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Upload Enterococcus clean-v2 segment dataset

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  1. README.md +3 -0
  2. data/enterococcus_clean_v2_host_assemblies/train-00000.parquet +3 -0
  3. data/enterococcus_clean_v2_host_contigs/train-00000.parquet +3 -0
  4. data/enterococcus_clean_v2_plasmid_to_assembly_links/train-00000.parquet +3 -0
  5. data/enterococcus_clean_v2_plasmids/train-00000.parquet +3 -0
  6. data/enterococcus_clean_v2_segments/train-00000.parquet +3 -0
  7. data/enterococcus_clean_v2_segments/train-00001.parquet +3 -0
  8. data/enterococcus_clean_v2_segments/train-00002.parquet +3 -0
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README.md CHANGED
@@ -57,12 +57,14 @@ Only `enterococcus_clean_v2_segments` contains the nucleotide segment sequence c
57
  | total canonical rows | 910900 |
58
  | host rows flagged by plasmid overlap | 27417 |
59
  | current clean-training eligible rows | 883483 |
 
60
  | selected Enterococcus clean-v2 NR plasmids | 2519 |
61
  | host assemblies with usable non-plasmid contigs | 1497 |
62
 
63
  ## Segment Flags
64
 
65
  - `segment_id`: unique integer primary key, contiguous from `0`.
 
66
  - `labels`: `1` for plasmid segments, `0` for host segments.
67
  - `training_eligible_current_clean`: current recommended training filter.
68
  - `filtered_by_plasmid`: host segment has a likely plasmid-overlap minimap2 hit.
@@ -91,3 +93,4 @@ flagged_hosts = segments.filter(lambda row: row["source_type"] == "host" and row
91
  Detailed JSON reports are stored under `reports/`.
92
  <!-- END ENTEROCOCCUS_CLEAN_V2_SEGMENT_DATASET -->
93
 
 
 
57
  | total canonical rows | 910900 |
58
  | host rows flagged by plasmid overlap | 27417 |
59
  | current clean-training eligible rows | 883483 |
60
+ | unique source sequence IDs | 5133 |
61
  | selected Enterococcus clean-v2 NR plasmids | 2519 |
62
  | host assemblies with usable non-plasmid contigs | 1497 |
63
 
64
  ## Segment Flags
65
 
66
  - `segment_id`: unique integer primary key, contiguous from `0`.
67
+ - `sequence_id`: source-sequence grouping ID, contiguous from `0`; segments from the same plasmid or host source contig share one value.
68
  - `labels`: `1` for plasmid segments, `0` for host segments.
69
  - `training_eligible_current_clean`: current recommended training filter.
70
  - `filtered_by_plasmid`: host segment has a likely plasmid-overlap minimap2 hit.
 
93
  Detailed JSON reports are stored under `reports/`.
94
  <!-- END ENTEROCOCCUS_CLEAN_V2_SEGMENT_DATASET -->
95
 
96
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