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yikunpku / RNA-MSM

Nucleic Acids Research 2024：RNA-MSM model is an unsupervised RNA language model based on multiple sequences that outputs both embedding and attention map to match different types of downstream tasks.
https://aigene.cloudbastion.cn/#/rna-msm
MIT License
49 stars 4 forks source link

ModuleNotFoundError: No module named 'msm.version' #9

Closed JinwnK closed 5 months ago

JinwnK commented 6 months ago

Hello, There is an error when I run the command:

$ conda activate rnamsm
(rnamsm) [kjw@master RNA-MSM]$ python RNA_MSM_Inference.py \
> data.root_path=/public/work/jinwen/4Gdb_test/RNA-MSM/test \
> data.MSA_path=/public/work/jinwen/4Gdb_test/RNA-MSM/test/results \
> data.model_path=/public/work/jinwen/4Gdb_test/RNA-MSM/test/pretrained \
> data.MSA_list=/public/work/jinwen/4Gdb_test/RNA-MSM/test/rna_id.txt
Traceback (most recent call last):
  File "RNA_MSM_Inference.py", line 5, in <module>
    from utils.tokenization import Vocab
  File "/public/work/jinwen/software/RNA-MSM/utils/tokenization.py", line 6, in <module>
    import msm
  File "/public/work/jinwen/software/RNA-MSM/msm/__init__.py", line 6, in <module>
    from .version import version as __version__  # noqa
ModuleNotFoundError: No module named 'msm.version'
Yanxu-Zhu commented 6 months ago

the same with me.Did you fix it？

JinwnK commented 6 months ago

the same with me.Did you fix it？

I haven't fixed it yet.

Yanxu-Zhu commented 6 months ago

Do you have any good rna models to recommend?

JinwnK commented 6 months ago

Do you have any good rna models to recommend?

I'm trying RNA-FM, RNAErnie.

Yanxu-Zhu commented 6 months ago

Thanks for your recommendation！

LiuJeremy commented 5 months ago

In the init.py file in the msm folder, you can add some annotations.

\# from .version import version as __version__  # noqa
from .data import Alphabet, BatchConverter, FastaBatchedDataset  # noqa
from .model import ProteinBertModel, MSATransformer  # noqa
\# from . import pretrained  # noqa
JinwnK commented 5 months ago

In the init.py file in the msm folder, you can add some annotations.

\# from .version import version as __version__  # noqa
from .data import Alphabet, BatchConverter, FastaBatchedDataset  # noqa
from .model import ProteinBertModel, MSATransformer  # noqa
\# from . import pretrained  # noqa

Thank you , it works!

ZhiyuanChen commented 5 months ago

Do you have any good rna models to recommend?

Maybe try https://multimolecule.danling.org/ I have everything implemented except for RNAErnie, which should be completed this week.