adding mindel promoter data and updating readme

README.md

@@ -36,29 +36,201 @@ experimental_conditions:
     duration_minutes: 6
     pre_induction_temperature_celsius: 25
     method: equal_volume_medium_transfer
+
 doi: https://doi.org/10.1038/s41586-021-03314-8
 citation: Rossi, MJ, Kuntala, PK, Lai, WKM, Yamada, N, Badjatia, N, Mittal, et al. 2021. A high-resolution protein architecture of the budding yeast genome. Nature.
+
+features:
+- applies_to:
+  - rossi_2021_metadata_replicate
+  - rossi_2021_metadata_sample
+  fields:
+  - name: treatment
+    dtype: string
+    description: >-
+      Experimental treatment applied prior to ChIP-exo. The majority of
+      samples are untreated; a subset of SAGA-associated factors received a
+      brief heat shock (equal volume of 37°C medium mixed into a 25°C culture,
+      6 min at 37°C).
+    role: experimental_condition
+  - name: growth_media
+    dtype: string
+    description: >-
+      Growth medium used in the experiment, as reported in yeastepigenome.org
+      sample metadata. The majority of samples used YPD (rich medium).
+    role: experimental_condition
+
+- applies_to:
+  - rossi_2021_metadata_replicate
+  - rossi_2021_metadata_sample
+  - rossi_2021_af_replicates
+  - rossi_2021_af_combined
+  - rossi_2021_af_replicates_mindel
+  - rossi_2021_af_combined_mindel
+  fields:
+  - name: regulator_locus_tag
+    dtype: string
+    description: Systematic gene name (ORF identifier) of the transcription factor
+  - name: regulator_symbol
+    dtype: string
+    description: Standard gene symbol of the transcription factor
+
+- applies_to:
+  - rossi_2021_af_replicates
+  - rossi_2021_af_combined
+  - rossi_2021_af_replicates_mindel
+  - rossi_2021_af_combined_mindel
+  fields:
+  - 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: seqnames
+    dtype: string
+    description: Chromosome identifier (e.g., chrI, chrII, chrXVI)
+  - name: start
+    dtype: int64
+    description: Promoter region start position (1-based coordinate)
+  - name: end
+    dtype: int64
+    description: Promoter region end position (1-based, inclusive)
+  - name: background_counts
+    dtype: int64
+    description: Read counts in the background/control sample for this peak region
+    role: quantitative_measure
+  - name: experiment_counts
+    dtype: int64
+    description: Read counts in the ChIP-exo experiment sample for this peak region
+    role: quantitative_measure
+  - name: total_background_counts
+    dtype: int64
+    description: Total read counts across the entire genome in the background sample
+    role: quantitative_measure
+  - name: total_experiment_counts
+    dtype: int64
+    description: Total read counts across the entire genome in the experiment sample
+    role: quantitative_measure
+  - name: enrichment
+    dtype: float64
+    description: Enrichment score for the binding peak
+    role: quantitative_measure
+  - name: poisson_pval
+    dtype: float64
+    description: P-value from Poisson distribution test for peak significance
+    role: quantitative_measure
+  - name: log_poisson_pval
+    dtype: float64
+    description: Log-transformed Poisson p-value
+    role: quantitative_measure
+  - name: hypergeometric_pval
+    dtype: float64
+    description: P-value from hypergeometric distribution test for peak significance
+    role: quantitative_measure
+  - name: log_hypergeometric_pval
+    dtype: float64
+    description: Log-transformed hypergeometric p-value
+    role: quantitative_measure
+  - name: poisson_qval
+    dtype: float64
+    description: FDR-adjusted q-value from Poisson test (multiple testing correction)
+    role: quantitative_measure
+  - name: hypergeometric_qval
+    dtype: float64
+    description: FDR-adjusted q-value from hypergeometric test (multiple testing correction)
+    role: quantitative_measure
+
+- applies_to:
+  - rossi_2021_af_replicates_mindel
+  - rossi_2021_af_combined_mindel
+  fields:
+  - name: width
+    dtype: int64
+    description: Width of the promoter region
+  - name: strand
+    dtype: string
+    description: Genomic strand of the promoter region (+ or -)
+  - name: mindel_name
+    dtype: string
+    description: Name of the promoter region as defined in the Mindel promoters
+  - name: promoter_sequence
+    dtype: string
+    description: Nucleotide sequence of the promoter region
+  - name: in_mahendrawada_features
+    dtype: bool
+    description: >-
+      TRUE if the promoter region was used in Mahendrawada 2025. Note that this
+      is equivalent to protein coding non dubious ORF
+  - name: promoter_exact_aligns
+    dtype: int64
+    description: >-
+      this is a feature from the Mindel data that I have not documented. It is a TODO.
+
 configs:
-- config_name: metadata
+- config_name: rossi_2021_metadata_replicate
   description: Metadata describing the tagged regulator in each experiment
   dataset_type: metadata
+  applies_to: ["genome_map"]
   data_files:
   - split: train
     path: rossi_2021_metadata.parquet
   dataset_info:
     features:
-    - name: regulator_locus_tag
-      dtype: string
-      description: Systematic gene name (ORF identifier) of the transcription factor
-    - name: regulator_symbol
-      dtype: string
-      description: Standard gene symbol of the transcription factor
-    - name: run_accession
+    - name: accession
       dtype: string
       description: GEO run accession identifier for the sample
+      role: sample_id
+    - name: sample_id
+      dtype: int64 
+      description: Unique identifier for the biological replicate. Note this is the
+      same as the sample_id in rossi_2021_metadata_sample
     - name: yeastepigenome_id
+      dtype: float64 
+      description: Sample identifier used by yeastepigenome.org
+    - name: antibody
+      dtype: string
+      description: Antibody used for ChIP-exo immunoprecipitation
+
+- config_name: rossi_2021_metadata_sample
+  description: Sample-level metadata for combined ChIP-exo experiments including experimental conditions
+  dataset_type: metadata
+  applies_to: ["rossi_2021_af_combined"]
+  data_files:
+  - split: train
+    path: rossi_2021_metadata_sample.parquet
+  dataset_info:
+    features:
+    - name: sample_id
+      dtype: int64
+      description: Unique identifier combining regulator and replicates
+    - name: multi_antibody
+      dtype: bool
+      description: TRUE if the set of replicates includes more than one type of antibody
+    - name: antibody
+      dtype: string
+      description: >-
+        Antibody used for ChIP-exo immunoprecipitation. If multi_antibody is TRUE,
+        then the antibodies in the set are separated by `;`
+
+- config_name: genome_map_control_meta
+  description: Sample accession metadata for ChIP-exo input/control coverage tracks
+  dataset_type: metadata
+  applies_to: ["genome_map_control"]
+  data_files:
+  - split: train
+    path: genome_map_control_meta.parquet
+  dataset_info:
+    features:
+    - name: accession
       dtype: string
+      description: SRA run accession identifier for the control sample
+    - name: yeastepigenome_id
+      dtype: float64
       description: Sample identifier used by yeastepigenome.org
+
 - config_name: genome_map
   description: "ChIP-exo 5' tag coverage data partitioned by sample accession"
   dataset_type: genome_map
@@ -67,6 +239,9 @@ configs:
     path: genome_map/*/*.parquet
   dataset_info:
     features:
+    - name: accession
+      dtype: string
+      description: GEO run accession identifier for the sample (partitioning column)
     - name: chr
       dtype: string
       description: Chromosome name (e.g., chrI, chrII, etc.)
@@ -77,259 +252,104 @@ configs:
       dtype: int32
       description: "Depth of coverage (number of 5' tags) at this genomic position"
 
-- config_name: rossi_2021_metadata
-  description: Replicate-level metadata for ChIP-exo experiments including experimental conditions and sample information
-  dataset_type: metadata
-  applies_to: ["rossi_2021_af_replicates"]
+- config_name: genome_map_control
+  description: "ChIP-exo 5' tag coverage data for input/control samples, partitioned by sample accession"
+  dataset_type: genome_map
   data_files:
   - split: train
-    path: rossi_2021_metadata.parquet
+    path: genome_map_control/*/*.parquet
   dataset_info:
     features:
-    - 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: run_accession
-      dtype: string
-      description: SRA run accession identifier for this biological replicate
-    - name: yeastepigenome_id
+    - name: accession
       dtype: string
-      description: Identifier from the Yeast Epigenome Project
-    - name: treatment
-      dtype: string
-      description: >-
-        Experimental treatment applied prior to ChIP-exo. The majority of
-        samples are untreated; a subset of SAGA-associated factors received a
-        brief heat shock (equal volume of 37°C medium mixed into a 25°C culture,
-        6 min at 37°C).
-      role: experimental_condition
-    - name: growth_media
-      dtype: string
-      description: >-
-        Growth medium used in the experiment, as reported in yeastepigenome.org
-        sample metadata. The majority of samples used YPD (rich medium).
-      role: experimental_condition
-    - name: antibody
-      dtype: string
-      description: Antibody used for ChIP-exo immunoprecipitation
-    - name: sample_id
+      description: GEO run accession identifier for the sample (partitioning column)
+    - name: chr
       dtype: string
-      description: Unique identifier for the biological replicate
+      description: Chromosome name (e.g., chrI, chrII, etc.)
+    - name: pos
+      dtype: int32
+      description: "Genomic position of the 5' tag"
+    - name: pileup
+      dtype: int32
+      description: "Depth of coverage (number of 5' tags) at this genomic position"
 
-- config_name: rossi_2021_metadata_sample
-  description: Sample-level metadata for combined ChIP-exo experiments including experimental conditions
-  dataset_type: metadata
-  applies_to: ["rossi_2021_af_combined"]
+- config_name: rossi_2021_af_replicates
+  description: ChIP-exo annotated features at biological replicate level with binding peaks and statistical significance metrics
+  dataset_type: annotated_features
+  genome_resources:
+    region_sets:
+      Kang:
+        path: https://huggingface.co/datasets/BrentLab/yeast_genome_resources/blob/main/yiming_promoters.bed
+        join_column: target_locus_tag
   data_files:
   - split: train
-    path: rossi_2021_metadata_sample.parquet
+    path: rossi_2021_af_replicates.parquet
   dataset_info:
     features:
-    - 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: treatment
-      dtype: string
-      description: >-
-        Experimental treatment applied prior to ChIP-exo. The majority of
-        samples are untreated; a subset of SAGA-associated factors received a
-        brief heat shock (equal volume of 37°C medium mixed into a 25°C culture,
-        6 min at 37°C).
-      role: experimental_condition
-    - name: growth_media
-      dtype: string
-      description: >-
-        Growth medium used in the experiment, as reported in yeastepigenome.org
-        sample metadata. The majority of samples used YPD (rich medium).
-      role: experimental_condition
-    - name: multi_antibody
-      dtype: bool
-      description: TRUE if the set of replicates includes more than one type of antibody
-    - name: antibody
-      dtype: string
-      description: >-
-        Antibody used for ChIP-exo immunoprecipitation. If multi_antibody is TRUE,
-        then the antibodies in the set are separated by `;`
     - name: sample_id
+      dtype: int64
+      description: Unique identifier for the biological replicate
+      role: sample_id
+    - name: run_accession
       dtype: string
-      description: Unique identifier combining regulator and replicates
+      description: SRA run accession identifier for this biological replicate
 
-- config_name: rossi_2021_af_replicates
+- config_name: rossi_2021_af_replicates_mindel
   description: ChIP-exo annotated features at biological replicate level with binding peaks and statistical significance metrics
   dataset_type: annotated_features
+  genome_resources:
+    region_sets:
+      Mindel:
+        path: https://huggingface.co/datasets/BrentLab/yeast_genome_resources/blob/main/mindel_promoters.csv.gz
+        join_column: target_locus_tag
   data_files:
   - split: train
-    path: rossi_2021_af_replicates.parquet
+    path: rossi_2021_af_replicates_mindel.parquet
   dataset_info:
     features:
     - name: sample_id
-      dtype: string
+      dtype: int64
       description: Unique identifier for the biological replicate
       role: sample_id
     - name: run_accession
       dtype: string
       description: SRA run accession identifier for this biological replicate
-    - 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: 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: seqnames
-      dtype: string
-      description: Chromosome identifier (e.g., chrI, chrII, chrXVI)
-    - name: start
-      dtype: int64
-      description: Promoter region start position (1-based coordinate)
-    - name: end
-      dtype: int64
-      description: Promoter region end position (1-based, inclusive)
-    - name: background_counts
-      dtype: int64
-      description: Read counts in the background/control sample for this peak region
-      role: quantitative_measure
-    - name: experiment_counts
-      dtype: int64
-      description: Read counts in the ChIP-exo experiment sample for this peak region
-      role: quantitative_measure
-    - name: total_background_counts
-      dtype: int64
-      description: Total read counts across the entire genome in the background sample
-      role: quantitative_measure
-    - name: total_experiment_counts
-      dtype: int64
-      description: Total read counts across the entire genome in the experiment sample
-      role: quantitative_measure
-    - name: enrichment
-      dtype: float64
-      description: Enrichment score for the binding peak
-      role: quantitative_measure
-    - name: poisson_pval
-      dtype: float64
-      description: P-value from Poisson distribution test for peak significance
-      role: quantitative_measure
-    - name: log_poisson_pval
-      dtype: float64
-      description: Log-transformed Poisson p-value
-      role: quantitative_measure
-    - name: hypergeometric_pval
-      dtype: float64
-      description: P-value from hypergeometric distribution test for peak significance
-      role: quantitative_measure
-    - name: log_hypergeometric_pval
-      dtype: float64
-      description: Log-transformed hypergeometric p-value
-      role: quantitative_measure
-    - name: poisson_qval
-      dtype: float64
-      description: FDR-adjusted q-value from Poisson test (multiple testing correction)
-      role: quantitative_measure
-    - name: hypergeometric_qval
-      dtype: float64
-      description: FDR-adjusted q-value from hypergeometric test (multiple testing correction)
-      role: quantitative_measure
 
 - config_name: rossi_2021_af_combined
   description: Combined ChIP-exo annotated features with binding peaks and statistical significance metrics aggregated across biological replicates
   dataset_type: annotated_features
+  genome_resources:
+    region_sets:
+      Kang:
+        path: https://huggingface.co/datasets/BrentLab/yeast_genome_resources/blob/main/yiming_promoters.bed
+        join_column: target_locus_tag
   data_files:
   - split: train
     path: rossi_2021_af_combined.parquet
   dataset_info:
     features:
     - name: sample_id
-      dtype: string
+      dtype: int64
       description: Unique identifier combining regulator and replicates
       role: sample_id
-    - 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: 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: seqnames
-      dtype: string
-      description: Chromosome identifier (e.g., chrI, chrII, chrXVI)
-    - name: start
-      dtype: int64
-      description: Promoter region start position (1-based coordinate)
-    - name: end
-      dtype: int64
-      description: Promoter region end position (1-based, inclusive)
-    - name: background_counts
-      dtype: int64
-      description: Combined read counts in the background/control sample for this peak region
-      role: quantitative_measure
-    - name: experiment_counts
-      dtype: int64
-      description: Combined read counts in the ChIP-exo experiment sample for this peak region
-      role: quantitative_measure
-    - name: total_background_counts
-      dtype: int64
-      description: Total read counts across the entire genome in the combined background sample
-      role: quantitative_measure
-    - name: total_experiment_counts
+
+- config_name: rossi_2021_af_combined_mindel
+  description: Combined ChIP-exo annotated features with binding peaks and statistical significance metrics aggregated across biological replicates
+  dataset_type: annotated_features
+  genome_resources:
+    region_sets:
+      Mindel:
+        path: https://huggingface.co/datasets/BrentLab/yeast_genome_resources/blob/main/mindel_promoters.csv.gz
+        join_column: target_locus_tag
+  data_files:
+  - split: train
+    path: rossi_2021_af_combined_mindel.parquet
+  dataset_info:
+    features:
+    - name: sample_id
       dtype: int64
-      description: Total read counts across the entire genome in the combined experiment sample
-      role: quantitative_measure
-    - name: enrichment
-      dtype: float64
-      description: Enrichment score for the binding peak calculated from combined replicates
-      role: quantitative_measure
-    - name: poisson_pval
-      dtype: float64
-      description: P-value from Poisson distribution test for peak significance
-      role: quantitative_measure
-    - name: log_poisson_pval
-      dtype: float64
-      description: Log-transformed Poisson p-value
-      role: quantitative_measure
-    - name: hypergeometric_pval
-      dtype: float64
-      description: P-value from hypergeometric distribution test for peak significance
-      role: quantitative_measure
-    - name: log_hypergeometric_pval
-      dtype: float64
-      description: Log-transformed hypergeometric p-value
-      role: quantitative_measure
-    - name: poisson_qval
-      dtype: float64
-      description: FDR-adjusted q-value from Poisson test (multiple testing correction)
-      role: quantitative_measure
-    - name: hypergeometric_qval
-      dtype: float64
-      description: FDR-adjusted q-value from hypergeometric test (multiple testing correction)
-      role: quantitative_measure
+      description: Unique identifier combining regulator and replicates
+      role: sample_id
 ---
 # Rossi 2021
 
@@ -338,99 +358,71 @@ This work was published in
 
 [Rossi MJ, Kuntala PK, Lai WKM, Yamada N, Badjatia N, Mittal C, Kuzu G, Bocklund K, Farrell NP, Blanda TR, Mairose JD, Basting AV, Mistretta KS, Rocco DJ, Perkinson ES, Kellogg GD, Mahony S, Pugh BF. A high-resolution protein architecture of the budding yeast genome. Nature. 2021 Apr;592(7853):309-314. doi: 10.1038/s41586-021-03314-8. Epub 2021 Mar 10. PMID: 33692541; PMCID: PMC8035251.](https://doi.org/10.1038/s41586-021-03314-8)
 
-## Usage
-
-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.
-
-### `tfbpapi`
+## Accessing Data
 
-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.
+The examples below require
+[labretriever](https://github.com/cmatKhan/labretriever#installation)
+(`pip install labretriever`) and/or the
+[HuggingFace Hub client](https://huggingface.co/docs/huggingface_hub/installation)
+(`pip install huggingface_hub`).
 
-### huggingface_cli/duckdb
+### Accessing Data with labretriever
 
-You can retrieves and displays the file paths for each configuration of
-the "BrentLab/rossi_2021" dataset from Hugging Face Hub.
+This repository is part of a collection configured as a unified database using
+[labretriever.VirtualDB](https://cmatkhan.github.io/labretriever/virtual_db_configuration/).
+Download the
+[collection config](https://github.com/BrentLab/tfbpshiny/blob/main/tfbpshiny/brentlab_yeast_collection.yaml)
+and use it to query the data directly in Python, or with an AI assistant using the
+[labretriever plugin](https://cmatkhan.github.io/labretriever/mcp_server/#quick-install-claude-code-plugin).
 
 ```python
-from huggingface_hub import ModelCard
-from pprint import pprint
+from labretriever.virtual_db import VirtualDB
+from labretriever.datacard import DataCard
 
-card = ModelCard.load("BrentLab/rossi_2021", repo_type="dataset")
+# Citation and metadata
+card = DataCard("BrentLab/rossi_2021")
+info = card.info()
+print(info["doi"])
+print(info["citation"])
 
-# cast to dict
-card_dict = card.data.to_dict()
+# path to the downloaded brentlab_yeast_collection.yaml
+vdb = VirtualDB("/path/to/brentlab_yeast_collection.yaml")
 
-# Get partition information
-dataset_paths_dict = {d.get("config_name"): d.get("data_files")[0].get("path") for d in card_dict.get("configs")}
-
-pprint(dataset_paths_dict)
+print(vdb.get_dataset_description("rossi"))
+vdb.query("SELECT * FROM rossi LIMIT 5")
 ```
 
-The entire repository is large. It may be preferable to only retrieve
-specific files or partitions. You can use the metadata files to choose
-which files to pull.
+### Direct parquet access
+
+The repository contains more data than what is exposed through the collection
+configuration. Use `DataCard.info()` to inspect available files, then download
+and query with DuckDB.
+
+Most files in this repository are single parquet files and can be read directly:
 
 ```python
 from huggingface_hub import snapshot_download
 import duckdb
-import os
-# Download only the metadata first
-repo_path = snapshot_download(
-    repo_id="BrentLab/rossi_2021",
-    repo_type="dataset",
-    allow_patterns="rossi_2021_metadata.parquet"
-)
-
-dataset_path = os.path.join(repo_path, "rossi_2021_metadata.parquet")
-conn = duckdb.connect()
-meta_res = conn.execute("SELECT * FROM read_parquet(?) LIMIT 10", [dataset_path]).df()
-print(meta_res)
-```
-
-We might choose to take a look at the file with accession SRR11466106:
 
-```python
-# Download only a specific sample's genome coverage data
 repo_path = snapshot_download(
     repo_id="BrentLab/rossi_2021",
     repo_type="dataset",
-    allow_patterns="genome_map/accession=SRR11466106/*.parquet"
+    allow_patterns="rossi_2021_af_combined.parquet",
 )
-
-# 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()
-print(result)
+conn = duckdb.connect()
+# returns a pandas DataFrame with the first 5 rows
+conn.execute(
+    "SELECT * FROM read_parquet(?) LIMIT 5",
+    [f"{repo_path}/rossi_2021_af_combined.parquet"],
+).df()
 ```
 
-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/rossi_2021"
-
-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
-)
+### Accessing using R
 
-print(f"\n✓ Repository downloaded to: {repo_path}")
+Clone the repository and read parquet files directly with
+[arrow](https://arrow.apache.org/docs/r/):
 
-# Construct path to the rossi_annotated_features parquet file
-parquet_path = os.path.join(repo_path, "yeastepigenome_annotatedfeatures.parquet")
-print(f"✓ Parquet file at: {parquet_path}")
+```r
+# install.packages("arrow")
+arrow::read_parquet("rossi_2021_af_combined.parquet")
 ```

rossi_2021_af_combined_mindel.parquet

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:de3ccc331bb962d8d740487edccfcd5106a41c48633a8c12d241918272cf22e9
+size 1360370384

rossi_2021_af_replicates_mindel.parquet

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:21e4bf08ec88ca283ec575f9058d9865fea9da07c629b71093ae348cddcaa1a2
+size 2064717545

rossi_2021_metadata.parquet

@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:ffd0d5ad6fdfcc19dbc0cd6a15d95a1c074e9484562c9613b263e8bf06f2ae4e
-size 33667
+oid sha256:0090a3d1543922c6001d65785e6babbd88c2a7f89dec242443a7d41a0447d2f4
+size 33637

scripts/genomecov_to_annotated_features.R

@@ -508,6 +508,8 @@ enrichment_analysis <- function(sample_set_id,
 # Main analysis workflow
 # ============================================================================
 
+PROMOTERS = "mindel"
+
 # Load data
 genomic_features <- arrow::read_parquet(
     "~/code/hf/yeast_genome_resources/brentlab_features.parquet")
@@ -529,10 +531,19 @@ sample_id_list <- genomecov$tagged$meta %>%
     unique()
 
 # Load regions
-regions_gr <- read_tsv(
-    "~/code/hf/yeast_genome_resources/yiming_promoters.bed",
-    col_names = c('chr', 'start', 'end', 'locus_tag', 'score', 'strand')) %>%
-    bed_to_granges()
+regions_list = list(
+    yiming = read_tsv(
+        "~/code/hf/yeast_genome_resources/yiming_promoters.bed",
+        col_names = c('chr', 'start', 'end', 'locus_tag', 'score', 'strand')) %>%
+        bed_to_granges(),
+    mindel = arrow::read_parquet("~/code/hf/yeast_genome_resources/mindel_promoters.parquet") |>
+        bed_to_granges()
+)
+
+regions_gr <- regions_list[[PROMOTERS]]
+
+# removes AAD6 and AAD16 from mindel. pseudogene no longer in annotations
+regions_gr = regions_gr[!is.na(regions_gr$target_locus_tag)]
 
 # Process control samples
 rossi_2021_control <- combine_control_af(genomecov$control, regions_gr)
@@ -555,72 +566,141 @@ annotated_feature_quants <- map(sample_id_list, ~{
 })
 names(annotated_feature_quants) <- sample_id_list
 
+if(PROMOTERS == "yiming"){
+    annotated_features_quants_replicates <- map(annotated_feature_quants, ~{
+        map(.x$replicates, as_tibble) %>%
+            list_rbind(names_to = "run_accession")}) %>%
+        list_rbind(names_to = "sample_id") %>%
+        mutate(sample_id = as.integer(sample_id)) %>%
+        left_join(
+            genomecov$tagged$meta %>%
+                ungroup() %>%
+                select(sample_id, regulator_locus_tag, regulator_symbol, run_accession) %>%
+                distinct(),
+            by = c("sample_id", "run_accession")) %>%
+        left_join(select(genomic_features, locus_tag, symbol)) %>%
+        dplyr::rename(target_locus_tag = locus_tag, target_symbol = symbol) %>%
+        dplyr::relocate(sample_id, run_accession, regulator_locus_tag, regulator_symbol,
+                        target_locus_tag, target_symbol) %>%
+        select(-c(score, width, strand))
+
+    # annotated_features_quants_replicates %>%
+    #     write_parquet(
+    #         "~/code/hf/rossi_2021/rossi_2021_af_replicates.parquet",
+    #         compression = "zstd",
+    #         write_statistics = TRUE,
+    #         chunk_size = 6708,
+    #         use_dictionary = c(
+    #             sample_id = TRUE,
+    #             run_accession = TRUE,
+    #             regulator_locus_tag = TRUE,
+    #             regulator_symbol = TRUE,
+    #             seqnames = TRUE,
+    #             target_locus_tag = TRUE,
+    #             target_symbol = TRUE
+    #         )
+    #     )
+
+} else if (PROMOTERS == "mindel") {
+    annotated_features_quants_replicates <- map(annotated_feature_quants, ~{
+        map(.x$replicates, as_tibble) %>%
+            list_rbind(names_to = "run_accession")}) %>%
+        list_rbind(names_to = "sample_id") %>%
+        mutate(sample_id = as.integer(sample_id)) %>%
+        left_join(
+            genomecov$tagged$meta %>%
+                ungroup() %>%
+                select(sample_id, regulator_locus_tag, regulator_symbol, run_accession) %>%
+                distinct(),
+            by = c("sample_id", "run_accession")) %>%
+        dplyr::relocate(sample_id, run_accession, regulator_locus_tag, regulator_symbol,
+                        target_locus_tag, target_symbol)
+
+    # annotated_features_quants_replicates %>%
+    #     write_parquet(
+    #         "~/code/hf/rossi_2021/rossi_2021_af_replicates_mindel.parquet",
+    #         compression = "zstd",
+    #         write_statistics = TRUE,
+    #         chunk_size = 5358,
+    #         use_dictionary = c(
+    #             sample_id = TRUE,
+    #             run_accession = TRUE,
+    #             regulator_locus_tag = TRUE,
+    #             regulator_symbol = TRUE,
+    #             seqnames = TRUE,
+    #             target_locus_tag = TRUE,
+    #             target_symbol = TRUE
+    #         )
+    #     )
+}
+
 # Extract and format replicate-level results
-annotated_features_quants_replicates <- map(annotated_feature_quants, ~{
-    map(.x$replicates, as_tibble) %>%
-        list_rbind(names_to = "run_accession")}) %>%
-    list_rbind(names_to = "sample_id") %>%
-    mutate(sample_id = as.integer(sample_id)) %>%
-    left_join(
-        genomecov$tagged$meta %>%
-            ungroup() %>%
-            select(sample_id, regulator_locus_tag, regulator_symbol, run_accession) %>%
-            distinct(),
-        by = c("sample_id", "run_accession")) %>%
-    left_join(select(genomic_features, locus_tag, symbol)) %>%
-    dplyr::rename(target_locus_tag = locus_tag, target_symbol = symbol) %>%
-    dplyr::relocate(sample_id, run_accession, regulator_locus_tag, regulator_symbol,
-                    target_locus_tag, target_symbol) %>%
-    select(-c(score, width, strand))
-
-# Write replicate-level results
-# annotated_features_quants_replicates %>%
-#     write_parquet(
-#         "~/code/hf/rossi_2021/rossi_2021_af_replicates.parquet",
-#         compression = "zstd",
-#         write_statistics = TRUE,
-#         chunk_size = 6708,
-#         use_dictionary = c(
-#             sample_id = TRUE,
-#             run_accession = TRUE,
-#             regulator_locus_tag = TRUE,
-#             regulator_symbol = TRUE,
-#             seqnames = TRUE,
-#             target_locus_tag = TRUE,
-#             target_symbol = TRUE
-#         )
-#     )
-
-# Extract and format combined results
-annotated_feature_quants_combined <- map(annotated_feature_quants, ~{
-    as_tibble(.x$combined)}) %>%
-    list_rbind(names_to = "sample_id") %>%
-    mutate(sample_id = as.integer(sample_id)) %>%
-    left_join(
-        genomecov$tagged$meta %>%
-            ungroup() %>%
-            select(sample_id, regulator_locus_tag, regulator_symbol) %>%
-            distinct(),
-        by = "sample_id") %>%
-    left_join(select(genomic_features, locus_tag, symbol)) %>%
-    dplyr::rename(target_locus_tag = locus_tag, target_symbol = symbol) %>%
-    dplyr::relocate(sample_id, regulator_locus_tag, regulator_symbol,
-                    target_locus_tag, target_symbol) %>%
-    select(-c(score, width, strand))
-
-# Write combined results
-# annotated_feature_quants_combined %>%
-#     write_parquet(
-#         "~/code/hf/rossi_2021/rossi_2021_af_combined.parquet",
-#         compression = "zstd",
-#         write_statistics = TRUE,
-#         chunk_size = 6708,
-#         use_dictionary = c(
-#             sample_id = TRUE,
-#             regulator_locus_tag = TRUE,
-#             regulator_symbol = TRUE,
-#             seqnames = TRUE,
-#             target_locus_tag = TRUE,
-#             target_symbol = TRUE
-#         )
-#     )
+
+if(PROMOTERS == 'yiming'){
+    # Extract and format combined results
+    annotated_feature_quants_combined <- map(annotated_feature_quants, ~{
+        as_tibble(.x$combined)}) %>%
+        list_rbind(names_to = "sample_id") %>%
+        mutate(sample_id = as.integer(sample_id)) %>%
+        left_join(
+            genomecov$tagged$meta %>%
+                ungroup() %>%
+                select(sample_id, regulator_locus_tag, regulator_symbol) %>%
+                distinct(),
+            by = "sample_id") %>%
+        left_join(select(genomic_features, locus_tag, symbol)) %>%
+        dplyr::rename(target_locus_tag = locus_tag, target_symbol = symbol) %>%
+        dplyr::relocate(sample_id, regulator_locus_tag, regulator_symbol,
+                        target_locus_tag, target_symbol) %>%
+        select(-c(score, width, strand))
+
+    # Write combined results
+    # annotated_feature_quants_combined %>%
+    #     write_parquet(
+    #         "~/code/hf/rossi_2021/rossi_2021_af_mindel_combined.parquet",
+    #         compression = "zstd",
+    #         write_statistics = TRUE,
+    #         chunk_size = 6708,
+    #         use_dictionary = c(
+    #             sample_id = TRUE,
+    #             regulator_locus_tag = TRUE,
+    #             regulator_symbol = TRUE,
+    #             seqnames = TRUE,
+    #             target_locus_tag = TRUE,
+    #             target_symbol = TRUE
+    #         )
+    #     )
+
+} else if(PROMOTERS == "mindel"){
+    # Extract and format combined results
+    annotated_feature_quants_combined <- map(annotated_feature_quants, ~{
+        as_tibble(.x$combined)}) %>%
+        list_rbind(names_to = "sample_id") %>%
+        mutate(sample_id = as.integer(sample_id)) %>%
+        left_join(
+            genomecov$tagged$meta %>%
+                ungroup() %>%
+                select(sample_id, regulator_locus_tag, regulator_symbol) %>%
+                distinct(),
+            by = "sample_id") %>%
+        dplyr::relocate(sample_id, regulator_locus_tag, regulator_symbol,
+                        target_locus_tag, target_symbol)
+
+    # Write combined results
+    # annotated_feature_quants_combined %>%
+    #     write_parquet(
+    #         "~/code/hf/rossi_2021/rossi_2021_af_combined_mindel.parquet",
+    #         compression = "zstd",
+    #         write_statistics = TRUE,
+    #         chunk_size = 5358,
+    #         use_dictionary = c(
+    #             sample_id = TRUE,
+    #             regulator_locus_tag = TRUE,
+    #             regulator_symbol = TRUE,
+    #             seqnames = TRUE,
+    #             target_locus_tag = TRUE,
+    #             target_symbol = TRUE
+    #         )
+    #     )
+
+}