._bootstrap>", line 1007, in _find_and_load
  File "<frozen importlib._bootstrap>", line 986, in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 680, in _load_unlocked
  File "<frozen importlib._bootstrap_external>", line 790, in exec_module
  File "<frozen importlib._bootstrap>", line 228, in _call_with_frames_removed
  File "/usr/lib/python3.9/site-packages/PhyloSuite-1.2.2-py3.9.egg/PhyloSuite/PhyloSuite.py", line 20, in <module>
    from src.main import MyMainWindow
  File "/usr/lib/python3.9/site-packages/PhyloSuite-1.2.2-py3.9.egg/PhyloSuite/src/main.py", line 23, in <module>
    from src.Lg_displaySettings import DisplaySettings
  File "/usr/lib/python3.9/site-packages/PhyloSuite-1.2.2-py3.9.egg/PhyloSuite/src/Lg_displaySettings.py", line 18, in <module>
    from src.handleGB import ArrayManager
  File "/usr/lib/python3.9/site-packages/PhyloSuite-1.2.2-py3.9.egg/PhyloSuite/src/handleGB.py", line 12, in <module>
    from Bio.Alphabet import generic_dna
  File "/home/ngotanw/.local/lib/python3.9/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.

OS: Arch Linux Python version: 3.9.2 Biopython version: 1.78

[dongzhang0725]

PhyloSuite is developed in Python 3.6.7, so you may try to install it with python 3.6 or python 3.7. By the way, you may also try the packaged version: http://phylosuite.jushengwu.com/installation_packages/PhyloSuite_v1.2.2_Linux.tar.gz .

NgoTanw @.***> 于2021年3月14日周日 下午5:08写道：

Unable to run PhyloSuite after installation. I get an error about Bio.Alphabet for both pip install and installation by source.

[ngotanw@RankA ~]$ PhyloSuite Traceback (most recent call last): File "/usr/bin/PhyloSuite", line 33, in sys.exit(load_entry_point('PhyloSuite==1.2.2', 'console_scripts', 'PhyloSuite')()) File "/usr/bin/PhyloSuite", line 25, in importlib_load_entry_point return next(matches).load() File "/usr/lib/python3.9/importlib/metadata.py", line 77, in load module = import_module(match.group('module')) File "/usr/lib/python3.9/importlib/init.py", line 127, in import_module return _bootstrap._gcd_import(name[level:], package, level) File "", line 1030, in _gcd_import File "", line 1007, in _find_and_load File "", line 986, in _find_and_load_unlocked File "", line 680, in _load_unlocked File "", line 790, in exec_module File "", line 228, in _call_with_frames_removed File "/usr/lib/python3.9/site-packages/PhyloSuite-1.2.2-py3.9.egg/PhyloSuite/PhyloSuite.py", line 20, in from src.main import MyMainWindow File "/usr/lib/python3.9/site-packages/PhyloSuite-1.2.2-py3.9.egg/PhyloSuite/src/main.py", line 23, in from src.Lg_displaySettings import DisplaySettings File "/usr/lib/python3.9/site-packages/PhyloSuite-1.2.2-py3.9.egg/PhyloSuite/src/Lg_displaySettings.py", line 18, in from src.handleGB import ArrayManager File "/usr/lib/python3.9/site-packages/PhyloSuite-1.2.2-py3.9.egg/PhyloSuite/src/handleGB.py", line 12, in from Bio.Alphabet import generic_dna File "/home/ngotanw/.local/lib/python3.9/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.

OS: Arch Linux Python version: 3.9.2 Biopython version: 1.78

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[NgoTanw]

Downgrading python to 3.7.2 didn't help. But the packaged version is getting things done. Although using the online features returns an SSLError.

[HannesOberreiter]

"Workaround" if you use (mini)conda. Install first an environment with Python 3.6.7, then install PhyloSuite and at last step install the specific version of biopython which still includes alphabet attribute.

# Create Env
conda create -n py36 python=3.6.7
# Activate Env
conda activate py36
# Install PhyloSuite
pip install PhyloSuite
# Overwrite biopython with specific version
pip install biopython==1.68
# Start PhyloSuite
PhyloSuite
# to deactivate environment
conda deactivate

Cheers Hannes

[dongzhang0725]

Nice input!