Update to Synthetic Networks

.gitignore

@@ -160,3 +160,14 @@ cython_debug/
 #  and can be added to the global gitignore or merged into this file.  For a more nuclear
 #  option (not recommended) you can uncomment the following to ignore the entire idea folder.
 #.idea/
+synthetic-data/human-interactome/9606.protein.links.full.v12.0.txt
+synthetic-data/human-interactome/9606.protein.links.full.v12.0.txt.gz
+synthetic-data/B_cell_activation/.Rhistory
+synthetic-data/.DS_Store
+
+.DS_Store
+.RData
+.Rhistory
+
+synthetic-data/interactomes/
+synthetic-data/spras-compatible-pathway-data/

README.md

@@ -1,2 +1,2 @@
 # spras-benchmarking
-Benchmarking datasets for the [SPRAS](https://github.com/Reed-CompBio/spras) project
+Benchmarking datasets for the [SPRAS](https://github.com/Reed-CompBio/spras) project

synthetic-data/README.md

@@ -0,0 +1,97 @@
+# Synthetic Data
+
+> All commands should be run from the `synthetic-data/` root directory.
+
+## Download STRING Human Interactome
+1. Download the STRING *Homo sapiens* `9606.protein.links.full.v12.0.txt.gz` database file from [STRING](https://string-db.org/cgi/download?sessionId=bL9sRTdIaUEt&species_text=Homo+sapiens&settings_expanded=0&min_download_score=0&filter_redundant_pairs=0&delimiter_type=txt).
+2. Move the downloaded file into the `human-interactome/` folder.
+3. From the synthetic-data/ directory, extract the file using:
+
+   ```
+   gunzip human-interactome/9606.protein.links.full.v12.0.txt.gz
+   ```
+
+## Download New PANTHER Pathways
+1. Visit [Pathway Commons](https://www.pathwaycommons.org/).
+2. Search for the desired pathway (e.g., "signaling") and filter the results by the **PANTHER pathway** data source.  
+   Example: [Search for "Signaling" filtered by PANTHER pathway](https://apps.pathwaycommons.org/search?datasource=panther&q=Signaling&type=Pathway)
+3. Click on the desired pathway and download the **Extended SIF** version of the pathway.
+4. In the `pathway-data/` folder, create a new subfolder named after the pathway you downloaded.
+5. Move the downloaded Extended SIF file to this new folder (as a `.txt` file). Rename the file to match the subfolder name exactly.
+
+## Sources and Targets
+
+[Sources](https://www.pnas.org/doi/full/10.1073/pnas.1808790115) are silico human surfaceomes receptors.
+
+[Targets](https://academic.oup.com/nar/article/51/D1/D39/6765312) are human transcription factors. 
+
+## Steps to Generate SPRAS-Compatible Pathways
+
+### 1. Process PANTHER Pathways
+
+1. Open `process_panther_pathway.R` and add the name of any new pathways to the `pathways` vector on **line 6**.
+2. From the `synthetic-data/` root directory, run the command:
+   ```
+   Rscript src/process_panther_pathway.R
+   ```
+3. This will create seven new files in each subfolder of the `pathway-data/` directory:
+- `DEL-EDGES.txt`
+- `DEL-NODES.txt`
+- `EDGES.txt`
+- `NODES.txt`
+- `PRIZES-100.txt`
+- `SOURCES.txt`
+- `TARGETS.txt`
+
+### 2. Convert Pathways to SPRAS-Compatible Format
+1.	In `SPRAS_compatible_files.py`, add the name of any new pathways to the `pathway_dirs` list on **line 8**.
+2.	From the synthetic-data/ directory, run the command:
+```
+python src/SPRAS_compatible_files.py
+```
+3. This will create a new folder named `spras-compatible-pathway-data`, containing subfolders for each PANTHER pathway in SPRAS-compatible format.  
+Each subfolder will include the following three files:
+- `<pathway_name>_gs_edges.txt`
+- `<pathway_name>_gs_nodes.txt`
+- `<pathway_name>_node_prizes.txt`
+
+4. From the synthetic-data/ directory, run the command:
+```
+python src/ratios.py
+```
+5. This will create a new file `data_ratio.txt` in `spras-compatible-pathway-data` to explain the edge to target/sources ratios.
+
+## Steps to get the interactomes
+### 1. Steps to get threshold interactomes
+1. From the synthetic-data/ directory, run the command:
+```
+python src/threshold_interactomes.py
+```
+2.	This will create a new folder named `interactomes`, containing a subfolder called `uniprot-threshold-interactomes`.
+The subfolder will include the following 12 files:
+- 10 thresholded interactomes: `uniprot_human_interactome_<threshold>.txt` (thresholds range from 1 to 900)
+- `proteins_missing_aliases.csv`: STRING IDs that are missing UniProt accession identifiers
+- `removed_edges.txt`: All edges removed from the uniprot_human_interactome_<threshold>.txt files
+
+### 2. Steps to get combined interactomes (Panther pathways and threshold interactomes)
+1. In `combine.py`, adjust the `pathway_dirs` list on **line 11** to be the pathways to be included in the combined networks
+2. From the synthetic-data/ directory, run the command:
+```
+python src/combine.py
+```
+3. This will create a new a subfolder called `uniprot-combined-threshold-interactomes` in `interactomes`.
+This subfolder will include 12 files:
+- 10 combined threshold interactomes combined with the chosen pathways: `uniprot_combined_interactome_<threshold>.txt` (thresholds range from 1 to 900)
+- `overlap_combined_info.csv`
+- `overlap_info.csv`
+
+# Pilot Data
+For the pilot data, use the list `["Wnt_signaling", "JAK_STAT_signaling", "Interferon_gamma_signaling", "FGF_signaling", "Ras"]` in both:
+- the list in `combine.py`
+- the list in `overlap_analytics.py`
+
+Make sure these pathways in the list are also added `["Wnt_signaling", "JAK_STAT_signaling", "Interferon_gamma_signaling", "FGF_signaling", "Ras"]`to:
+- the `pathways` vector in `ProcessPantherPathway.R`
+- the list in `SPRAS_compatible_files.py`
+
+**Once you’ve updated the pathway lists in all relevant scripts, run all the steps above to generate the Pilot dataset.**