Upload README.md with huggingface_hub

README.md

@@ -174,6 +174,36 @@ configs:
     - control_source
     - condition
     - regulator_locus_tag
+  experimental_conditions:
+    # Mahendrawada et al 2025: "30 °C culture"
+    temperature_celsius: 30
+    cultivation_method: unspecified
+    growth_phase_at_harvest:
+      # Mahendrawada et al 2025: "A600 of ~1.0"
+      od600: 1.0
+    media:
+      # Mahendrawada et al 2025: "synthetic complete (SC) media"
+      name: synthetic_complete
+      carbon_source: unspecified
+      nitrogen_source:
+        - compound: yeast_nitrogen_base
+          # Mahendrawada et al 2025: 1.7 g/L (without ammonium sulfate or amino acids (BD Difco))
+          concentration_percent: 0.17
+          specifications:
+            - without_ammonium_sulfate
+            - without_amino_acids
+        - compound: ammonium_sulfate
+          # Mahendrawada et al 2025: 5 g/L
+          concentration_percent: 0.5
+        - compound: amino_acid_dropout_mix
+          # Mahendrawada et al 2025: 0.6 g/L
+          concentration_percent: 0.06
+        - compound: adenine_sulfate
+          # Mahendrawada et al 2025: 40 μg/ml = 0.04 g/L
+          concentration_percent: 0.004
+        - compound: uracil
+          # Mahendrawada et al 2025: 2 μg/ml = 0.002 g/L
+          concentration_percent: 0.0002
   data_files:
   - split: train
     path: reprocess_diffcontrol_5prime.parquet
@@ -183,158 +213,8 @@ configs:
       dtype: string
       description: Source identifier for the control dataset (m2025 or h2021)
     - name: condition
-      dtype:
-        class_label:
-          names: ["standard",
-                  "30", "37",
-                  "SM", "WT", "WT_SM", 
-                  "admut", "admut_SM",
-                  "cAD", "cAD_SM",
-                  "dbdmut", "dbdmut_SM",
-                  "nAD", "nAD_SM",
-                  "ncAD", "ncAD_SM",
-                  "galactose", "raffinose"]
-      role: experimental_condition
-      description: Experimental condition. Standard is YPD (synthetic complete media).
-      definitions:
-        standard:
-          description: Baseline growth condition in synthetic complete media
-          growth_conditions:
-            media:
-              name: synthetic_complete
-              composition:
-                yeast_nitrogen_base_g_per_l: 1.7
-                yeast_nitrogen_base_specs:
-                  - without_amino_acids
-                  - without_ammonium_sulfate
-                ammonium_sulfate_g_per_l: 5
-                adenine_sulfate_ug_per_ml: 40
-                amino_acid_dropout_mix_g_per_l: 0.6
-                amino_acid_dropout_mix_composition:
-                  - compound: Tyrosine
-                    g_per_l: 2
-                  - compound: Serine
-                    g_per_l: 2
-                  - compound: Valine
-                    g_per_l: 2
-                  - compound: Isoleucine
-                    g_per_l: 2
-                  - compound: Phenylalanine
-                    g_per_l: 2
-                  - compound: Aspartic_acid
-                    g_per_l: 2
-                  - compound: Proline
-                    g_per_l: 2
-                  - compound: Arginine
-                    g_per_l: 4
-                  - compound: Threonine
-                    g_per_l: 4
-                uracil_ug_per_ml: 2
-                other_amino_acids_percent: 0.01
-        "30":
-          description: No heat shock control at 30°C
-          growth_conditions:
-            temperature_celsius: 30
-            duration_minutes: 10
-        "37":
-          description: Heat shock condition at elevated temperature
-          growth_conditions:
-            temperature_celsius: 37
-            duration_minutes: 10
-        SM:
-          description: Amino acid starvation stress induced by sulfometuron methyl
-          growth_conditions:
-            media:
-              name: synthetic_complete_minus_isoleucine_valine
-            chemical_stress:
-              agent: sulfometuron_methyl
-              concentration_ug_per_ml: 0.5
-              duration_minutes: 60
-        WT:
-          description: Wild-type negative control to distinguish specific TF effects from non-specific IAA/DMSO treatment effects
-          strain_type: wildtype
-        WT_SM:
-          description: Wild-type strain treated with sulfometuron methyl to induce amino acid starvation
-          strain_type: wildtype
-          chemical_stress:
-            agent: sulfometuron_methyl
-            concentration_ug_per_ml: 0.5
-            duration_minutes: 60
-        admut:
-          description: Gcn4 activation domain mutant with inactivated activation domains but intact DNA-binding domain
-          strain_type: gcn4_mutant
-          mutation_type: activation_domain_deleted
-        admut_SM:
-          description: Gcn4 activation domain mutant treated with sulfometuron methyl
-          strain_type: gcn4_mutant
-          mutation_type: activation_domain_deleted
-          chemical_stress:
-            agent: sulfometuron_methyl
-            concentration_ug_per_ml: 0.5
-            duration_minutes: 60
-        cAD:
-          description: Gcn4 central activation domain inactivated by missense mutations
-          strain_type: gcn4_mutant
-          mutation_type: central_activation_domain_inactivated
-        cAD_SM:
-          description: Gcn4 central activation domain mutant treated with sulfometuron methyl
-          strain_type: gcn4_mutant
-          mutation_type: central_activation_domain_inactivated
-          chemical_stress:
-            agent: sulfometuron_methyl
-            concentration_ug_per_ml: 0.5
-            duration_minutes: 60
-        dbdmut:
-          description: Gcn4 DNA-binding domain mutant with triple mutation to inhibit specific DNA binding
-          strain_type: gcn4_mutant
-          mutation_type: dna_binding_domain_inactivated
-        dbdmut_SM:
-          description: Gcn4 DNA-binding domain mutant treated with sulfometuron methyl
-          strain_type: gcn4_mutant
-          mutation_type: dna_binding_domain_inactivated
-          chemical_stress:
-            agent: sulfometuron_methyl
-            concentration_ug_per_ml: 0.5
-            duration_minutes: 60
-        nAD:
-          description: Gcn4 N-terminal activation domain inactivated by missense mutations
-          strain_type: gcn4_mutant
-          mutation_type: n_terminal_activation_domain_inactivated
-        nAD_SM:
-          description: Gcn4 N-terminal activation domain mutant treated with sulfometuron methyl
-          strain_type: gcn4_mutant
-          mutation_type: n_terminal_activation_domain_inactivated
-          chemical_stress:
-            agent: sulfometuron_methyl
-            concentration_ug_per_ml: 0.5
-            duration_minutes: 60
-        ncAD:
-          description: Gcn4 mutant with both N-terminal and central activation domains inactivated
-          strain_type: gcn4_mutant
-          mutation_type: n_terminal_and_central_activation_domains_inactivated
-        ncAD_SM:
-          description: Gcn4 N-terminal and central activation domain double mutant treated with sulfometuron methyl
-          strain_type: gcn4_mutant
-          mutation_type: n_terminal_and_central_activation_domains_inactivated
-          chemical_stress:
-            agent: sulfometuron_methyl
-            concentration_ug_per_ml: 0.5
-            duration_minutes: 60
-        galactose:
-          description: Galactose induction condition for Gal4 transcription factor activation
-          growth_conditions:
-            induction:
-              inducer: D-galactose
-              concentration_percent: 2
-              duration_hours: 2
-        raffinose:
-          description: Non-inducing baseline growth medium for Gal4 experiments
-          growth_conditions:
-            media:
-              name: yeast_extract_peptone
-              carbon_source:
-                compound: D-raffinose
-                concentration_percent: 2
+      dtype: string
+      description: Experimental condition. 'standard' is YPD.
     - name: regulator_locus_tag
       dtype: string
       description: Systematic gene name (ORF identifier) of the transcription factor
@@ -355,15 +235,12 @@ configs:
       description: Strand orientation (+ or -) of the promoter/target
     - name: input_vs_target_log2_fold_change
       dtype: float64
-      role: quantitative_measure
       description: Log2 fold change of TF-tagged sample vs control (from DESeq2)
     - name: input_vs_target_p_value
       dtype: float64
-      role: quantitative_measure
       description: P-value for differential enrichment (from DESeq2)
     - name: input_vs_target_adj_p_value
       dtype: float64
-      role: quantitative_measure
       description: Adjusted p-value (FDR-corrected) for differential enrichment (from DESeq2)
 
 - config_name: rna_seq
@@ -407,52 +284,84 @@ configs:
 
 This data is taken from the Supplement of
 
-[Mahendrawada, L., Warfield, L., Donczew, R. et al. Low overlap of transcription factor
-DNA binding and regulatory targets. Nature 642, 796–804 (2025).
-https://doi.org/10.1038/s41586-025-08916-0](https://doi.org/10.1038/s41586-025-08916-0)
+[Mahendrawada, L., Warfield, L., Donczew, R. et al. Low overlap of transcription factor DNA binding and regulatory targets. Nature 642, 796–804 (2025). https://doi.org/10.1038/s41586-025-08916-0](https://doi.org/10.1038/s41586-025-08916-0)
 
-Please note that all column descriptions, except for those containing "locus_tag" and
-"symbol", are copy/pasted directly from the supplement or methods section of this paper.
+Please note that all column descriptions, except for those containing "locus_tag" and "symbol", are copy/pasted directly from the supplement or
+methods section of this paper.
 
-This repo provides 5 datasets:
+## Dataset Details
 
-- **chec_mahendrawada_2025**: ChEC-seq transcription factor binding data with peak
-  scores (original authors' processed data).
-- **chec_reprocess_2025**: ChEC-seq transcription factor binding data reprocessed with
-  updated peak calling methodology.
-- **features_mahendrawada_2025**: Comprehensive genomic features and regulatory
-  characteristics for yeast genes.
-- **rnaseq_mahendrawada_2025**: Nascent RNA-seq differential expression data following
-  transcription factor depletion using 4TU metabolic labeling.
-- **reprocess_diffcontrol_5prime**: Comparing two different sets of control replicates,
-  m2025 from the Mahendrawada 2025 paper, and h2021 from a previous paper from the Hahn
-  lab.
+This repo provides three datasets:
 
-## Usage
+- **genomic_features**: These are the genomic features provided in Supplemental Table 2
+- **chec_seq**: binding location data provided in Supplemental Table 3. the `peak_score` is defined to be the ChEC signal around peak center'
+  (sum of ChEC signal from -150 to +150 bp from peak summit) normalized to Drosophila spike-in control. How these scores are assigned to features
+  isn't well described in either the supplement or Methods section, but it is reasonable to believe that it is done with HOMER.
+- **rna_seq**: Nascent RNA-seq differential expression data following transcription factor depletion using 4TU metabolic labeling filtered for
+  significantly affected genes (DESeq2, padj <0.1, FC >= 1.3)
+
+## Data Structure
+
+This dataset provides the following three parquet files
 
-The python package `tfbpapi` provides an interface to this data which eases
-examining the datasets, field definitions and other operations. You may also 
-download the parquet datasets directly from hugging face by clicking on
-"Files and Versions", or by using the huggingface_cli and duckdb directly.
-In both cases, this provides a method of retrieving dataset and field definitions.
+### ChEC-seq
 
-### `tfbpapi`
+| Field                 | Description                                                                                                                                |
+|-----------------------|--------------------------------------------------------------------------------------------------------------------------------------------|
+| `regulator_locus_tag` | Systematic gene name (ORF identifier) of the transcription factor                                                                         |
+| `regulator_symbol`    | Standard gene symbol of the transcription factor                                                                                           |
+| `target_locus_tag`    | Systematic gene name (ORF identifier) of the target gene                                                                                  |
+| `target_symbol`       | Standard gene symbol of the target gene                                                                                                    |
+| `peak_score`          | ChEC signal around peak center (sum of ChEC signal from -150 to +150 bp from peak summit) normalized to Drosophila spike-in control     |
 
-After [installing
-tfbpapi](https://github.com/BrentLab/tfbpapi/?tab=readme-ov-file#installation), you can
-adapt this [tutorial](https://brentlab.github.io/tfbpapi/tutorials/hfqueryapi_tutorial/)
-in order to explore the contents of this repository.
+### RNA-seq
 
-### huggingface_cli/duckdb
+| Field                 | Description                                                                                                                                |
+|-----------------------|--------------------------------------------------------------------------------------------------------------------------------------------|
+| `regulator_locus_tag` | Systematic gene name (ORF identifier) of the depleted transcription factor                                                                |
+| `regulator_symbol`    | Standard gene symbol of the depleted transcription factor                                                                                 |
+| `target_locus_tag`    | Systematic gene name (ORF identifier) of the differentially expressed target gene                                                         |
+| `target_symbol`       | Standard gene symbol of the differentially expressed target gene                                                                           |
+| `log2fc`              | Log2 fold change (IAA/DMSO) for significantly affected genes (DESeq2, padj <0.1, FC >= 1.3)                                             |
+
+### Features
+
+| Field                    | Description                                                                                                                                |
+|--------------------------|--------------------------------------------------------------------------------------------------------------------------------------------|
+| `gene_id`                | Systematic gene name (ORF identifier) from SGD (https://yeastgenome.org/)                                                                |
+| `SGD_id`                 | Unique identifier for each gene from SGD (https://yeastgenome.org/)                                                                      |
+| `gene_name`              | Common name of each gene                                                                                                                   |
+| `chr`                    | Chromosome number corresponding to gene                                                                                                    |
+| `strand`                 | Strandedness of the gene (+ or -)                                                                                                         |
+| `start`                  | Start position of the ORF                                                                                                                  |
+| `end`                    | End position of the ORF                                                                                                                    |
+| `TSS`                    | Transcription start site based on Park et al., 2014 (doi:10.1093/nar/gkt1366)                                                           |
+| `TATA_category`          | TATA box classification from Donczew et al., 2020 using consensus TATAWAW (doi:10.7554/eLife.50109)                                     |
+| `expression`             | Average signal normalized to gene length from Donczew et al., 2020 (doi:10.7554/eLife.50109)                                           |
+| `+1 nucleosome`          | Position of +1 nucleosome from Chereji et al., 2018 (doi:10.1186/S13059-018-1398-0)                                                     |
+| `-1 nucleosome`          | Position of -1 nucleosome from Chereji et al., 2018 (doi:10.1186/S13059-018-1398-0)                                                     |
+| `NDR Center`             | Center of nucleosome depleted region from Chereji et al., 2018 (doi:10.1186/S13059-018-1398-0)                                         |
+| `NDR Width`              | Width of nucleosome depletion region from Chereji et al., 2018 (doi:10.1186/S13059-018-1398-0)                                         |
+| `tail-dependence`        | Tail classification based on Mediator tail dependence from Warfield L, Donczew R et al., 2022 (doi:10.1016/j.molcel.2022.09.016)      |
+| `coactivator`            | Coactivator classification based on TFIID and/or SAGA dependence from Donczew et al., 2020 (doi:10.7554/eLife.50109)                   |
+| `LCID_center`            | Genes near boundaries of chromosomal interacting domains from Swygert et al., 2020 (doi:10.1016/j.molcel.2018.11.020)                  |
+| `Rossi_classes`          | Promoter classes from Rossi et al., 2021 (doi:10.1038/s41586-021-03314-8)                                                               |
+| `RP_category`            | Ribosomal protein (RP) and ribosomal biogenesis (RiBi) gene classification from Zencir et al., 2020 (doi:10.1093/NAR/GKAA852)          |
+| `binding_cluster`        | Clusters from unsupervised K-means clustering using binary binding data of 178 transcription factors                                     |
+| `list_of_TFS_bound`      | List of transcription factors bound to gene promoter (-400 to +200 bp from TSS; Homer peak calling)                                     |
+| `number_of_bound_tfs`    | Number of transcription factors bound to each promoter                                                                                     |
+| `locus_tag`              | Systematic gene identifier from yeast_genome_resources dataset                                                                             |
+| `symbol`                 | Standard gene symbol from yeast_genome_resources dataset                                                                                   |
+
+## Usage
 
-You can retrieves and displays the file paths for each configuration of
-the "BrentLab/mahendrawada_2025" dataset from Hugging Face Hub.
+There are three parquet files in this repo. This is a way of getting that information programmatically
 
 ```python
 from huggingface_hub import ModelCard
 from pprint import pprint
 
-card = ModelCard.load("BrentLab/mahendrawada_2025", repo_type="dataset")
+card = ModelCard.load("BrentLab/hughes_2006", repo_type="dataset")
 
 # cast to dict
 card_dict = card.data.to_dict()
@@ -463,29 +372,45 @@ dataset_paths_dict = {d.get("config_name"): d.get("data_files")[0].get("path") f
 pprint(dataset_paths_dict)
 ```
 
-If you wish to pull the entire repo, due to its size you may need to use an
-[authentication token](https://huggingface.co/docs/hub/en/security-tokens).
-If you do not have one, try omitting the token related code below and see if
-it works. Else, create a token and provide it like so:
+With the result
+
+```raw
+{'chec_seq': 'chec_mahendrawada_2025.parquet',
+ 'genomic_features': 'features_mahendrawada_2025.parquet',
+ 'rna_seq': 'rnaseq_mahendrawada_2025.parquet'}
+```
+
+I recommend using `huggingface_hub.snapshot_download` to pull the repository. After that, use your favorite
+method of interacting with `parquet` files (eg duckDB, but you could use dplyr in R or pandas, too).
 
 ```python
 from huggingface_hub import snapshot_download
+import duckdb
 import os
 
 repo_id = "BrentLab/mahendrawada_2025"
 
-hf_token = os.getenv("HF_TOKEN")
-
 # Download entire repo to local directory
 repo_path = snapshot_download(
     repo_id=repo_id,
-    repo_type="dataset",
-    token=hf_token
+    repo_type="dataset"
 )
 
-print(f"\n✓ Repository downloaded to: {repo_path}")
+print(f"Repository downloaded to: {repo_path}")
 
-# Construct path to the features_mahendrawada_2025.parquet parquet file
-parquet_path = os.path.join(repo_path, "features_mahendrawada_2025.parquet")
-print(f"✓ Parquet file at: {parquet_path}")
-```
+# Construct path to the checseq parquet file
+parquet_path = os.path.join(repo_path, "chec_mahendrawada_2025.parquet")
+print(f"Parquet file at: {parquet_path}")
+
+# Connect to DuckDB and query the parquet file
+conn = duckdb.connect()
+
+query = """
+SELECT * 
+FROM read_parquet(?)
+WHERE regulator_symbol = 'CST6'
+"""
+
+result = conn.execute(query, [parquet_path]).fetchall()
+print(f"Found {len(result)} rows for CST6")
+```