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ML-Bioinfo-CEITEC / genomic_benchmarks

Benchmarks for classification of genomic sequences
Apache License 2.0
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download_dataset doesn't work as expected on my CHPC system. #38

Open leannmlindsey opened 6 months ago

leannmlindsey commented 6 months ago

I was able to get download_dataset to work as expected on my macbook pro but when I try to use it on my university's CHPC system I get this error.

Do you have any idea what could be causing this? I am trying to repeat the experiments on the HyenaDNA paper and their code depends upon this function working properly.

(p100_hyena-dna) [u1323098@kp359:test_dir]$ python Python 3.8.18 | packaged by conda-forge | (default, Oct 10 2023, 15:44:36) [GCC 12.3.0] on linux Type "help", "copyright", "credits" or "license" for more information.

from genomic_benchmarks.data_check import list_datasets list_datasets() ['drosophila_enhancers_stark', 'dummy_mouse_enhancers_ensembl', 'human_ensembl_regulatory', 'demo_coding_vs_intergenomic_seqs', 'demo_human_or_worm', 'human_nontata_promoters', 'human_enhancers_ensembl', 'human_enhancers_cohn', 'human_ocr_ensembl'] from genomic_benchmarks.loc2seq import download_dataset download_dataset("human_nontata_promoters", version=0) Traceback (most recent call last): File "", line 1, in File "/uufs/chpc.utah.edu/common/home/u1323098/software/pkg/miniconda3/envs/p100_hyena-dna/lib/python3.8/site-packages/genomic_benchmarks/loc2seq/loc2seq.py", line 55, in download_dataset return download_from_cloud_cache((dataset_name, version), Path(dest_path) / dataset_name) File "/uufs/chpc.utah.edu/common/home/u1323098/software/pkg/miniconda3/envs/p100_hyena-dna/lib/python3.8/site-packages/genomic_benchmarks/loc2seq/cloud_caching.py", line 32, in download_from_cloud_cache gdown.download( File "/uufs/chpc.utah.edu/common/home/u1323098/software/pkg/miniconda3/envs/p100_hyena-dna/lib/python3.8/site-packages/gdown/download.py", line 259, in download filename_from_url = m.groups()[0] AttributeError: 'NoneType' object has no attribute 'groups'

davidboening commented 6 months ago

I had the same problem today, updating gdown fixed the issue: pip install --upgrade gdown I'm guessing this is due to some changes in the Google Drive API.