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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 11 new columns ({'1.1', '1', '1898', '0.1', '41', '1898.2', '1898.1', 'Tritim_EIv0.3_1183490', '97.84', 'TraesCS1D02G068300', '4.21e+03'}) and 11 missing columns ({'TraesCS1D02G189300', '193', '811', '22', '75.34', 'TRIDC5AG074060', '5', '6', '810', '1.45e+03', '831'}).
This happened while the csv dataset builder was generating data using
hf://datasets/Yoshigold/plant-msyn-data/mcscan_results/last_filtered_by_i1/test_8_1_25_once_more_once_more.triticum_timopheevii.filtered_by_i1.tsv (at revision 98e39d4bf8e0c4c109d0599c3c22c3d0790b2bd0)
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/python3.12/site-packages/datasets/builder.py", line 1831, in _prepare_split_single
writer.write_table(table)
File "/usr/local/lib/python3.12/site-packages/datasets/arrow_writer.py", line 714, in write_table
pa_table = table_cast(pa_table, self._schema)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/datasets/table.py", line 2272, in table_cast
return cast_table_to_schema(table, schema)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/datasets/table.py", line 2218, in cast_table_to_schema
raise CastError(
datasets.table.CastError: Couldn't cast
TraesCS1D02G068300: string
Tritim_EIv0.3_1183490: string
97.84: double
1898: int64
41: int64
0: int64
1: int64
1898.1: int64
1.1: int64
1898.2: int64
0.1: double
4.21e+03: double
-- schema metadata --
pandas: '{"index_columns": [{"kind": "range", "name": null, "start": 0, "' + 1599
to
{'TraesCS1D02G189300': Value('string'), 'TRIDC5AG074060': Value('string'), '75.34': Value('float64'), '811': Value('int64'), '193': Value('int64'), '5': Value('int64'), '6': Value('int64'), '810': Value('int64'), '22': Value('int64'), '831': Value('int64'), '0': Value('float64'), '1.45e+03': 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 1334, in compute_config_parquet_and_info_response
parquet_operations, partial, estimated_dataset_info = stream_convert_to_parquet(
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/src/services/worker/src/worker/job_runners/config/parquet_and_info.py", line 911, in stream_convert_to_parquet
builder._prepare_split(
File "/usr/local/lib/python3.12/site-packages/datasets/builder.py", line 1702, in _prepare_split
for job_id, done, content in self._prepare_split_single(
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/datasets/builder.py", line 1833, 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 11 new columns ({'1.1', '1', '1898', '0.1', '41', '1898.2', '1898.1', 'Tritim_EIv0.3_1183490', '97.84', 'TraesCS1D02G068300', '4.21e+03'}) and 11 missing columns ({'TraesCS1D02G189300', '193', '811', '22', '75.34', 'TRIDC5AG074060', '5', '6', '810', '1.45e+03', '831'}).
This happened while the csv dataset builder was generating data using
hf://datasets/Yoshigold/plant-msyn-data/mcscan_results/last_filtered_by_i1/test_8_1_25_once_more_once_more.triticum_timopheevii.filtered_by_i1.tsv (at revision 98e39d4bf8e0c4c109d0599c3c22c3d0790b2bd0)
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.
TraesCS1D02G189300 string | TRIDC5AG074060 string | 75.34 float64 | 811 int64 | 193 int64 | 5 int64 | 6 int64 | 810 int64 | 22 int64 | 831 int64 | 0 float64 | 1.45e+03 float64 |
|---|---|---|---|---|---|---|---|---|---|---|---|
TraesCS1D02G219600 | TRIDC5AG076810 | 75.43 | 863 | 202 | 6 | 82 | 938 | 1 | 859 | 0 | 1,410 |
TraesCS1D02G189400 | TRIDC5AG074040 | 74.63 | 749 | 178 | 8 | 10 | 752 | 50 | 792 | 0 | 1,270 |
TraesCS1D02G147700 | TRIDC5AG072370 | 58.78 | 1,036 | 361 | 15 | 7 | 991 | 10 | 1,030 | 0 | 1,260 |
TraesCS1D02G214100 | TRIDC5AG076150 | 69.99 | 733 | 198 | 7 | 1 | 727 | 11 | 727 | 0 | 1,190 |
TraesCS1D02G191600 | TRIDC5AG070190 | 77.19 | 640 | 138 | 6 | 12 | 645 | 2 | 639 | 0 | 1,080 |
TraesCS1D02G148200 | TRIDC5AG072160 | 67.49 | 729 | 210 | 5 | 1 | 726 | 1 | 705 | 0 | 1,070 |
TraesCS1D02G189200 | TRIDC5AG074170 | 74.23 | 586 | 133 | 5 | 18 | 587 | 6 | 589 | 0 | 982 |
TraesCS1D02G147200 | TRIDC5AG072520 | 73.66 | 577 | 145 | 2 | 4 | 578 | 19 | 590 | 0 | 976 |
TraesCS1D02G214200 | TRIDC5AG076160 | 71.67 | 586 | 155 | 6 | 16 | 593 | 35 | 617 | 0 | 965 |
TraesCS1D02G221100 | TRIDC5AG076790 | 77.67 | 515 | 111 | 3 | 4 | 516 | 5 | 517 | 0 | 926 |
TraesCS1D02G187900 | TRIDC5AG074340 | 72.66 | 567 | 143 | 7 | 63 | 622 | 15 | 576 | 0 | 863 |
TraesCS1D02G221600 | TRIDC5AG076720 | 57.73 | 705 | 265 | 12 | 64 | 755 | 57 | 741 | 0 | 836 |
TraesCS1D02G212800 | TRIDC5AG075850 | 62.78 | 626 | 198 | 17 | 16 | 621 | 27 | 637 | 0 | 771 |
TraesCS1D02G144900 | TRIDC5AG073190 | 54.43 | 654 | 248 | 11 | 66 | 676 | 4 | 650 | 0 | 668 |
TraesCS1D02G187600 | TRIDC5AG074560 | 78.78 | 377 | 75 | 1 | 1 | 377 | 65 | 436 | 0 | 665 |
TraesCS1D02G187100 | TRIDC5AG074640 | 79.46 | 331 | 66 | 1 | 27 | 357 | 72 | 400 | 0 | 645 |
TraesCS1D02G213900 | TRIDC5AG076090 | 63.13 | 453 | 149 | 6 | 51 | 486 | 6 | 457 | 0 | 624 |
TraesCS1D02G191800 | TRIDC5AG070280 | 68.41 | 364 | 110 | 3 | 188 | 549 | 45 | 405 | 0 | 560 |
TraesCS1D02G219700 | TRIDC5AG076830 | 78.6 | 271 | 58 | 0 | 26 | 296 | 23 | 293 | 0 | 531 |
TraesCS1D02G187500 | TRIDC5AG074570 | 69.11 | 314 | 95 | 1 | 10 | 321 | 17 | 330 | 0 | 524 |
TraesCS1D02G186900 | TRIDC5AG074760 | 54.87 | 452 | 168 | 8 | 1 | 418 | 5 | 454 | 0 | 491 |
TraesCS1D02G203700 | TRIDC5AG073590 | 64.76 | 332 | 114 | 3 | 1 | 331 | 1 | 330 | 0 | 483 |
TraesCS1D02G215500 | TRIDC5AG076250 | 83.77 | 228 | 35 | 1 | 54 | 279 | 57 | 284 | 0 | 476 |
TraesCS1D02G222200 | TRIDC5AG076570 | 63.2 | 375 | 115 | 11 | 24 | 381 | 30 | 398 | 0 | 466 |
TraesCS1D02G187700 | TRIDC5AG074530 | 68.39 | 310 | 78 | 7 | 1 | 294 | 1 | 306 | 0 | 462 |
TraesCS1D02G222000 | TRIDC5AG076660 | 70.77 | 260 | 56 | 4 | 2 | 246 | 5 | 259 | 0 | 432 |
TraesCS1D02G203000 | TRIDC5AG073390 | 80.28 | 213 | 42 | 0 | 1 | 213 | 9 | 221 | 0 | 424 |
TraesCS1D02G223200 | TRIDC5AG076310 | 55.99 | 384 | 120 | 12 | 1 | 357 | 1 | 362 | 0 | 385 |
TraesCS1D02G146000 | TRIDC5AG072730 | 53.9 | 410 | 144 | 15 | 47 | 437 | 14 | 397 | 0 | 376 |
TraesCS1D02G203200 | TRIDC5AG073460 | 92.55 | 161 | 12 | 0 | 1 | 161 | 16 | 176 | 0 | 375 |
TraesCS1D02G145100 | TRIDC5AG073210 | 94.51 | 164 | 9 | 0 | 1 | 164 | 4 | 167 | 0 | 367 |
TraesCS1D02G145900 | TRIDC5AG072800 | 82.26 | 186 | 30 | 1 | 349 | 531 | 25 | 210 | 0 | 358 |
TraesCS1D02G191000 | TRIDC5AG069990 | 62.71 | 295 | 80 | 7 | 92 | 381 | 1 | 270 | 0 | 345 |
TraesCS1D02G145700 | TRIDC5AG073050 | 92.86 | 154 | 11 | 0 | 1 | 154 | 28 | 181 | 0 | 333 |
TraesCS1D02G223000 | TRIDC5AG076330 | 53.65 | 315 | 122 | 7 | 36 | 347 | 28 | 321 | 0 | 329 |
TraesCS1D02G146100 | TRIDC5AG072570 | 97.86 | 140 | 3 | 0 | 1 | 140 | 32 | 171 | 0 | 320 |
TraesCS1D02G218900 | TRIDC5AG076970 | 66.17 | 201 | 58 | 4 | 5 | 196 | 9 | 208 | 0 | 252 |
TraesCS1D02G203900 | TRIDC5AG073630 | 50 | 328 | 97 | 13 | 4 | 291 | 17 | 317 | 0 | 245 |
TraesCS1D02G214000 | TRIDC5AG076110 | 62.89 | 194 | 61 | 4 | 100 | 289 | 11 | 197 | 0 | 228 |
TraesCS1D02G188700 | TRIDC5AG074270 | 58.13 | 203 | 56 | 6 | 1 | 200 | 1 | 177 | 0 | 212 |
TraesCS1D02G204100 | TRIDC5AG073680 | 52.02 | 198 | 85 | 5 | 5 | 197 | 3 | 195 | 0 | 204 |
TraesCS1D02G190700 | TRIDC5AG070070 | 52.51 | 219 | 49 | 7 | 2 | 165 | 3 | 221 | 0 | 186 |
TraesCS1D02G213300 | TRIDC5AG075920 | 69.07 | 97 | 29 | 1 | 23 | 118 | 3 | 99 | 0 | 160 |
TraesCS1D02G214500 | TRIDC5AG075900 | 50.63 | 158 | 40 | 3 | 102 | 222 | 35 | 191 | 0 | 159 |
TraesCS1D02G188900 | TRIDC5AG074150 | 72.38 | 105 | 22 | 4 | 6 | 109 | 5 | 103 | 0 | 152 |
TraesCS1D02G191500 | TRIDC5AG070120 | 49.7 | 167 | 70 | 3 | 65 | 221 | 44 | 206 | 0 | 150 |
TraesCS1D02G148400 | TRIDC5AG072140 | 58.97 | 117 | 44 | 2 | 75 | 191 | 4 | 116 | 0 | 147 |
TraesCS1D02G213203 | TRIDC5AG075860 | 48.99 | 149 | 58 | 5 | 5 | 143 | 8 | 148 | 0 | 137 |
TraesCS1D02G188800 | TRIDC5AG074260 | 32.03 | 462 | 227 | 18 | 10 | 390 | 6 | 461 | 0 | 135 |
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End of preview.
Plant Microsynteny Dataset (plant-msyn-data)
Pre-computed MCscan protein-based synteny analysis results for 30+ plant genomes.
Dataset Structure
plant-msyn-data/
├── mcscan_results/
│ ├── bed_files/ # Gene position files (*.bed) + database_genomes.txt whitelist
│ ├── i1_blocks/ # Synteny block files (*.i1.blocks)
│ ├── lifted_anchors/ # Syntenic anchor pair files (*.lifted.anchors)
│ ├── last_filtered_by_i1/ # I1-filtered LAST alignments
│ ├── pep_files/ # Protein FASTA files (*.pep)
│ ├── custom_meta/ # Custom genome metadata (user uploads)
│ └── custom_synteny_meta/ # Custom synteny project metadata
├── sql/
│ ├── search_catalogs/ # Per-genome SQLite catalogs for fast gene lookups
│ └── plantmsyn_metadata.db # Central metadata database
└── annotations/
└── [species_name]/
└── gene_annotation.tsv # Gene functional descriptions
Supported Genomes
The dataset includes synteny data for 30+ plant genomes including:
- Barley (Hordeum vulgare)
- Wheat (Triticum aestivum)
- Rice (Oryza sativa)
- Maize (Zea mays)
- Arabidopsis (Arabidopsis thaliana)
- And 25+ more species
Usage
This dataset is designed to be used with the Plant-mSyn web application.
To use programmatically:
from huggingface_hub import snapshot_download
# Download the full dataset
local_path = snapshot_download(
repo_id="yoshigold/plant-msyn-data",
repo_type="dataset"
)
File Formats
BED Files (*.bed)
Tab-separated files with gene positions:
- Column 1: Chromosome
- Column 2: Start position
- Column 3: End position
- Column 4: Gene ID
- Column 5: Score
- Column 6: Strand
Blocks Files (*.i1.blocks)
Tab-separated synteny block definitions linking genes between species.
Annotation Files (gene_annotation.tsv)
Tab-separated files with:
- Column 1: gene (Gene ID)
- Column 2: description (Functional annotation)
Citation
If you use this dataset, please cite:
- MCscan/JCVI: Tang et al. (2008) Synteny and Collinearity in Plant Genomes
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