No module named 'Bio.codonalign.codonalphabet'

[liupfskygre]

Hi there,
I try to install inStrain using conda,
got this error by calling inStrain -h

File "/home/dell/.conda/envs/instrain/bin/inStrain", line 19, in <module>
    import inStrain.controller
  File "/home/dell/.conda/envs/instrain/lib/python3.8/site-packages/inStrain/controller.py", line 20, in <module>
    import inStrain.profile
  File "/home/dell/.conda/envs/instrain/lib/python3.8/site-packages/inStrain/profile/__init__.py", line 5, in <module>
    import inStrain.profile.profile_controller
  File "/home/dell/.conda/envs/instrain/lib/python3.8/site-packages/inStrain/profile/profile_controller.py", line 14, in <module>
    import inStrain.SNVprofile
  File "/home/dell/.conda/envs/instrain/lib/python3.8/site-packages/inStrain/SNVprofile.py", line 21, in <module>
    import inStrain.profile.profile_utilities
  File "/home/dell/.conda/envs/instrain/lib/python3.8/site-packages/inStrain/profile/profile_utilities.py", line 27, in <module>
    import inStrain.GeneProfile
  File "/home/dell/.conda/envs/instrain/lib/python3.8/site-packages/inStrain/GeneProfile.py", line 26, in <module>
    from Bio.codonalign.codonalphabet import default_codon_table
ModuleNotFoundError: No module named 'Bio.codonalign.codonalphabet'

I have tryied reinstall biopython==1.73, 1.74 or 1.78, all gave same error,

any suggestion on this,

thanks.

Liu

[ecvanderwijk]

I also got that issue, but it got solved when I reinstalled inStrain using Conda.
conda remove inStrain
conda install -c bioconda inStrain
I hope that works for you.

[MrOlm]

This problem happens with Biopython version > 1.74. Are you sure that your attempts to download v1.74 were successful? You can check by typing "python" "import Bio" "print(Bio.version)"

You can also try and alter the version using the command pip install biopython=1.74

Best,
Matt

[liupfskygre]

Hi,
I try to reinstall as ecvanderwijk suggested and now it worked. Could be the install of biopython version issue, not properly installed.
thank you both.

Liu