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The dataset generation failed because of a cast error
Error code: DatasetGenerationCastError
Exception: DatasetGenerationCastError
Message: An error occurred while generating the dataset
All the data files must have the same columns, but at some point there are 7 new columns ({'tmscore', 'tmscore_biotite', 'same_subfamily', 'gene1', 'superposed_pairs_biotite', 'gene2', 'paralog'}) and 6 missing columns ({'effect', 'slow_growth', 'concordant', 'stress', 'sgd_dir', 'gene'}).
This happened while the csv dataset builder was generating data using
hf://datasets/HarriziSaad/BULMA/results/abc_struct_validation.csv (at revision 638ea388bc9e655093cf8cf4495055e546f568a4), ['hf://datasets/HarriziSaad/BULMA@638ea388bc9e655093cf8cf4495055e546f568a4/results/validation.csv', 'hf://datasets/HarriziSaad/BULMA@638ea388bc9e655093cf8cf4495055e546f568a4/results/abc_struct_validation.csv', 'hf://datasets/HarriziSaad/BULMA@638ea388bc9e655093cf8cf4495055e546f568a4/results/abc_struct_validation_summary.csv']
Please either edit the data files to have matching columns, or separate them into different configurations (see docs at https://hf.co/docs/hub/datasets-manual-configuration#multiple-configurations)
Traceback: Traceback (most recent call last):
File "/usr/local/lib/python3.14/site-packages/datasets/builder.py", line 1848, in _prepare_split_single
writer.write_table(table)
~~~~~~~~~~~~~~~~~~^^^^^^^
File "/usr/local/lib/python3.14/site-packages/datasets/arrow_writer.py", line 784, in write_table
self._write_table(pa_table, writer_batch_size=writer_batch_size)
~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.14/site-packages/datasets/arrow_writer.py", line 795, in _write_table
pa_table = table_cast(pa_table, self._schema)
File "/usr/local/lib/python3.14/site-packages/datasets/table.py", line 2378, in table_cast
return cast_table_to_schema(table, schema)
File "/usr/local/lib/python3.14/site-packages/datasets/table.py", line 2306, in cast_table_to_schema
raise CastError(
...<3 lines>...
)
datasets.table.CastError: Couldn't cast
gene1: string
gene2: string
same_subfamily: bool
tmscore: double
paralog: bool
tmscore_biotite: double
superposed_pairs_biotite: int64
-- schema metadata --
pandas: '{"index_columns": [{"kind": "range", "name": null, "start": 0, "' + 1122
to
{'stress': Value('string'), 'gene': Value('string'), 'effect': Value('float64'), 'sgd_dir': Value('int64'), 'concordant': Value('int64'), 'slow_growth': Value('float64')}
because column names don't match
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/src/services/worker/src/worker/job_runners/config/parquet_and_info.py", line 1369, in compute_config_parquet_and_info_response
parquet_operations, partial, estimated_dataset_info = stream_convert_to_parquet(
~~~~~~~~~~~~~~~~~~~~~~~~~^
builder, max_dataset_size_bytes=max_dataset_size_bytes
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
)
^
File "/src/services/worker/src/worker/job_runners/config/parquet_and_info.py", line 948, in stream_convert_to_parquet
builder._prepare_split(split_generator=splits_generators[split], file_format="parquet")
~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.14/site-packages/datasets/builder.py", line 1694, in _prepare_split
for job_id, done, content in self._prepare_split_single(
~~~~~~~~~~~~~~~~~~~~~~~~~~^
gen_kwargs=gen_kwargs, job_id=job_id, **_prepare_split_args
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
):
^
File "/usr/local/lib/python3.14/site-packages/datasets/builder.py", line 1850, in _prepare_split_single
raise DatasetGenerationCastError.from_cast_error(
...<4 lines>...
)
datasets.exceptions.DatasetGenerationCastError: An error occurred while generating the dataset
All the data files must have the same columns, but at some point there are 7 new columns ({'tmscore', 'tmscore_biotite', 'same_subfamily', 'gene1', 'superposed_pairs_biotite', 'gene2', 'paralog'}) and 6 missing columns ({'effect', 'slow_growth', 'concordant', 'stress', 'sgd_dir', 'gene'}).
This happened while the csv dataset builder was generating data using
hf://datasets/HarriziSaad/BULMA/results/abc_struct_validation.csv (at revision 638ea388bc9e655093cf8cf4495055e546f568a4), ['hf://datasets/HarriziSaad/BULMA@638ea388bc9e655093cf8cf4495055e546f568a4/results/validation.csv', 'hf://datasets/HarriziSaad/BULMA@638ea388bc9e655093cf8cf4495055e546f568a4/results/abc_struct_validation.csv', 'hf://datasets/HarriziSaad/BULMA@638ea388bc9e655093cf8cf4495055e546f568a4/results/abc_struct_validation_summary.csv']
Please either edit the data files to have matching columns, or separate them into different configurations (see docs at https://hf.co/docs/hub/datasets-manual-configuration#multiple-configurations)Need help to make the dataset viewer work? Make sure to review how to configure the dataset viewer, and open a discussion for direct support.
stress string | gene string | effect float64 | sgd_dir int64 | concordant int64 | slow_growth float64 |
|---|---|---|---|---|---|
oxidative | YAL002W | 2.409524 | -1 | 1 | 0.481726 |
oxidative | YAL011W | 0.455086 | -1 | 1 | 0.673299 |
oxidative | YAL020C | -1.22663 | 1 | 1 | -0.597068 |
oxidative | YAL021C | 6.680334 | -1 | 1 | 0.828493 |
oxidative | YAL024C | 8.267511 | -1 | 1 | 0.641747 |
oxidative | YAL026C | 2.871661 | 1 | 0 | 0.833142 |
oxidative | YAL039C | 0.448263 | 1 | 0 | -0.031998 |
oxidative | YAL042W | -0.798548 | -1 | 0 | -0.166429 |
oxidative | YAL055W | 3.258199 | -1 | 1 | -0.146092 |
oxidative | YAL058W | 7.734242 | 1 | 0 | -0.202358 |
oxidative | YAL059W | -1.872198 | 1 | 1 | -0.678331 |
oxidative | YAL064C-A | -0.236426 | -1 | 0 | -0.075967 |
oxidative | YAL068C | 1.699604 | 1 | 0 | -0.127242 |
oxidative | YAR018C | 2.258892 | -1 | 1 | 0.091905 |
oxidative | YAR042W | 2.475787 | -1 | 1 | 0.09255 |
oxidative | YBL001C | 0.519451 | -1 | 1 | -0.122162 |
oxidative | YBL008W | 3.035395 | -1 | 1 | 0.378802 |
oxidative | YBL009W | 0.863778 | -1 | 1 | 0.34931 |
oxidative | YBL010C | -0.449439 | -1 | 0 | 0.054768 |
oxidative | YBL015W | -0.143678 | -1 | 0 | -0.146152 |
oxidative | YBL017C | 0.849109 | -1 | 1 | 0.07832 |
oxidative | YBL019W | 0.500158 | -1 | 1 | 0.128858 |
oxidative | YBL021C | -1.485206 | -1 | 0 | -0.020022 |
oxidative | YBL022C | 3.815298 | -1 | 1 | 0.846712 |
oxidative | YBL024W | 5.54187 | -1 | 1 | 0.343688 |
oxidative | YBL028C | 2.605624 | -1 | 1 | 0.217531 |
oxidative | YBL029W | 4.316994 | -1 | 1 | -0.255591 |
oxidative | YBL031W | 1.681393 | -1 | 1 | 0.641569 |
oxidative | YBL032W | 5.128289 | -1 | 1 | -0.258123 |
oxidative | YBL036C | 1.207114 | -1 | 1 | 0.059385 |
oxidative | YBL037W | 2.234998 | -1 | 1 | 0.384981 |
oxidative | YBL043W | 2.851816 | -1 | 1 | 0.05473 |
oxidative | YBL046W | 13.106831 | -1 | 1 | 0.840459 |
oxidative | YBL047C | 7.930327 | -1 | 1 | 0.376114 |
oxidative | YBL048W | -0.734753 | -1 | 0 | -0.118975 |
oxidative | YBL051C | 9.545362 | -1 | 1 | 0.446508 |
oxidative | YBL052C | 1.540819 | -1 | 1 | 0.225683 |
oxidative | YBL053W | -2.281133 | -1 | 0 | 0.011217 |
oxidative | YBL054W | 0.108273 | -1 | 1 | 0.332451 |
oxidative | YBL056W | 1.541275 | -1 | 1 | 0.011833 |
oxidative | YBL057C | 0.37862 | -1 | 1 | -0.037941 |
oxidative | YBL059W | 0.869975 | -1 | 1 | 0.07977 |
oxidative | YBL060W | -1.435992 | -1 | 0 | 0.199544 |
oxidative | YBL061C | 2.230312 | -1 | 1 | 0.284863 |
oxidative | YBL062W | 0.703733 | -1 | 1 | 0.481764 |
oxidative | YBL063W | -0.617356 | -1 | 0 | -0.032024 |
oxidative | YBL064C | 3.735271 | -1 | 1 | 0.162942 |
oxidative | YBL065W | -0.21784 | -1 | 0 | 0.06249 |
oxidative | YBL066C | 1.776416 | -1 | 1 | -0.027234 |
oxidative | YBL067C | 2.845616 | -1 | 1 | 0.494785 |
oxidative | YBL068W | -1.327565 | -1 | 0 | 0.114443 |
oxidative | YBL069W | -3.684444 | -1 | 0 | -0.018716 |
oxidative | YBL070C | 2.831506 | -1 | 1 | 0.112924 |
oxidative | YBL072C | 0.974439 | -1 | 1 | -0.827748 |
oxidative | YBL075C | 1.488358 | -1 | 1 | -0.032285 |
oxidative | YBL078C | -1.098166 | -1 | 0 | 0.067008 |
oxidative | YBL079W | 0.421164 | 1 | 0 | 0.036274 |
oxidative | YBL081W | 2.549203 | -1 | 1 | -0.315751 |
oxidative | YBL085W | -0.504528 | -1 | 0 | -0.163504 |
oxidative | YBL087C | -1.37843 | 1 | 1 | -0.299978 |
oxidative | YBL088C | 6.674034 | -1 | 1 | 0.049419 |
oxidative | YBL089W | -1.888035 | 1 | 1 | 0.073257 |
oxidative | YBL091C | 1.106616 | -1 | 1 | 0.177616 |
oxidative | YBL091C-A | 1.093104 | -1 | 1 | 0.074943 |
oxidative | YBL094C | 4.03252 | -1 | 1 | 0.114288 |
oxidative | YBR003W | -0.709828 | -1 | 0 | -0.203272 |
oxidative | YBR020W | -0.764181 | -1 | 0 | 0.057239 |
oxidative | YBR027C | -6.177703 | -1 | 0 | 0.636299 |
oxidative | YBR031W | -1.038648 | 1 | 1 | -0.75172 |
oxidative | YBR035C | -0.731736 | -1 | 0 | 0.391376 |
oxidative | YBR036C | -0.152926 | 1 | 1 | 0.431467 |
oxidative | YBR037C | -0.98627 | -1 | 0 | -0.068005 |
oxidative | YBR044C | -0.141791 | -1 | 0 | 0.118536 |
oxidative | YBR046C | 0.564537 | -1 | 1 | 0.041251 |
oxidative | YBR058C | 12.670307 | 1 | 0 | -0.085314 |
oxidative | YBR066C | 0.920099 | 1 | 0 | -0.047857 |
oxidative | YBR077C | -0.997014 | -1 | 0 | 0.253399 |
oxidative | YBR078W | 1.34583 | -1 | 1 | 0.273323 |
oxidative | YBR083W | 0.323282 | -1 | 1 | 0.285105 |
oxidative | YBR084W | -1.807229 | 1 | 1 | 0.135634 |
oxidative | YBR098W | 10.822899 | -1 | 1 | 0.711342 |
oxidative | YBR099C | 8.712726 | -1 | 1 | 0.268723 |
oxidative | YBR101C | 2.741623 | -1 | 1 | -0.221123 |
oxidative | YBR103W | 10.559639 | 1 | 0 | 0.635288 |
oxidative | YBR119W | -2.916199 | -1 | 0 | 0.125497 |
oxidative | YBR128C | -5.439806 | 1 | 1 | 0.164416 |
oxidative | YBR129C | -0.055247 | -1 | 0 | -0.152749 |
oxidative | YBR131W | 1.74985 | -1 | 1 | 0.535104 |
oxidative | YBR133C | -1.347353 | 1 | 1 | -0.144186 |
oxidative | YBR141C | -1.203154 | -1 | 0 | -0.140498 |
oxidative | YBR144C | 0.09465 | 1 | 0 | -0.22567 |
oxidative | YBR151W | 0.721667 | -1 | 1 | 0.245812 |
oxidative | YBR164C | -0.775426 | -1 | 0 | 0.513038 |
oxidative | YBR173C | -0.400743 | 1 | 1 | 0.086278 |
oxidative | YBR174C | 1.291986 | -1 | 1 | 0.522831 |
oxidative | YBR183W | 1.462163 | -1 | 1 | 0.107964 |
oxidative | YBR187W | 1.632713 | -1 | 1 | 0.096804 |
oxidative | YBR188C | -0.410436 | -1 | 0 | 0.02328 |
oxidative | YBR195C | 3.280984 | -1 | 1 | 0.100566 |
oxidative | YBR207W | -0.428289 | -1 | 0 | -0.130151 |
End of preview.
BULMA
Data and code for: Harrizi, S.; Nait Irahal, I.; Kabine, M. Genome-Wide Chemogenomic Analysis Reveals Agent-Specific Context-Dependence of Gene Function and Individualised ABC Transporter Roles in Saccharomyces cerevisiae. Release R1.
Reproduction
pip install -r requirements.txt
bash run_all.sh
Scripts in code/ run in numerical order and regenerate every number, table and figure source file in results/ from data/raw/. Public third-party data are downloaded to data/external/ on first run. results/summary_numbers.md lists every statistic quoted in the manuscript; Table S4 of the manuscript maps each section, figure and table to its script.
Contents
data/raw/ input data
data/derived/ fixed random reference sample
code/ analysis scripts
results/ derived tables and figure source data
Licence
CC BY 4.0. Input data remain under the terms of their sources.
Contact
Saad Harrizi, Université Hassan II de Casablanca. ORCID 0009-0007-1426-0371.
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