adding two new promoter sets

README.md

@@ -92,6 +92,21 @@ features:
             - gene: TYE7
               description: TYE7 deletion strain
 
+- applies_to:
+  - annotated_feature_reprocess_intergenic
+  - annotated_feature_reprocess_intergenic_analysis
+  fields:
+  - name: ir_name
+    dtype: string
+    description: >-
+      Unique identifier of the intergenic region. See
+      yeast_genome_resources/intergenic_regions_metadata_5_1.csv for details on
+      the region (location, etc). Note that these intergenic regions are defined
+      as the region between the end of one ORF and the start of the next, and
+      are named according to the locus tags of the flanking ORFs (e.g.,
+      YAL001C-YAL002W). A intergenic  region is assigned to a promoter only when
+      the 5' end is continuous with the region.
+
 - applies_to:
   - annotated_feature
   - annotated_feature_meta
@@ -99,6 +114,8 @@ features:
   - genome_map_meta
   - annotated_feature_reprocess_yiming
   - annotated_feature_reprocess_mindel
+  - annotated_feature_reprocess_start_codon_500
+  - annotated_feature_reprocess_intergenic
   fields:
   - name: batch
     dtype: string
@@ -111,6 +128,8 @@ features:
   - genome_map_meta
   - 2026_analysis_set
   - annotated_feature_reprocess_mindel_analysis
+  - annotated_feature_reprocess_start_codon_500bp_analysis
+  - annotated_feature_reprocess_intergenic_analysis
   fields:
   - name: regulator_locus_tag
     dtype: string
@@ -128,6 +147,10 @@ features:
   - annotated_feature_reprocess_yiming
   - annotated_feature_reprocess_mindel
   - annotated_feature_reprocess_mindel_analysis
+  - annotated_feature_reprocess_start_codon_500
+  - annotated_feature_reprocess_start_codon_500bp_analysis
+  - annotated_feature_reprocess_intergenic
+  - annotated_feature_reprocess_intergenic_analysis
   fields:
   - name: target_locus_tag
     dtype: string
@@ -145,6 +168,10 @@ features:
   - annotated_feature_reprocess_yiming
   - annotated_feature_reprocess_mindel
   - annotated_feature_reprocess_mindel_analysis
+  - annotated_feature_reprocess_start_codon_500
+  - annotated_feature_reprocess_start_codon_500bp_analysis
+  - annotated_feature_reprocess_intergenic
+  - annotated_feature_reprocess_intergenic_analysis
   fields:
   - name: experiment_hops
     dtype: float64 
@@ -181,6 +208,10 @@ features:
   - annotated_feature_reprocess_yiming
   - annotated_feature_reprocess_mindel
   - annotated_feature_reprocess_mindel_analysis
+  - annotated_feature_reprocess_start_codon_500
+  - annotated_feature_reprocess_start_codon_500bp_analysis
+  - annotated_feature_reprocess_intergenic
+  - annotated_feature_reprocess_intergenic_analysis
   fields:
   - name: total_background_hops
     dtype: float64
@@ -413,7 +444,7 @@ configs:
 - config_name: genome_map_meta
   description: Metadata for genome map datasets including regulator information and experimental details
   dataset_type: metadata
-  applies_to: ["genome_map", "annotated_feature_reprocess_yiming", "annotated_feature_reprocess_mindel"]
+  applies_to: ["genome_map", "annotated_feature_reprocess_yiming", "annotated_feature_reprocess_mindel", "annotated_feature_reprocess_start_codon_500", "annotated_feature_reprocess_intergenic"]
   data_files:
   - split: train
     path: genome_map_meta.parquet
@@ -484,6 +515,57 @@ configs:
       description: >-
         Genome map identifier linking to the genome_map and genome_map_meta dataset
 
+- config_name: annotated_feature_reprocess_start_codon_500
+  description: >-
+    This is the genome_map data quantified against the promoters defined
+    as 500bp upstream of the start codon for each gene 
+    (see BrentLab/yeast_genome_resources) using
+    scripts/quantify_regions_500bp_intergenic.R.
+  dataset_type: annotated_features
+  data_files:
+  - split: train
+    path: annotated_feature_reprocess_start_codon_500/*/*.parquet
+  genome_resources:
+    region_sets:
+      start_codon_500bp:
+        path: https://huggingface.co/datasets/BrentLab/yeast_genome_resources/blob/main/start_codon_500bp_upstream_promoters.bed
+        join_column: target_locus_tag
+  partitioning:
+    enabled: true
+    partition_by: ["batch"]
+    path_template: "annotated_feature_reprocess_start_codon_500/batch={batch}/*.parquet"
+  dataset_info:
+    features:
+    - name: genome_map_id
+      dtype: int64
+      description: >-
+        Genome map identifier linking to the genome_map and genome_map_meta dataset
+
+- config_name: annotated_feature_reprocess_intergenic
+  description: >-
+    This is the genome_map data quantified against the promoters defined
+    as the full intergenic region upstream of each gene (see
+    BrentLab/yeast_genome_resources) using scripts/quantify_regions_500bp_intergenic.R.
+  dataset_type: annotated_features
+  data_files:
+  - split: train
+    path: annotated_feature_reprocess_intergenic/*/*.parquet
+  genome_resources:
+    region_sets:
+      intergenic:
+        path: https://huggingface.co/datasets/BrentLab/yeast_genome_resources/blob/main/intergenic_regions_metadata_5_1.csv
+        join_column: ir_name
+  partitioning:
+    enabled: true
+    partition_by: ["batch"]
+    path_template: "annotated_feature_reprocess_intergenic/batch={batch}/*.parquet"
+  dataset_info:
+    features:
+    - name: genome_map_id
+      dtype: int64
+      description: >-
+        Genome map identifier linking to the genome_map and genome_map_meta dataset
+
 - config_name: annotated_feature_reprocess_mindel_analysis
   description: >-
     This is the analysis set for the mindel data. It is generated using the same logic as the 2026_analysis_set, but using the results from the reprocessing against the mindel promoters. A passing replicate has >=3000 hops had a dto empirical pvalue < 0.01 against either kemmeren or hackett. Where a given regulator had multiple passing replicates, those replicates were combined (see annotated_feature_combined). This dataset should be used when you want to use data that can be reproduced directly from the genome_map data included in this repo, using the mindel promoter definitions. See scripts/quantify_regions.R as well as BrentLab/yeast_comparative_analysis/scripts for details of how this was conducted.
@@ -508,6 +590,54 @@ configs:
         if they have more than 3k hopes (single or combined), then they are
         included in the analysis set.
       role: sample_id
+
+- config_name: annotated_feature_reprocess_start_codon_500bp_analysis
+  description: >-
+    This is the analysis set for promoters created with 500bp regions upstream
+    of the start codon. It uses the same passing replicates as the 2025_analysis_set. see R/scripts/quantify_regions_500bp_intergenic.R for details of how this was conducted.
+  dataset_type: annotated_features
+  metadata_fields: ["combined_id","regulator_locus_tag","regulator_symbol", "total_experiment_hops", "total_background_hops"]
+  data_files:
+  - split: train
+    path: annotated_feature_reprocess_start_codon_500bp_analysis.parquet
+  genome_resources:
+    region_sets:
+      start_codon_500bp:
+        path: https://huggingface.co/datasets/BrentLab/yeast_genome_resources/blob/main/start_codon_500bp_upstream_promoters.bed
+        join_column: target_locus_tag
+  dataset_info:
+    features:
+    - name: combined_id
+      dtype: string
+      description: >-
+        The genome map identifier of either a single passing, or multiple
+        passing replicates (hyphen-delimited) that were combined for the
+        2026 analysis set.
+      role: sample_id
+
+- config_name: annotated_feature_reprocess_intergenic_analysis
+  description: >-
+    This is the analysis set for promoters created with the full intergenic 
+    region upstream of a given target. It uses the same passing replicates as the 2025_analysis_set. see R/scripts/quantify_regions_500bp_intergenic.R for details of how this was conducted.
+  dataset_type: annotated_features
+  metadata_fields: ["combined_id","regulator_locus_tag","regulator_symbol", "total_experiment_hops", "total_background_hops"]
+  data_files:
+  - split: train
+    path: annotated_feature_reprocess_intergenic_analysis.parquet
+  genome_resources:
+    region_sets:
+      intergenic:
+        path: https://huggingface.co/datasets/BrentLab/yeast_genome_resources/blob/main/intergenic_regions_metadata_5_1.csv
+        join_column: ir_name
+  dataset_info:
+    features:
+    - name: combined_id
+      dtype: string
+      description: >-
+        The genome map identifier of either a single passing, or multiple
+        passing replicates (hyphen-delimited) that were combined for the
+        2026 analysis set.
+      role: sample_id
 ---
 # Calling Cards
 

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