Update README.md

README.md

@@ -131,75 +131,59 @@ This collects the ChEC-seq data from the following GEO series:
 - [GSE209631](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE209631)
 - [GSE222268](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE222268)
 
-The metadata for each is parsed out from the SraRunTable, or in the case of GSE222268, the NCBI series matrix file
-(the genotype isn't in the SraRunTable)
+The metadata for each is parsed out from the SraRunTable, or in the case of GSE222268,
+the NCBI series matrix file (the genotype isn't in the SraRunTable)
 
-The [Barkai lab](https://barkailab.wixsite.com/barkai) refers to this set as their binding compendium.
+The [Barkai lab](https://barkailab.wixsite.com/barkai) refers to this set as their
+binding compendium.
 
 The genotypes for GSE222268 are not clear enough to me currently to parse well.
 
-## Dataset Details
+This repo provides 4 datasets:
 
-`genome_map` stores the pileup of 5' end tags. See the Series and associated cited paper for details, but it is a
-standard processing pipeline to count 5' ends.  
+- **GSE178430_metadata**: Metadata for GSE178430.
+- **GSE209631_metadata**: ChEC-seq experiment metadata for transcription factor variant
+  studies.
+- **GSE222268_metadata**: General experiment metadata for genomic studies.
+- **genome_map**: Genomic coverage data with pileup counts at specific positions.
 
-The `<series_accession>_metadata.parquet` files store metadata. You may use the field `accession` to extract the corresponding
-data.
-
-See `scripts/` for more parsing details.
-
-## Data Structure
-
-### genome_map/
+## Usage
 
-This is a parquet dataset which is partitioned by Series and Accession
+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.
 
-| Field      | Description                                                    |
-|------------|----------------------------------------------------------------|
-| `seqnames` | Chromosome or sequence name (e.g., chrI, chrII, etc.)          |
-| `start`    | Start position of the genomic interval (1-based coordinates)   |
-| `end`      | End position of the genomic interval (1-based coordinates)     |
-| `pileup`   | Number of reads or signal intensity at this genomic position   |
+### `tfbpapi`
 
-### [GSE178430](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE179430) Metadata
+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.
 
-| Field                        | Description                                                                    |
-|------------------------------|--------------------------------------------------------------------------------|
-| `accession`                  | Sample accession identifier                                                    |
-| `regulator_locus_tag`        | Systematic gene name (ORF identifier) of the tagged transcription factor      |
-| `regulator_symbol`           | Standard gene symbol of the tagged transcription factor                       |
-| `strainid`                   | Strain identifier used in the experiment                                       |
-| `instrument`                 | Sequencing instrument used for data generation                                 |
-| `genotype`                   | Full genotype description of the experimental strain                           |
-| `dbd_donor_symbol`           | Gene symbol of the DNA-binding domain donor (for chimeric constructs)         |
-| `ortholog_donor`             | Ortholog donor information for cross-species constructs                       |
-| `paralog_deletion_symbol`    | Gene symbol of deleted paralog in the strain background                       |
-| `paralog_resistance_cassette`| Antibiotic resistance cassette used for paralog deletion                      |
+### huggingface_cli/duckdb
 
-### [GSE209631](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE209631) Metadata
+You can retrieves and displays the file paths for each configuration of
+the "BrentLab/barkai_compendium" dataset from Hugging Face Hub.
 
-| Field                 | Description                                                                    |
-|-----------------------|--------------------------------------------------------------------------------|
-| `accession`           | Sample accession identifier                                                    |
-| `regulator_locus_tag` | Systematic gene name (ORF identifier) of the tagged transcription factor      |
-| `regulator_symbol`    | Standard gene symbol of the tagged transcription factor                       |
-| `variant_type`        | Type of transcription factor variant tested in the experiment                  |
+```python
+from huggingface_hub import ModelCard
+from pprint import pprint
 
-### [GSE222268](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE222268) Metadata
+card = ModelCard.load("BrentLab/barkai_compendium", repo_type="dataset")
 
-| Field                 | Description                                                                    |
-|-----------------------|--------------------------------------------------------------------------------|
-| `title`               | Experiment title or sample description                                         |
-| `accession`           | GEO sample accession identifier                                                |
-| `extract_protocol_ch1`| Protocol used for sample extraction and preparation                            |
-| `description`         | Detailed description of the experimental sample or condition                   |
-| `instrument_model`    | Model of sequencing instrument used for data generation                        |
+# cast to dict
+card_dict = card.data.to_dict()
 
+# Get partition information
+dataset_paths_dict = {d.get("config_name"): d.get("data_files")[0].get("path") for d in card_dict.get("configs")}
 
-## Usage
+pprint(dataset_paths_dict)
+```
 
-The entire repository is large. It may be preferrable to only retrieve specific files or partitions. You can
-use the metadata files to choose which files to pull.
+The entire repository is large. It may be preferrable to only retrieve specific files or
+partitions. You canuse the metadata files to choose which files to pull.
 
 ```python
 from huggingface_hub import snapshot_download
@@ -210,11 +194,11 @@ import os
 repo_path = snapshot_download(
     repo_id="BrentLab/barkai_compendium",
     repo_type="dataset",
-    allow_patterns="_metadata.parquet"
+    allow_patterns="*metadata.parquet"
 )
 
 dataset_path = os.path.join(repo_path, "GSE178430_metadata.parquet")
-con = duckdb.connect()
+conn = duckdb.connect()
 meta_res = conn.execute("SELECT * FROM read_parquet(?) LIMIT 10", [dataset_path]).df()
 
 print(meta_res)
@@ -230,7 +214,7 @@ repo_path = snapshot_download(
     allow_patterns="genome_map/series=GSE179430/accession=GSM5417602/*parquet"  # Only the parquet data
 )
 
-# The rest works the same
+# Query the specific partition
 dataset_path = os.path.join(repo_path, "genome_map")
 result = conn.execute("SELECT * FROM read_parquet(?) LIMIT 10", 
                      [f"{dataset_path}/**/*.parquet"]).df()
@@ -238,4 +222,26 @@ result = conn.execute("SELECT * FROM read_parquet(?) LIMIT 10",
 print(result)
 ```
 
-**Dataset Author and Contact**: Chase Mateusiak [@cmatKhan](https://github.com/cmatkhan/)
+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:
+
+```python
+repo_id = "BrentLab/barkai_compendium"
+
+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
+)
+
+print(f"\n✓ Repository downloaded to: {repo_path}")
+
+# Construct path to the genome_map parquet file
+parquet_path = os.path.join(repo_path, "genome_map.parquet")
+print(f"✓ Parquet file at: {parquet_path}")
+```