| --- |
| pretty_name: Enterococcus clean-v2 plasmid segment dataset |
| tags: |
| - biology |
| - genomics |
| - plasmid |
| - enterococcus |
| - prokbert |
| language: |
| - en |
| configs: |
| - config_name: enterococcus_clean_v2_host_assemblies |
| data_files: |
| - split: train |
| path: data/enterococcus_clean_v2_host_assemblies/train-*.parquet |
| - config_name: enterococcus_clean_v2_host_contigs |
| data_files: |
| - split: train |
| path: data/enterococcus_clean_v2_host_contigs/train-*.parquet |
| - config_name: enterococcus_clean_v2_plasmid_to_assembly_links |
| data_files: |
| - split: train |
| path: data/enterococcus_clean_v2_plasmid_to_assembly_links/train-*.parquet |
| - config_name: enterococcus_clean_v2_plasmids |
| data_files: |
| - split: train |
| path: data/enterococcus_clean_v2_plasmids/train-*.parquet |
| - config_name: enterococcus_clean_v2_segments |
| data_files: |
| - split: train |
| path: data/enterococcus_clean_v2_segments/train-*.parquet |
| --- |
| |
| <!-- BEGIN ENTEROCOCCUS_CLEAN_V2_SEGMENT_DATASET --> |
| # Enterococcus Clean-v2 Segment Dataset |
|
|
| This dataset contains the Enterococcus clean-v2 NR plasmid training segments and their sampled host candidate segments. Problematic host segments are not dropped from the canonical export; they are retained and tagged. |
|
|
| ## Configs |
|
|
| | config | split | rows | has_sequence | |
| | --- | --- | --- | --- | |
| | enterococcus_clean_v2_host_assemblies | train | 1497 | False | |
| | enterococcus_clean_v2_host_contigs | train | 4530 | False | |
| | enterococcus_clean_v2_plasmid_to_assembly_links | train | 7916 | False | |
| | enterococcus_clean_v2_plasmids | train | 2519 | False | |
| | enterococcus_clean_v2_segments | train | 910900 | True | |
| |
| Only `enterococcus_clean_v2_segments` contains the nucleotide segment sequence column. |
|
|
| ## Counts |
|
|
| | metric | value | |
| | --- | ---: | |
| | plasmid segment rows | 182180 | |
| | host candidate rows | 728720 | |
| | total canonical rows | 910900 | |
| | host rows flagged by plasmid overlap | 27417 | |
| | current clean-training eligible rows | 883483 | |
| | unique source sequence IDs | 5133 | |
| | selected Enterococcus clean-v2 NR plasmids | 2519 | |
| | host assemblies with usable non-plasmid contigs | 1497 | |
|
|
| ## Segment Flags |
|
|
| - `segment_id`: unique integer primary key, contiguous from `0`. |
| - `sequence_id`: source-sequence grouping ID, contiguous from `0`; segments from the same plasmid or host source contig share one value. |
| - `labels`: `1` for plasmid segments, `0` for host segments. |
| - `training_eligible_current_clean`: current recommended training filter. |
| - `filtered_by_plasmid`: host segment has a likely plasmid-overlap minimap2 hit. |
| - `is_problematic_segment`: currently equivalent to a host segment flagged by plasmid overlap. |
| - `problematic_reasons`: text reason for problematic rows, currently `host_plasmid_overlap`. |
|
|
| ## Loading |
|
|
| ```python |
| from datasets import load_dataset |
| |
| segments = load_dataset("neuralbioinfo/enterococcus-plasmid-training", "enterococcus_clean_v2_segments", split="train") |
| clean = segments.filter(lambda row: row["training_eligible_current_clean"]) |
| flagged_hosts = segments.filter(lambda row: row["source_type"] == "host" and row["filtered_by_plasmid"]) |
| ``` |
|
|
| ## Provenance |
|
|
| - Source clean-v2 plasmid DB: `clean_v2_len2k_4mb_nochrom_broadhq20` |
| - Taxonomic scope: Enterococcus genus taxid `1350` |
| - Segment length: `4000` |
| - Plasmid coverage: `2.0` |
| - Host candidate ratio: `4x` |
| - Host-overlap filter: minimap2 against selected Enterococcus clean-v2 NR plasmids. |
|
|
| Detailed JSON reports are stored under `reports/`. |
| <!-- END ENTEROCOCCUS_CLEAN_V2_SEGMENT_DATASET --> |
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