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DBNascent

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genomics

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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 9 new columns ({'Other seq', '3D seq', 'Published?', 'Median QC score', 'Protocols', 'ChIP-seq', 'ATAC-seq', 'RNA-seq', 'Organisms'}) and 8 missing columns ({'Sample name', 'Read depth', 'Treatment', 'QC score', 'Replicate', 'Protocol', 'Cell type', 'Organism'}).

This happened while the csv dataset builder was generating data using

hf://datasets/funlab/DBNascent/datasets.csv (at revision 2b150727f77de6fa2e9f105d664e2ff4e69efa38)

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 "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/builder.py", line 2011, in _prepare_split_single
                  writer.write_table(table)
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/arrow_writer.py", line 585, in write_table
                  pa_table = table_cast(pa_table, self._schema)
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/table.py", line 2302, in table_cast
                  return cast_table_to_schema(table, schema)
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/table.py", line 2256, in cast_table_to_schema
                  raise CastError(
              datasets.table.CastError: Couldn't cast
              Paper identifier: string
              Protocols: string
              Organisms: string
              Published?: string
              Median QC score: double
              ATAC-seq: string
              RNA-seq: string
              ChIP-seq: string
              3D seq: string
              Other seq: string
              -- schema metadata --
              pandas: '{"index_columns": [{"kind": "range", "name": null, "start": 0, "' + 1456
              to
              {'Sample name': Value(dtype='string', id=None), 'Paper identifier': Value(dtype='string', id=None), 'Organism': Value(dtype='string', id=None), 'Protocol': Value(dtype='string', id=None), 'Cell type': Value(dtype='string', id=None), 'Treatment': Value(dtype='string', id=None), 'Replicate': Value(dtype='int64', id=None), 'Read depth': Value(dtype='string', id=None), 'QC score': Value(dtype='int64', id=None)}
              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 1577, in compute_config_parquet_and_info_response
                  parquet_operations = convert_to_parquet(builder)
                File "/src/services/worker/src/worker/job_runners/config/parquet_and_info.py", line 1191, in convert_to_parquet
                  builder.download_and_prepare(
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/builder.py", line 1027, in download_and_prepare
                  self._download_and_prepare(
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/builder.py", line 1122, in _download_and_prepare
                  self._prepare_split(split_generator, **prepare_split_kwargs)
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/builder.py", line 1882, in _prepare_split
                  for job_id, done, content in self._prepare_split_single(
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/builder.py", line 2013, in _prepare_split_single
                  raise DatasetGenerationCastError.from_cast_error(
              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 9 new columns ({'Other seq', '3D seq', 'Published?', 'Median QC score', 'Protocols', 'ChIP-seq', 'ATAC-seq', 'RNA-seq', 'Organisms'}) and 8 missing columns ({'Sample name', 'Read depth', 'Treatment', 'QC score', 'Replicate', 'Protocol', 'Cell type', 'Organism'}).
              
              This happened while the csv dataset builder was generating data using
              
              hf://datasets/funlab/DBNascent/datasets.csv (at revision 2b150727f77de6fa2e9f105d664e2ff4e69efa38)
              
              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.

Sample name string	Paper identifier string	Organism string	Protocol string	Cell type string	Treatment string	Replicate int64	Read depth string	QC score int64
ERR769522	Laitem2015cdk9	H. sapiens	GRO-seq	HeLa (cell line)	DRB (30min)	1	20M	4
ERR769523	Laitem2015cdk9	H. sapiens	GRO-seq	HeLa (cell line)	KM05283 (30min)	1	23M	4
ERR769524	Laitem2015cdk9	H. sapiens	GRO-seq	HeLa (cell line)	null	1	24M	2
ERR769525	Laitem2015cdk9	H. sapiens	GRO-seq	HeLa (cell line)	null	2	26M	2
SRM497904	Hah2013enhancer	H. sapiens	GRO-seq	MCF7 (cell line)	ethanol	1	40M	3
SRM497907	Hah2013enhancer	H. sapiens	GRO-seq	MCF7 (cell line)	ethanol	2	49M	2
SRM497911	Hah2013enhancer	H. sapiens	GRO-seq	MCF7 (cell line)	17-beta-estradiol (10min)	1	41M	2
SRM497912	Hah2013enhancer	H. sapiens	GRO-seq	MCF7 (cell line)	17-beta-estradiol (10min)	2	52M	3
SRM497914	Hah2013enhancer	H. sapiens	GRO-seq	MCF7 (cell line)	17-beta-estradiol (40min)	1	46M	2
SRM497917	Hah2013enhancer	H. sapiens	GRO-seq	MCF7 (cell line)	17-beta-estradiol (40min)	2	38M	2
SRR064994	Core2012defining	D. melanogaster	GRO-seq	S2 (cell line)	null	1	6M	4
SRR065240	Escoubet-lozach2011mechanisms	M. musculus	GRO-seq	peritoneal macrophage (primary)	DMSO (1hr)	1	8M	4
SRR065241	Escoubet-lozach2011mechanisms	M. musculus	GRO-seq	peritoneal macrophage (primary)	Kdo2-Lipid A (1hr)	1	8M	4
SRR073010	Larschan2011x	D. melanogaster	GRO-seq	S2 (cell line)	null	2	11M	4
SRR091798	Ji2011transcriptional	M. musculus	GRO-seq	C2C12 (cell line)	null	1	17M	2
SRR097862	Min2011regulating	M. musculus	GRO-seq	ESC (cell line)	null	3	8M	4
SRR097863	Min2011regulating	M. musculus	GRO-seq	MEF (primary)	null	1	8M	4
SRR097864	Min2011regulating	M. musculus	GRO-seq	MEF (primary)	null	2	7M	4
SRR10063517	Linnakuosmanen2020nrf2	H. sapiens	GRO-seq	HAEC (primary)	growth media (6hr)	1	19M	2
SRR10063518	Linnakuosmanen2020nrf2	H. sapiens	GRO-seq	HAEC (primary)	growth media (6hr)	2	9M	4
SRR10063519	Linnakuosmanen2020nrf2	H. sapiens	GRO-seq	HAEC (primary)	hypoxia (6hr)	1	18M	2
SRR10063520	Linnakuosmanen2020nrf2	H. sapiens	GRO-seq	HAEC (primary)	hypoxia (6hr)	2	8M	4
SRR10063521	Linnakuosmanen2020nrf2	H. sapiens	GRO-seq	HAEC (primary)	oxPAPC (6hr)	1	15M	3
SRR10063522	Linnakuosmanen2020nrf2	H. sapiens	GRO-seq	HAEC (primary)	oxPAPC (6hr)	2	11M	3
SRR10063523	Linnakuosmanen2020nrf2	H. sapiens	GRO-seq	HAEC (primary)	hypoxia (6hr) , oxPAPC (6hr)	1	16M	2
SRR10063524	Linnakuosmanen2020nrf2	H. sapiens	GRO-seq	HAEC (primary)	hypoxia (6hr) , oxPAPC (6hr)	2	16M	2
SRR10063525	Linnakuosmanen2020nrf2	H. sapiens	GRO-seq	HUVEC (primary)	growth media (6hr)	1	19M	2
SRR10063526	Linnakuosmanen2020nrf2	H. sapiens	GRO-seq	HUVEC (primary)	growth media (6hr)	2	15M	2
SRR10063527	Linnakuosmanen2020nrf2	H. sapiens	GRO-seq	HUVEC (primary)	hypoxia (6hr)	1	15M	3
SRR10063528	Linnakuosmanen2020nrf2	H. sapiens	GRO-seq	HUVEC (primary)	hypoxia (6hr)	2	17M	2
SRR10063529	Linnakuosmanen2020nrf2	H. sapiens	GRO-seq	HUVEC (primary)	hypoxia (6hr)	3	13M	3
SRR10063530	Linnakuosmanen2020nrf2	H. sapiens	GRO-seq	HUVEC (primary)	oxPAPC (6hr)	1	99M	4
SRR10063531	Linnakuosmanen2020nrf2	H. sapiens	GRO-seq	HUVEC (primary)	oxPAPC (6hr)	2	14M	3
SRR10063532	Linnakuosmanen2020nrf2	H. sapiens	GRO-seq	HUVEC (primary)	oxPAPC (6hr)	3	12M	3
SRR10063533	Linnakuosmanen2020nrf2	H. sapiens	GRO-seq	HUVEC (primary)	hypoxia (6hr) , oxPAPC (6hr)	1	51M	4
SRR10063534	Linnakuosmanen2020nrf2	H. sapiens	GRO-seq	HUVEC (primary)	hypoxia (6hr) , oxPAPC (6hr)	2	16M	2
SRR10063535	Linnakuosmanen2020nrf2	H. sapiens	GRO-seq	HUVEC (primary)	hypoxia (6hr) , oxPAPC (6hr)	3	14M	3
SRR10063536	Linnakuosmanen2020nrf2	H. sapiens	GRO-seq	HASM (primary)	growth media (6hr)	1	14M	3
SRR10063537	Linnakuosmanen2020nrf2	H. sapiens	GRO-seq	HASM (primary)	growth media (6hr)	2	23M	2
SRR10063540	Linnakuosmanen2020nrf2	H. sapiens	GRO-seq	HASM (primary)	oxPAPC (6hr)	1	17M	2
SRR10063541	Linnakuosmanen2020nrf2	H. sapiens	GRO-seq	HASM (primary)	oxPAPC (6hr)	2	7M	4
SRR10063544	Linnakuosmanen2020nrf2	H. sapiens	GRO-seq	CD14+ macrophage (primary)	growth media (6hr)	1	19M	2
SRR10063545	Linnakuosmanen2020nrf2	H. sapiens	GRO-seq	CD14+ macrophage (primary)	growth media (6hr)	2	26M	2
SRR10063548	Linnakuosmanen2020nrf2	H. sapiens	GRO-seq	CD14+ macrophage (primary)	oxPAPC (6hr)	1	18M	2
SRR10067473	Kelly2020unpublished	M. musculus	PRO-seq	ESC (cell line)	null	1	41M	2
SRR10067474	Kelly2020unpublished	M. musculus	PRO-seq	ESC (cell line)	null	2	23M	1
SRR10067475	Kelly2020unpublished	M. musculus	PRO-seq	ESC (cell line)	JQ1 (2hr)	1	29M	2
SRR10067476	Kelly2020unpublished	M. musculus	PRO-seq	ESC (cell line)	JQ1 (2hr)	2	15M	2
SRR10067477	Kelly2020unpublished	M. musculus	PRO-seq	ESC (cell line)	LBH589 (2hr)	1	51M	2
SRR10067478	Kelly2020unpublished	M. musculus	PRO-seq	ESC (cell line)	LBH589 (2hr)	2	10M	3
SRR10067479	Kelly2020unpublished	M. musculus	PRO-seq	ESC (cell line)	LBH589 (6hr)	1	30M	1
SRR10067480	Kelly2020unpublished	M. musculus	PRO-seq	ESC (cell line)	LBH589 (6hr)	2	42M	2
SRR1015583	Luo2014dynamic	H. sapiens	GRO-seq	AC16 (cell line)	null	1	22M	1
SRR1015584	Luo2014dynamic	H. sapiens	GRO-seq	AC16 (cell line)	null	2	23M	1
SRR1015585	Luo2014dynamic	H. sapiens	GRO-seq	AC16 (cell line)	TNF-alpha (10min)	1	21M	1
SRR1015586	Luo2014dynamic	H. sapiens	GRO-seq	AC16 (cell line)	TNF-alpha (10min)	2	18M	2
SRR1015587	Luo2014dynamic	H. sapiens	GRO-seq	AC16 (cell line)	TNF-alpha (30min)	1	16M	2
SRR1015588	Luo2014dynamic	H. sapiens	GRO-seq	AC16 (cell line)	TNF-alpha (30min)	2	21M	1
SRR1015589	Luo2014dynamic	H. sapiens	GRO-seq	AC16 (cell line)	TNF-alpha (2hr)	1	20M	2
SRR1015590	Luo2014dynamic	H. sapiens	GRO-seq	AC16 (cell line)	TNF-alpha (2hr)	2	24M	1
SRR1015591	Luo2014dynamic	H. sapiens	GRO-seq	AC16 (cell line)	DMSO (15min)	1	77M	1
SRR1015592	Luo2014dynamic	H. sapiens	GRO-seq	AC16 (cell line)	DMSO (15min)	2	55M	1
SRR1015593	Luo2014dynamic	H. sapiens	GRO-seq	AC16 (cell line)	null	1	130M	3
SRR1015594	Luo2014dynamic	H. sapiens	GRO-seq	AC16 (cell line)	null	2	154M	4
SRR10282967	Komarov2020epigenetic	D. melanogaster	GRO-seq	ovary (tissue)	null	1	25M	3
SRR10282968	Komarov2020epigenetic	D. melanogaster	GRO-seq	ovary (tissue)	null	1	23M	3
SRR10298307	Li2021comprehensive	H. sapiens	GRO-seq	MCF7 (cell line)	null	1	64M	2
SRR10298308	Li2021comprehensive	H. sapiens	GRO-seq	MCF7 (cell line)	null	2	49M	1
SRR10298309	Li2021comprehensive	H. sapiens	GRO-seq	MDA-MB-231 (cell line)	null	1	59M	1
SRR10298310	Li2021comprehensive	H. sapiens	GRO-seq	MDA-MB-231 (cell line)	null	2	115M	2
SRR10312745	Li2020human	H. sapiens	PRO-seq	foreskin fibroblast (primary)	DMSO (6hr) , HCMV strain Towne IE2 BAC (4day)	1	28M	2
SRR10312746	Li2020human	H. sapiens	PRO-seq	foreskin fibroblast (primary)	HCMV strain Towne IE2 BAC (4day) , dTag7 (6hr)	1	29M	3
SRR10312747	Li2020human	H. sapiens	PRO-seq	foreskin fibroblast (primary)	DMSO (6hr) , HCMV strain Towne IE2F BAC (4day)	1	29M	2
SRR10312748	Li2020human	H. sapiens	PRO-seq	foreskin fibroblast (primary)	HCMV strain Towne IE2F BAC (4day) , dTag7 (6hr)	1	25M	3
SRR10312749	Li2020human	H. sapiens	PRO-seq	foreskin fibroblast (primary)	DMSO (6hr) , HCMV strain Towne IE2 BAC (4day) , flavopiridol (1hr)	1	27M	3
SRR10312750	Li2020human	H. sapiens	PRO-seq	foreskin fibroblast (primary)	HCMV strain Towne IE2 BAC (4day) , dTag7 (6hr) , flavopiridol (1hr)	1	28M	3
SRR10312751	Li2020human	H. sapiens	PRO-seq	foreskin fibroblast (primary)	DMSO (6hr) , HCMV strain Towne IE2F BAC (4day) , flavopiridol (1hr)	1	28M	3
SRR10312752	Li2020human	H. sapiens	PRO-seq	foreskin fibroblast (primary)	HCMV strain Towne IE2F BAC (4day) , dTag7 (6hr) , flavopiridol (1hr)	1	31M	3
SRR10312753	Li2020human	H. sapiens	PRO-seq	foreskin fibroblast (primary)	DMSO (6hr) , HCMV strain TB40/E IE2F (3day)	1	38M	4
SRR10312754	Li2020human	H. sapiens	PRO-seq	foreskin fibroblast (primary)	HCMV strain TB40/E IE2F (3day) , dTag7 (6hr)	1	43M	3
SRR10312755	Li2020human	H. sapiens	PRO-seq	foreskin fibroblast (primary)	DMSO (6hr) , HCMV strain TB40/E IE2F (3day) , flavopiridol (1hr)	1	40M	3
SRR10312756	Li2020human	H. sapiens	PRO-seq	foreskin fibroblast (primary)	HCMV strain TB40/E IE2F (3day) , dTag7 (6hr) , flavopiridol (1hr)	1	36M	4
SRR10312757	Li2020human	H. sapiens	PRO-seq	foreskin fibroblast (primary)	DMSO (6hr) , HCMV strain TB40/E IE2F (3day)	2	38M	4
SRR10312758	Li2020human	H. sapiens	PRO-seq	foreskin fibroblast (primary)	HCMV strain TB40/E IE2F (3day) , dTag7 (6hr)	2	26M	5
SRR10312759	Li2020human	H. sapiens	PRO-seq	foreskin fibroblast (primary)	DMSO (6hr) , HCMV strain TB40/E IE2F (3day) , phosphonoformic acid (6hr)	1	42M	3
SRR10312760	Li2020human	H. sapiens	PRO-seq	foreskin fibroblast (primary)	HCMV strain TB40/E IE2F (3day) , dTag7 (6hr) , phosphonoformic acid (6hr)	1	39M	4
SRR10312761	Li2020human	H. sapiens	PRO-seq	foreskin fibroblast (primary)	HCMV strain TB40/E IE2 (1day)	1	36M	3
SRR10312762	Li2020human	H. sapiens	PRO-seq	foreskin fibroblast (primary)	HCMV strain TB40/E IE2 (3day)	1	33M	3
SRR10312763	Li2020human	H. sapiens	PRO-seq	foreskin fibroblast (primary)	HCMV strain TB40/E IE2 (3day) , phosphonoformic acid (3day)	1	24M	4
SRR10354624	Jaeger2020selective	H. sapiens	PRO-seq	KBM7 (cell line)	DMSO (2hr)	1	77M	1
SRR10354625	Jaeger2020selective	H. sapiens	PRO-seq	KBM7 (cell line)	DMSO (2hr)	2	67M	1
SRR10354626	Jaeger2020selective	H. sapiens	PRO-seq	KBM7 (cell line)	dTAG7 (2hr)	1	74M	2
SRR10354627	Jaeger2020selective	H. sapiens	PRO-seq	KBM7 (cell line)	dTAG7 (2hr)	2	83M	1
SRR10354653	Jaeger2020selective	H. sapiens	other	KBM7 (cell line)	4-thiouridine (5min) , DMSO (2hr)	1	57M	1
SRR10354654	Jaeger2020selective	H. sapiens	other	KBM7 (cell line)	4-thiouridine (5min) , DMSO (2hr)	2	60M	1
SRR10354655	Jaeger2020selective	H. sapiens	other	KBM7 (cell line)	4-thiouridine (5min) , dTAG7 (2hr)	1	63M	1
SRR10354656	Jaeger2020selective	H. sapiens	other	KBM7 (cell line)	4-thiouridine (5min) , dTAG7 (2hr)	2	69M	1
SRR10354657	Jaeger2020selective	H. sapiens	other	KBM7 (cell line)	4-thiouridine (5min) , NVP2 (30min)	1	59M	2
SRR10354658	Jaeger2020selective	H. sapiens	other	KBM7 (cell line)	4-thiouridine (5min) , NVP2 (30min)	2	55M	1
SRR10354659	Jaeger2020selective	H. sapiens	other	KBM7 (cell line)	4-thiouridine (5min) , NVP2 (30min) , dTAG7 (2hr)	1	58M	1

End of preview.

Data pulled from https://nascent.colorado.edu/home/

Querying with DuckDB

duckdb -csv -c "SELECT * FROM read_csv_auto('~/src/fg/DBNascent/all_samples.csv') WHERE Protocol == 'GRO-seq' AND \"Cell type\" ILIKE '%HeLa%'"
# Write the output to a file
# > hela_groseq.csv

Sample name	Paper identifier	Organism	Protocol	Cell type	Treatment	Replicate	Read depth	QC score
ERR769522	Laitem2015cdk9	H. sapiens	GRO-seq	HeLa (cell line)	DRB (30min)	1	20M	4
ERR769523	Laitem2015cdk9	H. sapiens	GRO-seq	HeLa (cell line)	KM05283 (30min)	1	23M	4
ERR769524	Laitem2015cdk9	H. sapiens	GRO-seq	HeLa (cell line)	NaN	1	24M	2
ERR769525	Laitem2015cdk9	H. sapiens	GRO-seq	HeLa (cell line)	NaN	2	26M	2
SRR1342250	Gardini2014integrator	H. sapiens	GRO-seq	HeLa (cell line)	EGF (30min) , serum starvation (1day)	1	58M	3
SRR1342251	Gardini2014integrator	H. sapiens	GRO-seq	HeLa (cell line)	EGF (30min) , doxycycline (4day) , serum starvation (1day)	1	45M	1
SRR1342252	Gardini2014integrator	H. sapiens	GRO-seq	HeLa (cell line)	EGF (30min) , serum starvation (1day)	2	114M	4
SRR1342253	Gardini2014integrator	H. sapiens	GRO-seq	HeLa (cell line)	EGF (30min) , doxycycline (4day) , serum starvation (1day)	2	71M	3
SRR1596500	Andersson2014nuclear	H. sapiens	GRO-seq	HeLa (cell line)	NaN	1	21M	1
SRR1596501	Andersson2014nuclear	H. sapiens	GRO-seq	HeLa (cell line)	NaN	2	33M	1
SRR2059423	Zhang2016regulation	H. sapiens	GRO-seq	HeLa (cell line)	NaN	1	56M	3
SRR2059424	Zhang2016regulation	H. sapiens	GRO-seq	HeLa (cell line)	NaN	1	85M	3
SRR5109939	Bouvyliivrand2017analysis	H. sapiens	GRO-seq	HeLa (cell line)	NaN	1	22M	1
SRR7010982	Fei2018ndf	H. sapiens	GRO-seq	HeLa (cell line)	NaN	1	64M	2
SRR7010983	Fei2018ndf	H. sapiens	GRO-seq	HeLa (cell line)	NaN	1	76M	2
SRR7010984	Fei2018ndf	H. sapiens	GRO-seq	HeLa (cell line)	NaN	2	66M	2
SRZ10004434	Bahat2019targeting	H. sapiens	GRO-seq	HeLa (cell line)	DMSO (90min)	1	141M	2
SRZ10004438	Bahat2019targeting	H. sapiens	GRO-seq	HeLa (cell line)	DMSO (90min)	2	124M	2
SRZ10004442	Bahat2019targeting	H. sapiens	GRO-seq	HeLa (cell line)	Spt5-Pol II small-molecule inhibitor 21 (90min)	1	138M	2
SRZ1693611	Duttke2015human	H. sapiens	GRO-seq	HeLa (cell line)	NaN	1	68M	4

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