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The dataset generation failed
Error code: DatasetGenerationError
Exception: UnicodeDecodeError
Message: 'utf-8' codec can't decode byte 0x89 in position 0: invalid start byte
Traceback: Traceback (most recent call last):
File "/usr/local/lib/python3.14/site-packages/datasets/builder.py", line 1827, in _prepare_split_single
for key, table in generator:
^^^^^^^^^
File "/src/services/worker/src/worker/job_runners/config/parquet_and_info.py", line 613, in wrapped
for item in generator(*args, **kwargs):
~~~~~~~~~^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.14/site-packages/datasets/packaged_modules/text/text.py", line 98, in _generate_tables
batch = f.read(self.config.chunksize)
File "/usr/local/lib/python3.14/site-packages/datasets/utils/file_utils.py", line 844, in read_with_retries
out = read(*args, **kwargs)
File "<frozen codecs>", line 325, in decode
UnicodeDecodeError: 'utf-8' codec can't decode byte 0x89 in position 0: invalid start byte
The above exception was the direct cause of the following exception:
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 1880, in _prepare_split_single
raise DatasetGenerationError("An error occurred while generating the dataset") from e
datasets.exceptions.DatasetGenerationError: An error occurred while generating the datasetNeed help to make the dataset viewer work? Make sure to review how to configure the dataset viewer, and open a discussion for direct support.
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RBP_ID Family_ID RSource_ID Motif_ID MSource_ID DBID RBP_Name RBP_Species RBP_Status Family_Name RBDs RBD_Count Cutoff DBID Motif_Type MSource_Identifier MSource_Type MSource_Author MSource_Year PMID MSource_Version RBPSource_Name RBPSource_URL RBPSource_Year RBPSource_Month RBPSource_Day |
T000001_2.00 F01_2.00 TS49_2.00 . . EuGene.1500010227 EuGene.1500010227 Micromonas_sp_RCC299 N C2H2 ZF,CCCH ZF,KH zf-C2H2,zf-CCCH,KH_1 3 0.70 . . . . . . . . JGI:Phytozome https://phytozome.jgi.doe.gov/pz/portal.html 2018 Apr 12 |
T000002_2.00 F02_2.00 TS73_2.00 . . OESDEN_02641 OESDEN_02641 Oesophagostomum_dentatum N C2H2 ZF,CCCH ZF,RRM zf-C2H2,zf-CCCH,RRMs_3D 3 0.70 . . . . . . . . WormBase:ParaSite http://parasite.wormbase.org/ 2015 Oct 22 |
T000003_2.00 F03_2.00 TS04_2.00 . . AMAG_15521 AMAG_15521 Allomyces_macrogynus N C2H2 ZF,CCCH ZF zf-C2H2,zf-CCCH 2 0.70 . . . . . . . . Broad http://www.broadinstitute.org/ 2016 May 1 |
T000004_2.00 F03_2.00 TS04_2.00 . . AMAG_20117 AMAG_20117 Allomyces_macrogynus N C2H2 ZF,CCCH ZF zf-C2H2,zf-CCCH 2 0.70 . . . . . . . . Broad http://www.broadinstitute.org/ 2016 May 1 |
T000005_2.00 F03_2.00 TS04_2.00 . . AMSG_02404 AMSG_02404 Thecamonas_trahens N C2H2 ZF,CCCH ZF zf-C2H2,zf-CCCH 2 0.70 . . . . . . . . Broad http://www.broadinstitute.org/ 2016 May 1 |
T000006_2.00 F03_2.00 TS04_2.00 . . SPPG_08277 SPPG_08277 Spizellomyces_punctatus N C2H2 ZF,CCCH ZF zf-C2H2,zf-CCCH 2 0.70 . . . . . . . . Broad http://www.broadinstitute.org/ 2016 May 1 |
T000007_2.00 F03_2.00 TS04_2.00 . . SPRG_08635 SPRG_08635 Saprolegnia_parasitica N C2H2 ZF,CCCH ZF zf-C2H2,zf-CCCH 2 0.70 . . . . . . . . Broad http://www.broadinstitute.org/ 2016 May 1 |
T000008_2.00 F03_2.00 TS12_2.00 . . ALNC14_095790 ALNC14_095790 Albugo_laibachii N C2H2 ZF,CCCH ZF zf-C2H2,zf-CCCH 2 0.70 . . . . . . . . Ensembl http://www.ensembl.org/ 2018 Dec 8 |
T000009_2.00 F03_2.00 TS12_2.00 . . F443_12247 F443_12247 Phytophthora_parasitica N C2H2 ZF,CCCH ZF zf-C2H2,zf-CCCH 2 0.70 . . . . . . . . Ensembl http://www.ensembl.org/ 2018 Dec 8 |
T000010_2.00 F03_2.00 TS12_2.00 . . FGRRES_13848_M FGRRES_13848_M Fusarium_graminearum N C2H2 ZF,CCCH ZF zf-C2H2,zf-CCCH 2 0.70 . . . . . . . . Ensembl http://www.ensembl.org/ 2018 Dec 8 |
T000011_2.00 F03_2.00 TS12_2.00 . . maker-par_contig_923-fgenesh-gene-0.4 maker-par_contig_923-fgenesh-gene-0.4 Pythium_arrhenomanes N C2H2 ZF,CCCH ZF zf-C2H2,zf-CCCH 2 0.70 . . . . . . . . Ensembl http://www.ensembl.org/ 2018 Dec 8 |
T000012_2.00 F03_2.00 TS12_2.00 . . maker-pir_contig_136-fgenesh-gene-0.1 maker-pir_contig_136-fgenesh-gene-0.1 Pythium_irregulare N C2H2 ZF,CCCH ZF zf-C2H2,zf-CCCH 2 0.70 . . . . . . . . Ensembl http://www.ensembl.org/ 2018 Dec 8 |
T000013_2.00 F03_2.00 TS12_2.00 . . maker-pir_contig_1426-snap-gene-0.4 maker-pir_contig_1426-snap-gene-0.4 Pythium_irregulare N C2H2 ZF,CCCH ZF zf-C2H2,zf-CCCH 2 0.70 . . . . . . . . Ensembl http://www.ensembl.org/ 2018 Dec 8 |
T000014_2.00 F03_2.00 TS12_2.00 . . maker-piw_contig_1667-fgenesh-gene-0.1 maker-piw_contig_1667-fgenesh-gene-0.1 Pythium_iwayamai N C2H2 ZF,CCCH ZF zf-C2H2,zf-CCCH 2 0.70 . . . . . . . . Ensembl http://www.ensembl.org/ 2018 Dec 8 |
T000015_2.00 F03_2.00 TS12_2.00 . . maker-pve_contig_366-fgenesh-gene-0.0 maker-pve_contig_366-fgenesh-gene-0.0 Pythium_vexans N C2H2 ZF,CCCH ZF zf-C2H2,zf-CCCH 2 0.70 . . . . . . . . Ensembl http://www.ensembl.org/ 2018 Dec 8 |
T000016_2.00 F03_2.00 TS12_2.00 . . Physo158324 Physo158324 Phytophthora_sojae N C2H2 ZF,CCCH ZF zf-C2H2,zf-CCCH 2 0.70 . . . . . . . . Ensembl http://www.ensembl.org/ 2018 Dec 8 |
T000017_2.00 F03_2.00 TS12_2.00 . . PITG_06616 PITG_06616 Phytophthora_infestans N C2H2 ZF,CCCH ZF zf-C2H2,zf-CCCH 2 0.70 . . . . . . . . Ensembl http://www.ensembl.org/ 2018 Dec 8 |
T000018_2.00 F03_2.00 TS12_2.00 . . PYU1_G003637 PYU1_G003637 Pythium_ultimum N C2H2 ZF,CCCH ZF zf-C2H2,zf-CCCH 2 0.70 . . . . . . . . Ensembl http://www.ensembl.org/ 2018 Dec 8 |
T000019_2.00 F03_2.00 TS12_2.00 . . PYU1_G012529 PYU1_G012529 Pythium_ultimum N C2H2 ZF,CCCH ZF zf-C2H2,zf-CCCH 2 0.70 . . . . . . . . Ensembl http://www.ensembl.org/ 2018 Dec 8 |
T000020_2.00 F03_2.00 TS71_2.00 . . estExt_fgenesh1_pm.C_190131 estExt_fgenesh1_pm.C_190131 Phytophthora_capsici N C2H2 ZF,CCCH ZF zf-C2H2,zf-CCCH 2 0.70 . . . . . . . . Superfamily http://supfam.cs.bris.ac.uk/SUPERFAMILY/ 2010 Oct 26 |
T000021_2.00 F03_2.00 TS73_2.00 . . ECANG7_04631 ECANG7_04631 Echinococcus_canadensis N C2H2 ZF,CCCH ZF zf-C2H2,zf-CCCH 2 0.70 . . . . . . . . WormBase:ParaSite http://parasite.wormbase.org/ 2015 Oct 22 |
T000022_2.00 F04_2.00 TS12_2.00 . . fgenesh_masked-piw_contig_3591-abinit-gene-0.8 fgenesh_masked-piw_contig_3591-abinit-gene-0.8 Pythium_iwayamai N C2H2 ZF,CCHC ZF zf-C2H2,zf-CCHC 2 0.70 . . . . . . . . Ensembl http://www.ensembl.org/ 2018 Dec 8 |
T000023_2.00 F04_2.00 TS12_2.00 . . maker-piw_contig_1224-snap-gene-0.6 maker-piw_contig_1224-snap-gene-0.6 Pythium_iwayamai N C2H2 ZF,CCHC ZF zf-C2H2,zf-CCHC 2 0.70 . . . . . . . . Ensembl http://www.ensembl.org/ 2018 Dec 8 |
T000024_2.00 F04_2.00 TS12_2.00 . . SPU_017846 SPU_017846 Strongylocentrotus_purpuratus N C2H2 ZF,CCHC ZF zf-C2H2,zf-CCHC 2 0.70 . . . . . . . . Ensembl http://www.ensembl.org/ 2018 Dec 8 |
T000025_2.00 F04_2.00 TS12_2.00 . . SPU_017847 SPU_017847 Strongylocentrotus_purpuratus N C2H2 ZF,CCHC ZF zf-C2H2,zf-CCHC 2 0.70 . . . . . . . . Ensembl http://www.ensembl.org/ 2018 Dec 8 |
T000026_2.00 F04_2.00 TS12_2.00 . . SPU_017848 SPU_017848 Strongylocentrotus_purpuratus N C2H2 ZF,CCHC ZF zf-C2H2,zf-CCHC 2 0.70 . . . . . . . . Ensembl http://www.ensembl.org/ 2018 Dec 8 |
T000027_2.00 F04_2.00 TS12_2.00 . . SPU_017849 SPU_017849 Strongylocentrotus_purpuratus N C2H2 ZF,CCHC ZF zf-C2H2,zf-CCHC 2 0.70 . . . . . . . . Ensembl http://www.ensembl.org/ 2018 Dec 8 |
T000028_2.00 F04_2.00 TS12_2.00 . . SPU_017850 SPU_017850 Strongylocentrotus_purpuratus N C2H2 ZF,CCHC ZF zf-C2H2,zf-CCHC 2 0.70 . . . . . . . . Ensembl http://www.ensembl.org/ 2018 Dec 8 |
T000029_2.00 F04_2.00 TS12_2.00 . . SPU_020846 SPU_020846 Strongylocentrotus_purpuratus N C2H2 ZF,CCHC ZF zf-C2H2,zf-CCHC 2 0.70 . . . . . . . . Ensembl http://www.ensembl.org/ 2018 Dec 8 |
T000030_2.00 F04_2.00 TS12_2.00 . . TRIUR3_32111 TRIUR3_32111 Triticum_urartu N C2H2 ZF,CCHC ZF zf-C2H2,zf-CCHC 2 0.70 . . . . . . . . Ensembl http://www.ensembl.org/ 2018 Dec 8 |
T000031_2.00 F04_2.00 TS19_2.00 . . Alligator_sinensis_CCG003433.1 Alligator_sinensis_CCG003433.1 Alligator_sinensis N C2H2 ZF,CCHC ZF zf-C2H2,zf-CCHC 2 0.70 . . . . . . . . GigaDB http://gigadb.org/dataset/100166 2015 Oct 22 |
T000032_2.00 F04_2.00 TS69_2.00 . . XP_002942387 XP_002942387 Xenopus_tropicalis N C2H2 ZF,CCHC ZF zf-C2H2,zf-CCHC 2 0.70 . . . . . . . . Misc http://hugheslab.med.utoronto.ca/ 2018 Jan 19 |
T000033_2.00 F04_2.00 TS72_2.00 . . PPAI002507 PPAI002507 Phlebotomus_papatasi N C2H2 ZF,CCHC ZF zf-C2H2,zf-CCHC 2 0.70 . . . . . . . . Vectorbase https://www.vectorbase.org/ 2015 Oct 22 |
T000034_2.00 F04_2.00 TS73_2.00 . . scaffold181-EXSNAP2012.15 scaffold181-EXSNAP2012.15 Pristionchus_exspectatus N C2H2 ZF,CCHC ZF zf-C2H2,zf-CCHC 2 0.70 . . . . . . . . WormBase:ParaSite http://parasite.wormbase.org/ 2015 Oct 22 |
T000035_2.00 F05_2.00 TS12_2.00 . . GSMUA_AchrUn_randomG03750_001 GSMUA_AchrUn_randomG03750_001 Musa_acuminata N C2H2 ZF,KH zf-C2H2,KH_1 2 0.70 . . . . . . . . Ensembl http://www.ensembl.org/ 2018 Dec 8 |
T000036_2.00 F05_2.00 TS71_2.00 . . XP_002157333.1 XP_002157333.1 Hydra_magnipapillata N C2H2 ZF,KH zf-C2H2,KH_1 2 0.70 . . . . . . . . Superfamily http://supfam.cs.bris.ac.uk/SUPERFAMILY/ 2010 Oct 26 |
T000037_2.00 F06_2.00 TS46_2.00 . . fgenesh2_pg.scaffold_109000029 fgenesh2_pg.scaffold_109000029 Branchiostoma_floridae N C2H2 ZF,NHL zf-C2H2,NHL 2 0.70 . . . . . . . . JGI http://genome.jgi-psf.org/ 2012 Mar 17 |
T000038_2.00 F06_2.00 TS46_2.00 . . fgenesh2_pg.scaffold_133000053 fgenesh2_pg.scaffold_133000053 Branchiostoma_floridae N C2H2 ZF,NHL zf-C2H2,NHL 2 0.70 . . . . . . . . JGI http://genome.jgi-psf.org/ 2012 Mar 17 |
T000039_2.00 F06_2.00 TS46_2.00 . . fgenesh2_pg.scaffold_144000004 fgenesh2_pg.scaffold_144000004 Branchiostoma_floridae N C2H2 ZF,NHL zf-C2H2,NHL 2 0.70 . . . . . . . . JGI http://genome.jgi-psf.org/ 2012 Mar 17 |
T000040_2.00 F06_2.00 TS73_2.00 . . L892_g21682 L892_g21682 Steinernema_scapterisci N C2H2 ZF,NHL zf-C2H2,NHL 2 0.70 . . . . . . . . WormBase:ParaSite http://parasite.wormbase.org/ 2015 Oct 22 |
T000041_2.00 F07_2.00 TS73_2.00 . . D917_04749 D917_04749 Trichinella_nativa N C2H2 ZF,RanBP ZF,RRM zf-C2H2,zf-RanBP,RRMs_3D 3 0.70 . . . . . . . . WormBase:ParaSite http://parasite.wormbase.org/ 2015 Oct 22 |
T000042_2.00 F08_2.00 TS49_2.00 . . EuGene.0900010172 EuGene.0900010172 Micromonas_sp_RCC299 N C2H2 ZF,RanBP ZF zf-C2H2,zf-RanBP 2 0.70 . . . . . . . . JGI:Phytozome https://phytozome.jgi.doe.gov/pz/portal.html 2018 Apr 12 |
T000043_2.00 F08_2.00 TS69_2.00 . . Contig13849.0.g86 Contig13849.0.g86 Oxytricha_trifallax N C2H2 ZF,RanBP ZF zf-C2H2,zf-RanBP 2 0.70 . . . . . . . . Misc http://hugheslab.med.utoronto.ca/ 2018 Jan 19 |
T000044_2.00 F08_2.00 TS69_2.00 . . Contig14898.0.g56 Contig14898.0.g56 Oxytricha_trifallax N C2H2 ZF,RanBP ZF zf-C2H2,zf-RanBP 2 0.70 . . . . . . . . Misc http://hugheslab.med.utoronto.ca/ 2018 Jan 19 |
T000045_2.00 F09_2.00 TS04_2.00 . . WUBG_07684 WUBG_07684 Wuchereria_bancrofti N C2H2 ZF,RRM zf-C2H2,RRMs_3D 2 0.70 . . . . . . . . Broad http://www.broadinstitute.org/ 2016 May 1 |
T000046_2.00 F09_2.00 TS12_2.00 . . Bo3g023850 Bo3g023850 Brassica_oleracea N C2H2 ZF,RRM zf-C2H2,RRMs_3D 2 0.70 . . . . . . . . Ensembl http://www.ensembl.org/ 2018 Dec 8 |
T000047_2.00 F09_2.00 TS12_2.00 . . CGI_10011751 CGI_10011751 Crassostrea_gigas N C2H2 ZF,RRM zf-C2H2,RRMs_3D 2 0.70 . . . . . . . . Ensembl http://www.ensembl.org/ 2018 Dec 8 |
T000048_2.00 F09_2.00 TS12_2.00 . . EFV56476 EFV56476 Trichinella_spiralis N C2H2 ZF,RRM zf-C2H2,RRMs_3D 2 0.70 . . . . . . . . Ensembl http://www.ensembl.org/ 2018 Dec 8 |
T000049_2.00 F09_2.00 TS12_2.00 . . K443DRAFT_292260 K443DRAFT_292260 Laccaria_amethystina N C2H2 ZF,RRM zf-C2H2,RRMs_3D 2 0.70 . . . . . . . . Ensembl http://www.ensembl.org/ 2018 Dec 8 |
T000050_2.00 F09_2.00 TS12_2.00 . . ML01246a ML01246a Mnemiopsis_leidyi N C2H2 ZF,RRM zf-C2H2,RRMs_3D 2 0.70 . . . . . . . . Ensembl http://www.ensembl.org/ 2018 Dec 8 |
T000051_2.00 F09_2.00 TS12_2.00 M00261_2.00 MS14_2.00 PGSC0003DMG400030803 PGSC0003DMG400030803 Solanum_tuberosum I C2H2 ZF,RRM zf-C2H2,RRMs_3D 2 0.70 RNCMPT00284 RNAcompete RNA_Zoo RNAcompete Ray 2013 23846655 NULL Ensembl http://www.ensembl.org/ 2018 Dec 8 |
T000052_2.00 F09_2.00 TS19_2.00 . . Ogr13363 Ogr13363 Ophisaurus_gracilis N C2H2 ZF,RRM zf-C2H2,RRMs_3D 2 0.70 . . . . . . . . GigaDB http://gigadb.org/dataset/100166 2015 Oct 22 |
T000053_2.00 F09_2.00 TS47_2.00 . . Ocbimv22000154m.g Ocbimv22000154m.g Octopus_bimaculoides N C2H2 ZF,RRM zf-C2H2,RRMs_3D 2 0.70 . . . . . . . . JGI:Metazome https://metazome.jgi.doe.gov/pz/portal.html 2015 Oct 22 |
T000054_2.00 F09_2.00 TS47_2.00 . . Ocbimv22039846m.g Ocbimv22039846m.g Octopus_bimaculoides N C2H2 ZF,RRM zf-C2H2,RRMs_3D 2 0.70 . . . . . . . . JGI:Metazome https://metazome.jgi.doe.gov/pz/portal.html 2015 Oct 22 |
T000055_2.00 F09_2.00 TS69_2.00 . . Contig15516.0.0.g97 Contig15516.0.0.g97 Oxytricha_trifallax N C2H2 ZF,RRM zf-C2H2,RRMs_3D 2 0.70 . . . . . . . . Misc http://hugheslab.med.utoronto.ca/ 2018 Jan 19 |
T000056_2.00 F09_2.00 TS71_2.00 . . estExt_fgeneshTM_pg.C_11526 estExt_fgeneshTM_pg.C_11526 Tremella_mesenterica N C2H2 ZF,RRM zf-C2H2,RRMs_3D 2 0.70 . . . . . . . . Superfamily http://supfam.cs.bris.ac.uk/SUPERFAMILY/ 2010 Oct 26 |
T000057_2.00 F09_2.00 TS72_2.00 . . LLOJ005865 LLOJ005865 Lutzomyia_longipalpis N C2H2 ZF,RRM zf-C2H2,RRMs_3D 2 0.70 . . . . . . . . Vectorbase https://www.vectorbase.org/ 2015 Oct 22 |
T000058_2.00 F09_2.00 TS73_2.00 . . ASU_06187 ASU_06187 Ascaris_suum N C2H2 ZF,RRM zf-C2H2,RRMs_3D 2 0.70 . . . . . . . . WormBase:ParaSite http://parasite.wormbase.org/ 2015 Oct 22 |
T000059_2.00 F09_2.00 TS73_2.00 . . MhA1_Contig53.frz3.gene55 MhA1_Contig53.frz3.gene55 Meloidogyne_hapla N C2H2 ZF,RRM zf-C2H2,RRMs_3D 2 0.70 . . . . . . . . WormBase:ParaSite http://parasite.wormbase.org/ 2015 Oct 22 |
T000060_2.00 F09_2.00 TS73_2.00 . . nAv.1.0.1.g09713 nAv.1.0.1.g09713 Acanthocheilonema_viteae N C2H2 ZF,RRM zf-C2H2,RRMs_3D 2 0.70 . . . . . . . . WormBase:ParaSite http://parasite.wormbase.org/ 2015 Oct 22 |
T000061_2.00 F09_2.00 TS73_2.00 . . nLs.2.1.2.g07665 nLs.2.1.2.g07665 Litomosoides_sigmodontis N C2H2 ZF,RRM zf-C2H2,RRMs_3D 2 0.70 . . . . . . . . WormBase:ParaSite http://parasite.wormbase.org/ 2015 Oct 22 |
T000062_2.00 F09_2.00 TS73_2.00 . . PTRK_0001316100 PTRK_0001316100 Parastrongyloides_trichosuri N C2H2 ZF,RRM zf-C2H2,RRMs_3D 2 0.70 . . . . . . . . WormBase:ParaSite http://parasite.wormbase.org/ 2015 Oct 22 |
T000063_2.00 F09_2.00 TS73_2.00 . . RSKR_0000562600 RSKR_0000562600 Rhabditophanes_kr3021 N C2H2 ZF,RRM zf-C2H2,RRMs_3D 2 0.70 . . . . . . . . WormBase:ParaSite http://parasite.wormbase.org/ 2015 Oct 22 |
T000064_2.00 F10_2.00 TS17_2.00 . . TVAG_237340 TVAG_237340 Trichomonas_vaginalis N C2H2 ZF,SAM zf-C2H2,SAM_1 2 0.70 . . . . . . . . EuPathDB http://eupathdb.org/ 2015 Mar 30 |
T000065_2.00 F10_2.00 TS19_2.00 . . Alligator_sinensis_CCG018601.1 Alligator_sinensis_CCG018601.1 Alligator_sinensis N C2H2 ZF,SAM zf-C2H2,SAM_1 2 0.70 . . . . . . . . GigaDB http://gigadb.org/dataset/100166 2015 Oct 22 |
T000066_2.00 F11_2.00 TS12_2.00 M00700_2.00 MS06_2.00 ENSG00000056097 ZFR Homo_sapiens D C2H2 ZF zf-C2H2 1 0.70 ZFR_linear_1 HTR-SELEX Jolma2020_RBPs HTR-SELEX Jolma 2020 32703884 NULL Ensembl http://www.ensembl.org/ 2018 Dec 8 |
T000066_2.00 F11_2.00 TS12_2.00 M00701_2.00 MS06_2.00 ENSG00000056097 ZFR Homo_sapiens D C2H2 ZF zf-C2H2 1 0.70 ZFR_linear_2 HTR-SELEX Jolma2020_RBPs HTR-SELEX Jolma 2020 32703884 NULL Ensembl http://www.ensembl.org/ 2018 Dec 8 |
T000066_2.00 F11_2.00 TS12_2.00 M00702_2.00 MS06_2.00 ENSG00000056097 ZFR Homo_sapiens D C2H2 ZF zf-C2H2 1 0.70 ZFR_linear_3 HTR-SELEX Jolma2020_RBPs HTR-SELEX Jolma 2020 32703884 NULL Ensembl http://www.ensembl.org/ 2018 Dec 8 |
T000066_2.00 F11_2.00 TS12_2.00 M00703_2.00 MS06_2.00 ENSG00000056097 ZFR Homo_sapiens D C2H2 ZF zf-C2H2 1 0.70 ZFR_linear_4 HTR-SELEX Jolma2020_RBPs HTR-SELEX Jolma 2020 32703884 NULL Ensembl http://www.ensembl.org/ 2018 Dec 8 |
T000067_2.00 F11_2.00 TS69_2.00 M00446_2.00 MS12_2.00 XB-GENE-6252591 gtf3a Xenopus_laevis D C2H2 ZF zf-C2H2 1 0.70 1123_20095591 SELEX RBPDB RBPDB Cook 2011 21036867 v1.2.1 Misc http://hugheslab.med.utoronto.ca/ 2018 Jan 19 |
T000068_2.00 F12_2.00 TS73_2.00 . . DICVIV_06115 DICVIV_06115 Dictyocaulus_viviparus N CCCH ZF,CCHC ZF,KH,RRM zf-CCCH,zf-CCHC,KH_1,RRMs_3D 4 0.70 . . . . . . . . WormBase:ParaSite http://parasite.wormbase.org/ 2015 Oct 22 |
T000069_2.00 F13_2.00 TS12_2.00 . . EMIHUDRAFT_462691 EMIHUDRAFT_462691 Emiliania_huxleyi N CCCH ZF,CCHC ZF,RanBP ZF zf-CCCH,zf-CCHC,zf-RanBP 3 0.70 . . . . . . . . Ensembl http://www.ensembl.org/ 2018 Dec 8 |
T000070_2.00 F14_2.00 TS73_2.00 . . ANCCAN_03839 ANCCAN_03839 Ancylostoma_caninum N CCCH ZF,CCHC ZF,RRM zf-CCCH,zf-CCHC,RRMs_3D 3 0.70 . . . . . . . . WormBase:ParaSite http://parasite.wormbase.org/ 2015 Oct 22 |
T000071_2.00 F15_2.00 TS04_2.00 . . AMAG_01018 AMAG_01018 Allomyces_macrogynus N CCCH ZF,CCHC ZF zf-CCCH,zf-CCHC 2 0.70 . . . . . . . . Broad http://www.broadinstitute.org/ 2016 May 1 |
T000072_2.00 F15_2.00 TS04_2.00 . . AMAG_02531 AMAG_02531 Allomyces_macrogynus N CCCH ZF,CCHC ZF zf-CCCH,zf-CCHC 2 0.70 . . . . . . . . Broad http://www.broadinstitute.org/ 2016 May 1 |
T000073_2.00 F15_2.00 TS04_2.00 . . AMSG_00318 AMSG_00318 Thecamonas_trahens N CCCH ZF,CCHC ZF zf-CCCH,zf-CCHC 2 0.70 . . . . . . . . Broad http://www.broadinstitute.org/ 2016 May 1 |
T000074_2.00 F15_2.00 TS04_2.00 . . CpipJ_CPIJ009192 CpipJ_CPIJ009192 Culex_pipiens N CCCH ZF,CCHC ZF zf-CCCH,zf-CCHC 2 0.70 . . . . . . . . Broad http://www.broadinstitute.org/ 2016 May 1 |
T000075_2.00 F15_2.00 TS04_2.00 . . RO3G_08870 RO3G_08870 Rhizopus_oryzae N CCCH ZF,CCHC ZF zf-CCCH,zf-CCHC 2 0.70 . . . . . . . . Broad http://www.broadinstitute.org/ 2016 May 1 |
T000076_2.00 F15_2.00 TS04_2.00 . . SPPG_01134 SPPG_01134 Spizellomyces_punctatus N CCCH ZF,CCHC ZF zf-CCCH,zf-CCHC 2 0.70 . . . . . . . . Broad http://www.broadinstitute.org/ 2016 May 1 |
T000077_2.00 F15_2.00 TS04_2.00 . . WUBG_01564 WUBG_01564 Wuchereria_bancrofti N CCCH ZF,CCHC ZF zf-CCCH,zf-CCHC 2 0.70 . . . . . . . . Broad http://www.broadinstitute.org/ 2016 May 1 |
T000078_2.00 F15_2.00 TS12_2.00 . . A1Q1_05026 A1Q1_05026 Trichosporon_asahii N CCCH ZF,CCHC ZF zf-CCCH,zf-CCHC 2 0.70 . . . . . . . . Ensembl http://www.ensembl.org/ 2018 Dec 8 |
T000079_2.00 F15_2.00 TS12_2.00 . . ACEP13561 ACEP13561 Atta_cephalotes N CCCH ZF,CCHC ZF zf-CCCH,zf-CCHC 2 0.70 . . . . . . . . Ensembl http://www.ensembl.org/ 2018 Dec 8 |
T000080_2.00 F15_2.00 TS12_2.00 . . ACYPI000730 ACYPI000730 Acyrthosiphon_pisum N CCCH ZF,CCHC ZF zf-CCCH,zf-CCHC 2 0.70 . . . . . . . . Ensembl http://www.ensembl.org/ 2018 Dec 8 |
T000081_2.00 F15_2.00 TS12_2.00 . . ACYPI007246 ACYPI007246 Acyrthosiphon_pisum N CCCH ZF,CCHC ZF zf-CCCH,zf-CCHC 2 0.70 . . . . . . . . Ensembl http://www.ensembl.org/ 2018 Dec 8 |
T000082_2.00 F15_2.00 TS12_2.00 . . ADAC006702 ADAC006702 Anopheles_darlingi N CCCH ZF,CCHC ZF zf-CCCH,zf-CCHC 2 0.70 . . . . . . . . Ensembl http://www.ensembl.org/ 2018 Dec 8 |
T000083_2.00 F15_2.00 TS12_2.00 . . AGABI2DRAFT_62161 AGABI2DRAFT_62161 Agaricus_bisporus N CCCH ZF,CCHC ZF zf-CCCH,zf-CCHC 2 0.70 . . . . . . . . Ensembl http://www.ensembl.org/ 2018 Dec 8 |
T000084_2.00 F15_2.00 TS12_2.00 . . AGAP013044 AGAP013044 Anopheles_gambiae N CCCH ZF,CCHC ZF zf-CCCH,zf-CCHC 2 0.70 . . . . . . . . Ensembl http://www.ensembl.org/ 2018 Dec 8 |
T000085_2.00 F15_2.00 TS12_2.00 . . Aqu1.218275 Aqu1.218275 Amphimedon_queenslandica N CCCH ZF,CCHC ZF zf-CCCH,zf-CCHC 2 0.70 . . . . . . . . Ensembl http://www.ensembl.org/ 2018 Dec 8 |
T000086_2.00 F15_2.00 TS12_2.00 . . BGIBMGA011920 BGIBMGA011920 Bombyx_mori N CCCH ZF,CCHC ZF zf-CCCH,zf-CCHC 2 0.70 . . . . . . . . Ensembl http://www.ensembl.org/ 2018 Dec 8 |
T000087_2.00 F15_2.00 TS12_2.00 . . Bm3301 Bm3301 Brugia_malayi N CCCH ZF,CCHC ZF zf-CCCH,zf-CCHC 2 0.70 . . . . . . . . Ensembl http://www.ensembl.org/ 2018 Dec 8 |
T000088_2.00 F15_2.00 TS12_2.00 . . BN946_scf185007.g274 BN946_scf185007.g274 Trametes_cinnabarina N CCCH ZF,CCHC ZF zf-CCCH,zf-CCHC 2 0.70 . . . . . . . . Ensembl http://www.ensembl.org/ 2018 Dec 8 |
T000089_2.00 F15_2.00 TS12_2.00 . . BOTBODRAFT_106517 BOTBODRAFT_106517 Botryobasidium_botryosum N CCCH ZF,CCHC ZF zf-CCCH,zf-CCHC 2 0.70 . . . . . . . . Ensembl http://www.ensembl.org/ 2018 Dec 8 |
T000090_2.00 F15_2.00 TS12_2.00 . . CapteG180092 CapteG180092 Capitella_teleta N CCCH ZF,CCHC ZF zf-CCCH,zf-CCHC 2 0.70 . . . . . . . . Ensembl http://www.ensembl.org/ 2018 Dec 8 |
T000091_2.00 F15_2.00 TS12_2.00 . . CBG06226 CBG06226 Caenorhabditis_briggsae N CCCH ZF,CCHC ZF zf-CCCH,zf-CCHC 2 0.70 . . . . . . . . Ensembl http://www.ensembl.org/ 2018 Dec 8 |
T000092_2.00 F15_2.00 TS12_2.00 . . CBN21927 CBN21927 Caenorhabditis_brenneri N CCCH ZF,CCHC ZF zf-CCCH,zf-CCHC 2 0.70 . . . . . . . . Ensembl http://www.ensembl.org/ 2018 Dec 8 |
T000093_2.00 F15_2.00 TS12_2.00 . . CBN24449 CBN24449 Caenorhabditis_brenneri N CCCH ZF,CCHC ZF zf-CCCH,zf-CCHC 2 0.70 . . . . . . . . Ensembl http://www.ensembl.org/ 2018 Dec 8 |
T000094_2.00 F15_2.00 TS12_2.00 . . CERSUDRAFT_110762 CERSUDRAFT_110762 Ceriporiopsis_subvermispora N CCCH ZF,CCHC ZF zf-CCCH,zf-CCHC 2 0.70 . . . . . . . . Ensembl http://www.ensembl.org/ 2018 Dec 8 |
T000095_2.00 F15_2.00 TS12_2.00 . . CJA04615 CJA04615 Caenorhabditis_japonica N CCCH ZF,CCHC ZF zf-CCCH,zf-CCHC 2 0.70 . . . . . . . . Ensembl http://www.ensembl.org/ 2018 Dec 8 |
T000096_2.00 F15_2.00 TS12_2.00 . . CNB01070 CNB01070 Cryptococcus_neoformans N CCCH ZF,CCHC ZF zf-CCCH,zf-CCHC 2 0.70 . . . . . . . . Ensembl http://www.ensembl.org/ 2018 Dec 8 |
End of preview.
YAML Metadata Warning:empty or missing yaml metadata in repo card
Check out the documentation for more information.
RNA tasks and grounding targets: data pipeline
Jupyter notebooks that build six RNA task datasets, their train/validation/test splits and the
grounding targets used to evaluate attribution maps, starting from the raw source files in
raw_data.zip.
Contents
| path | purpose |
|---|---|
data/<task>/<task>.ipynb |
builds the task dataset from raw/ into processed/ |
data/<task>/splits.ipynb |
assigns train/validation/test, written to splits/ |
data/<task>/grounding.ipynb |
builds the grounding target B, null masks and shuffled controls in grounding/processed/ (all tasks except m6a) |
data/docs/ground_truth_spec.md |
how B is constructed; read by the grounding notebooks |
raw_data.zip |
every raw input file, at the path the notebooks expect |
pyproject.toml, uv.lock, .python-version |
Python 3.12 environment, managed with uv |
No grounding set is built for m6a (section T3 of the spec). crp has no test split: the OK7a
table (crp_ok7a.parquet) is the held-out evaluation set.
Running
About 20 GB of free disk space is needed (compressed and unpacked raw data, plus about 7 GB of outputs).
Unpack the raw data in this folder. This creates
data/<task>/raw/anddata/<task>/grounding/raw/:unzip raw_data.zipCreate the environment:
uv syncFor each task, run the notebooks in order:
<task>.ipynb, thensplits.ipynb, thengrounding.ipynb. Fromdata/<task>/:uv run jupyter nbconvert --to notebook --execute --inplace <notebook>.ipynb
Each notebook checks the checksums of what it reads, so running them out of order stops with an error. A full run took about 45 minutes on the Linux machine the outputs were built on: about 13 minutes for the build and split notebooks and 32 for grounding, most of it pas (18) and spl (8).
Requirements
- Memory:
crp/splits.ipynbandpas/grounding.ipynbneed well over 16 GB of RAM (32 GB is a safe size); the crp 11-mer pair enumeration allocates several arrays of about 6 GB each. The other notebooks run in 16 GB. - Operating system: the outputs were produced on Linux. The notebooks also run on Windows, where
Python writes the
.jsonlmirrors with CRLF line endings; those files, and the checksums the previews record for them, then differ from a Linux run, while the parquet files are identical.
Outputs
Each output table is written as <name>.parquet, a <name>.jsonl mirror, and
<name>.preview.jsonl: a _meta record (schema, row counts, checksums, build rules) followed by the
first five rows. The spl build does not write spl.jsonl, which would be about 0.6 GB. All files of
a task join on row_index, the 0-based row position in processed/<task>.parquet. Figures are only
shown inline in the notebooks.
Licence
The code and documentation are released under the MIT licence (LICENSE). The raw data in
raw_data.zip comes from the sources listed above and remains under their terms.
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