Comments (2)
konstin
commented on May 27, 2024
Also requires 3.7, even though all dependencies should work on 3.6. There isn't a python package, so if we don't want to vendor their code, we need to create a python package.
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sacdallago
commented on May 27, 2024
TBH, although ugly, for some of these things I'm happy even sys-calling them. After all: we are doing them a favor by integrating their tools, "worst comes to worst" they can collaborate with us! Easiest solution! Sys-calls (to e.g. docker containers) could be an interesting extension of the pipeline
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Related Issues (20)
- Add support for ESM-2 and ESMFold HOT 3
- Update jax-unirep dependency version
- Protocol prottrans_t5_xl_u50: URLError: <urlopen error [Errno 113] No route to host> HOT 1
- OSError: Unable to open file (truncated file: eof = 63504384, sblock->base_addr = 0, stored_eof = 374434776)
- Custom embeddings
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- Can not install bio-embedding in wsl HOT 2
- Can not install bioembedings on ubuntu? Please help HOT 1
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- Error during first step - greenlet size changed, may indicate binary incompatibility. HOT 1
- 3D Protein Embeddings
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- Cant install bio_embeddings in colab HOT 2
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- Protocol prottrans_t5_xl_u50: PermissionError: [Errno 13] Permission denied: 'C:\\Users\\user\\AppData\\Local\\Temp\\tmpk7e1m0jg' HOT 1
- from where comes the models in "bio_embeddings/utilities /defaults.yml", where is docs, parameters, dataset ?
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- Cannot Import Any Embedder "load()" has been removed, use yaml = YAML(typ='rt') yaml.load(...)
- Protocol prottrans_bert_bfd: OSError: Unable to load weights from pytorch checkpoint file for .catch/bio_embeddings/prottrans_bert_bfd/model_directory/pytorch_model.bin' at '.catch/bio_embeddings/prottrans_bert_bfd/model_directory/pytorch_model.bin'. If you tried to load a PyTorch model from a TF 2.0 checkpoint, please set from_tf=True.
- Can Word2Vec be used for 4, 5 and 6 kmer? If possible, which file I need to changed and which parameter. I am seeking Guidance on Adapting Word2Vec Code for 4kmer Sequences
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