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dongzhang0725 / PhyloSuite

PhyloSuite is an integrated and scalable desktop platform for streamlined molecular sequence data management and evolutionary phylogenetics studies
GNU General Public License v3.0
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Bio.Alphabet Related #27

Closed starsareintherose closed 2 years ago

starsareintherose commented 3 years ago 
░▒▓ ~/Dow/py/p/p/u/bin ▓▒░ ./PhyloSuite   ░▒▓ ✔  10:54:54 ▓▒░
Traceback (most recent call last):
  File "/home/guoyi/Downloads/py/pkg/phylosuite/usr/bin/./PhyloSuite", line 33, in <module>
    sys.exit(load_entry_point('PhyloSuite==1.2.2', 'console_scripts', 'PhyloSuite')())
  File "/home/guoyi/Downloads/py/pkg/phylosuite/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 855, in exec_module
  File "<frozen importlib._bootstrap>", line 228, in _call_with_frames_removed
  File "/usr/lib/python3.9/site-packages/PhyloSuite/PhyloSuite.py", line 20, in <module>
    from src.main import MyMainWindow
  File "/usr/lib/python3.9/site-packages/PhyloSuite/src/main.py", line 23, in <module>
    from src.Lg_displaySettings import DisplaySettings
  File "/usr/lib/python3.9/site-packages/PhyloSuite/src/Lg_displaySettings.py", line 18, in <module>
    from src.handleGB import ArrayManager
  File "/usr/lib/python3.9/site-packages/PhyloSuite/src/handleGB.py", line 12, in <module>
    from Bio.Alphabet import generic_dna
  File "/usr/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.
dongzhang0725 commented 3 years ago

biopython 用1.71版本，python用3.6.7版本

月季花中的星辰 @.***> 于2021年5月11日周二 上午10:58写道：

░▒▓ ~/Dow/py/p/p/u/bin ▓▒░ ./PhyloSuite ░▒▓ ✔ 10:54:54 ▓▒░

Traceback (most recent call last):

File "/home/guoyi/Downloads/py/pkg/phylosuite/usr/bin/./PhyloSuite", line 33, in 

sys.exit(load_entry_point('PhyloSuite==1.2.2', 'console_scripts', 'PhyloSuite')())

File "/home/guoyi/Downloads/py/pkg/phylosuite/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 855, in exec_module

File "", line 228, in _call_with_frames_removed

File "/usr/lib/python3.9/site-packages/PhyloSuite/PhyloSuite.py", line 20, in 

from src.main import MyMainWindow

File "/usr/lib/python3.9/site-packages/PhyloSuite/src/main.py", line 23, in 

from src.Lg_displaySettings import DisplaySettings

File "/usr/lib/python3.9/site-packages/PhyloSuite/src/Lg_displaySettings.py", line 18, in 

from src.handleGB import ArrayManager

File "/usr/lib/python3.9/site-packages/PhyloSuite/src/handleGB.py", line 12, in 

from Bio.Alphabet import generic_dna

File "/usr/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.

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