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taxonomy_genus

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Update README.md

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@@ -35,13 +35,12 @@ configs:
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  UniProt search (7/22/2025): * (Swiss-Prot reviewed entries only) download TSV with Taxonomic lineage (Ids), sequence, and length.
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  Curation steps:
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-
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- Filtered for sequence length >=20 and <=2048
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- Extract Taxonomic IDs (domain, kingdom, phylum, class, order, family, genus, species) from taxonomic_lineage_ids column
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- Keep entry, genus, and sequence information
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- Drop N/A
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- CD-HIT using Docker at 80% similarity threshold and n=5
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- Keep representative sequences
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- Create labels based on spcecies
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- Remove genuses/examples with fewer than 100 samples
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- Stratified split: first get test set (5,000), then eval (5,000), rest is train
 
35
  UniProt search (7/22/2025): * (Swiss-Prot reviewed entries only) download TSV with Taxonomic lineage (Ids), sequence, and length.
36
 
37
  Curation steps:
38
+ - Filtered for sequence length >=20 and <=2048
39
+ - Extract Taxonomic IDs (domain, kingdom, phylum, class, order, family, genus, species) from taxonomic_lineage_ids column
40
+ - Keep entry, genus, and sequence information
41
+ - Drop N/A
42
+ - CD-HIT using Docker at 80% similarity threshold and n=5
43
+ - Keep representative sequences
44
+ - Create labels based on spcecies
45
+ - Remove genuses/examples with fewer than 100 samples
46
+ - Stratified split: first get test set (5,000), then eval (5,000), rest is train