| # TE-Seq Data v1 |
|
|
| Transposable Element locus sequences from the human genome (GRCh38). |
|
|
| ## Dataset Summary |
|
|
| | Property | Value | |
| |----------|-------| |
| | Total records | 4,693,511 | |
| | File size | ~894 MB | |
| | Sequence column | `sequence` (consume verbatim; no padding trimming) | |
| | Labels | `family` (1,180 unique), `class` (13 unique) | |
|
|
| ## Schema |
|
|
| | Column | Type | Description | |
| |--------|------|-------------| |
| | `sequence` | string | DNA sequence (consume as-is) | |
| | `family` | string | TE family label (primary training target) | |
| | `class` | string | TE class (e.g., SINE, LINE, LTR, DNA) | |
| | `chrom`, `start`, `end` | string/int | Genomic coordinates | |
| | `strand` | string | + or - | |
| | `subfamily` | string | Subfamily label | |
| | Other columns | | Locus metadata (ID, loci, group, N1, N2, TE_chrom, TE_start, TE_end) | |
| |
| ## File Status: Corrected Splits vs Legacy Root |
| |
| Use the corrected split shards for all current DeepGenopix training, simulator, and benchmark jobs: |
| |
| - `train/te_seqdata.parquet` |
| - `val/te_seqdata.parquet` |
| - `test/te_seqdata.parquet` |
| - `split_summary.json` |
| - `te_seqdata.recovered.parquet` for corrected raw sibling access |
|
|
| Do not use the root `te_seqdata.parquet` for new jobs. It is retained only as a legacy snapshot for backward compatibility and was intentionally left untouched when the corrected split was uploaded. The corrected split excludes the remaining 405 unresolved unlabeled rows. |
|
|
| Current canonical split-input revision for reproducible jobs: `f107d46c5a61087eb3fb19b4e3e75fdef0b74fdd`. |
|
|
| ## Usage |
|
|
| Use this dataset as the raw input for `run_parquet_etl()` in DeepGenopix: |
|
|
| ```python |
| from deepgenopix.etl import run_parquet_etl |
| run_parquet_etl( |
| "te_seqdata.parquet", |
| output_dir="data/processed/te_visuals/<run_id>", |
| sequence_col="sequence", |
| label_col="family", # or "class" |
| ) |
| ``` |
|
|
| ## Class Distribution |
|
|
| - SINE: 1,770,903 |
| - LINE: 1,516,226 |
| - LTR: 720,177 |
| - DNA: 483,994 |
| - Satellite: 7,018 |
| - Other: ~2,000 each or fewer |
|
|
| ## Splits |
|
|
| The ETL builds stratified train/val/test splits automatically: |
| - Tier 1 (< 30 samples): all → train |
| - Tier 2 (30–200): floor-20 val, 10% test, rest → train |
| - Tier 3 (> 200): 10% val, 10% test, rest → train |
