updating readme, revising some of hte metdata, and removing the composite batch from annotated features

README.md

@@ -79,40 +79,6 @@ configs:
       dtype: string
       description: Experimental batch identifier for controlling batch effects
 
-- config_name: genome_map
-  description: Genome-wide calling cards insertion density data partitioned by batch
-  dataset_type: genome_map
-  data_files:
-  - split: train
-    path: genome_map/*/*.parquet
-  dataset_info:
-    features:
-    - name: id
-      dtype: string
-      description: Unique identifier for each genomic interval
-    - name: chr
-      dtype: string
-      description: Chromosome name (e.g., chrI, chrII, etc.)
-    - name: start
-      dtype: float64
-      description: Start position of genomic interval
-    - name: end
-      dtype: float64
-      description: End position of genomic interval
-    - name: depth
-      dtype: float64
-      description: Number of transposon insertion events (read depth) in this genomic interval
-    - name: strand
-      dtype: string
-      description: Strand information (+ or -) for the genomic interval
-    - name: batch
-      dtype: string
-      description: Experimental batch identifier
-    partitioning:
-      enabled: true
-      partition_by: ["batch"]
-      path_template: "genome_map/batch={batch}/*.parquet"
-
 - config_name: annotated_features_meta
   description: Metadata for annotated features datasets including regulator informatioand data quality indicators
   dataset_type: metadata
@@ -158,10 +124,136 @@ configs:
       dtype: string
       description: Unique identifier for the metadata record
 
+- config_name: annotated_features_combined
+  description: >-
+    Calling Cards replicate data combined at the qbed (genome map) level, with enrichment
+    and significance called via callingCardsTools. Partitioned by genome_map_id_set,
+    where each partition corresponds to a set of combined replicate genome maps for
+    a single regulator.
+  dataset_type: annotated_features
+  data_files:
+  - split: train
+    path: annotated_features_combined/*/*.parquet
+  dataset_info:
+    partitioning:
+      enabled: true
+      partition_by: ["genome_map_id_set"]
+      path_template: "annotated_features_combined/genome_map_id_set={genome_map_id_set}/*.parquet"
+    features:
+    - name: genome_map_id_set
+      dtype: string
+      description: >-
+        Hyphen-delimited set of genome map IDs corresponding to the combined replicates for this
+        regulator (partition key)
+    - name: target_locus_tag
+      dtype: string
+      description: Systematic gene identifier for the target gene
+      role: target_identifier
+    - name: target_symbol
+      dtype: string
+      description: Standard gene symbol for the target gene
+      role: target_identifier
+    - name: experiment_hops
+      dtype: float64
+      description: Number of transposon insertion events (hops) at target locus in the experimental sample
+      role: quantitative_measure
+    - name: background_hops
+      dtype: float64
+      description: Number of transposon insertion events (hops) at target locus in the background control
+      role: quantitative_measure
+    - name: background_total_hops
+      dtype: float64
+      description: Total number of background hops across all loci in the control sample
+      role: quantitative_measure
+    - name: experiment_total_hops
+      dtype: float64
+      description: Total number of experimental hops across all loci in the experimental sample
+      role: quantitative_measure
+    - name: callingcards_enrichment
+      dtype: float64
+      description: Enrichment score calculated as ratio of normalized experimental to background hops
+      role: quantitative_measure
+    - name: poisson_pval
+      dtype: float64
+      description: P-value from Poisson test for statistical significance of binding enrichment
+      role: quantitative_measure
+    - name: hypergeometric_pval
+      dtype: float64
+      description: P-value from hypergeometric test for statistical significance of binding enrichment
+      role: quantitative_measure
+
+- config_name: annotated_features_combined_meta
+  description: Sample-level metadata for combined Calling Cards experiments including regulator information, QC flags, and experimental conditions
+  dataset_type: metadata
+  applies_to: ["annotated_features_combined"]
+  data_files:
+  - split: train
+    path: annotated_features_combined_meta.parquet
+  dataset_info:
+    features:
+    - name: genome_map_id_set
+      dtype: string
+      description: Hyphen-delimited set of genome map IDs used as the partition key in annotated_features_combined
+    - name: pss_id
+      dtype: string
+      description: Passing sample set identifier grouping replicates used in this combined analysis
+    - name: binding_id
+      dtype: string
+      description: Unique identifier for this combined binding measurement record
+    - name: regulator_locus_tag
+      dtype: string
+      description: Systematic gene identifier for the transcription factor
+      role: regulator_identifier
+    - name: regulator_symbol
+      dtype: string
+      description: Standard gene symbol for the transcription factor
+      role: regulator_identifier
+    - name: batch
+      dtype: string
+      description: Experimental batch identifier for controlling batch effects
+    - name: condition
+      dtype: string
+      description: Experimental condition for this sample
+      role: experimental_condition
+
+- config_name: genome_map
+  description: Genome-wide calling cards insertion density data partitioned by batch
+  dataset_type: genome_map
+  data_files:
+  - split: train
+    path: genome_map/*/*.parquet
+  dataset_info:
+    features:
+    - name: id
+      dtype: string
+      description: Unique identifier for each genomic interval
+    - name: chr
+      dtype: string
+      description: Chromosome name (e.g., chrI, chrII, etc.)
+    - name: start
+      dtype: float64
+      description: Start position of genomic interval
+    - name: end
+      dtype: float64
+      description: End position of genomic interval
+    - name: depth
+      dtype: float64
+      description: Number of transposon insertion events (read depth) in this genomic interval
+    - name: strand
+      dtype: string
+      description: Strand information (+ or -) for the genomic interval
+    - name: batch
+      dtype: string
+      description: Experimental batch identifier
+    partitioning:
+      enabled: true
+      partition_by: ["batch"]
+      path_template: "genome_map/batch={batch}/*.parquet"
+
 - config_name: genome_map_meta
   description: Metadata for genome map datasets including regulator information and experimental details
   dataset_type: metadata
-  applies_to: ["genome_map"]
+  applies_to: ["genome_map", "annotated_features_orig_reprocess"]
   data_files:
   - split: train
     path: genome_map_meta.parquet
@@ -170,10 +262,9 @@ configs:
     - name: id
       dtype: string
       description: Unique identifier for the metadata record
-    - name: db_id
+    - name: binding_id
       dtype: string
-      description: current django managed database identifier for the dataset
-      role: experimental_condition
+      description: current django managed database identifier for the dataset to the 'binding' table
     - name: regulator_locus_tag
       dtype: string
       description: Systematic identifier for the regulatory factor
@@ -189,11 +280,134 @@ configs:
     - name: replicate
       dtype: int64
       description: Biological replicate number, within batch
-      role: experimental_condition
     - name: notes
       dtype: string
       description: Additional notes or comments about the experiment
-      role: experimental_condition
+    - name: condition
+          dtype:
+            class_label:
+              names: ["standard", "rapa", "starvation",
+                      "glu_1_gal_1", "del_MET28",
+                      "glu_1_gal_2", "del_FKH2",
+                      "del_TYE7"]
+          description: >-
+            Experimental condition of the sample, including standard growth, rapamycin treatment,
+            nutrient starvation, mixed carbon source conditions, and gene deletion strains
+          role: experimental_condition
+          definitions:
+            standard:
+              media:
+                name: synthetic_complete
+                carbon_source:
+                  - compound: D-glucose
+                    concentration_percent: 2
+            rapa:
+              perturbation_method:
+                type: chemical_treatment
+                compound: rapamycin
+                description: Rapamycin treatment to inhibit TORC1 signaling
+            starvation:
+              description: "Nutrient starvation condition - specific media composition not defined in source"
+            glu_1_gal_1:
+              media:
+                carbon_source:
+                  - compound: D-glucose
+                    concentration_percent: 1
+                  - compound: D-galactose
+                    concentration_percent: 1
+            glu_1_gal_2:
+              media:
+                carbon_source:
+                  - compound: D-glucose
+                    concentration_percent: 1
+                  - compound: D-galactose
+                    concentration_percent: 2
+            del_MET28:
+              genotype:
+                deletions:
+                  - gene: MET28
+                    description: MET28 deletion strain
+            del_FKH2:
+              genotype:
+                deletions:
+                  - gene: FKH2
+                    description: FKH2 deletion strain
+            del_TYE7:
+              genotype:
+                deletions:
+                  - gene: TYE7
+                    description: TYE7 deletion strain
+
+- config_name: annotated_features_orig_reprocess
+  description: >-
+    Calling Cards annotated features reprocessed from the original qbed genome maps
+    using scripts/quantify_regions.R. Each record corresponds to a single genome map
+    (replicate-level), where the id field links to genome_map_meta. Includes log-transformed
+    p-values and FDR-adjusted q-values not present in the original annotated_features_combined.
+  dataset_type: annotated_features
+  data_files:
+  - split: train
+    path: annotated_features_orig_reprocess/*/*.parquet
+  dataset_info:
+    features:
+    - name: id
+      dtype: int64
+      description: Genome map identifier linking to the genome_map and genome_map_meta dataset
+    - name: target_locus_tag
+      dtype: string
+      description: Systematic gene identifier for the target gene
+      role: target_identifier
+    - name: target_symbol
+      dtype: string
+      description: Standard gene symbol for the target gene
+      role: target_identifier
+    - name: experiment_hops
+      dtype: float64
+      description: Number of transposon insertion events (hops) at target locus in the experimental sample
+      role: quantitative_measure
+    - name: background_hops
+      dtype: float64
+      description: Number of transposon insertion events (hops) at target locus in the background control
+      role: quantitative_measure
+    - name: total_background_hops
+      dtype: float64
+      description: Total number of background hops across all loci in the control sample
+      role: quantitative_measure
+    - name: total_experiment_hops
+      dtype: float64
+      description: Total number of experimental hops across all loci in the experimental sample genomic (not mito) chromosomes
+      role: quantitative_measure
+    - name: callingcards_enrichment
+      dtype: float64
+      description: Enrichment score calculated as ratio of normalized experimental to background hops
+      role: quantitative_measure
+    - name: poisson_pval
+      dtype: float64
+      description: P-value from Poisson test for statistical significance of binding enrichment
+      role: quantitative_measure
+    - name: log_poisson_pval
+      dtype: float64
+      description: Log-transformed Poisson p-value. This has greater numeric resolution for significant loci
+      role: quantitative_measure
+    - name: poisson_qval
+      dtype: float64
+      description: FDR-adjusted q-value from Poisson test (multiple testing correction)
+      role: quantitative_measure
+    - name: hypergeometric_pval
+      dtype: float64
+      description: P-value from hypergeometric test for statistical significance of binding enrichment
+      role: quantitative_measure
+    - name: log_hypergeometric_pval
+      dtype: float64
+      description: Log-transformed hypergeometric p-value
+      role: quantitative_measure
+    - name: hypergeometric_qval
+      dtype: float64
+      description: FDR-adjusted q-value from hypergeometric test (multiple testing correction)
+      role: quantitative_measure
+    - name: batch
+      dtype: string
+      description: Experimental batch identifier for controlling batch effects (parition key)
 ---
 # Calling Cards
 
@@ -339,4 +553,4 @@ print(f"\n✓ Repository downloaded to: {repo_path}")
 
 # Construct path to the annotated_features_meta parquet file
 parquet_path = os.path.join(repo_path, "annotated_features_meta.parquet")
-print(f"✓ Parquet file at: {parquet_path}")
+print(f"✓ Parquet file at: {parquet_path}")

annotated_features/batch=composite/part-0.parquet

@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
-oid sha256:1e2c8e64e8686b346ae4e6d5f239990bda0c3c30ae51e021d33e88debf5e1b6a
-size 4926318

annotated_features_combined_meta.parquet

@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:e9d88e9b78b8658374c3ec068fa51e439ce86eefc56c2936bfb45cea8dfd8bd2
-size 5068
+oid sha256:1f58b2c09c3061d035b5d6d09f8efa10dd758465204650513ce2c4d29606faa1
+size 6401

annotated_features_meta.parquet

@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:e044dfe82b2b0ea4b67b60f3ea7acbcfad3410c9b8289a4d89a90a022c2d63a4
-size 27016
+oid sha256:b0805253b44b0bea473a19bfbd6c38fe3ded123154f728a1c092f40ee97e878c
+size 24549