refactor: hiv

cache/directory.py

@@ -172,6 +172,27 @@ def download(self, output: str | PathLike):
             online="https://depmap.org/portal/download/api/download?file_name=downloads-by-canonical-id%2Fpublic-25q2-c5ef.104%2FOmicsCNGeneWGS.csv&dl_name=OmicsCNGeneWGS.csv&bucket=depmap-external-downloads",
         ),
     },
+    "KEGG": {
+        # For some reason, KEGG requires a Referer header: opening this URL otherwise fails.
+        "ko03250.xml": CacheItem(
+            name="KEGG 03250",
+            cached="https://drive.google.com/uc?id=16dtWKHCQMp2qrLfFDE7nVhbwBCr2H5a9",
+            online="https://www.kegg.jp/kegg-bin/download?entry=ko03250&format=kgml",
+            online_headers = [('Referer', 'https://www.kegg.jp/pathway/ko03250')],
+        )
+    },
+    "HIV1": {
+        "prize_05.tsv": CacheItem(
+            name="HIV_05 prizes",
+            cached="https://drive.google.com/uc?id=1jVWNRPfYkbqimO44GdzXYB3-7NXhet1m",
+            online="https://raw.githubusercontent.com/gitter-lab/hiv1-aurkb/ac9278d447e4188eea3bf4b24c4c4e0c19b0c6d9/Results/base_analysis/prize_05.csv"
+        ),
+        "prize_060.tsv": CacheItem(
+            name="HIV_060 prizes",
+            cached="https://drive.google.com/uc?id=1Aucgp7pcooGr9oT4m2bvYEuYW6186WxQ",
+            online="https://raw.githubusercontent.com/gitter-lab/hiv1-aurkb/ac9278d447e4188eea3bf4b24c4c4e0c19b0c6d9/Results/base_analysis/prize_060.csv"
+        )
+    },
     "iRefIndex": {
         # This can also be obtained from the SPRAS repo
         # (https://github.com/Reed-CompBio/spras/blob/b5d7a2499afa8eab14c60ce0f99fa7e8a23a2c64/input/phosphosite-irefindex13.0-uniprot.txt).

configs/dmmm.yaml

@@ -43,12 +43,12 @@ datasets:
   # TODO: use old paramaters for datasets
   # HIV: https://github.com/Reed-CompBio/spras-benchmarking/blob/0293ae4dc0be59502fac06b42cfd9796a4b4413e/hiv-benchmarking/spras-config/config.yaml
   - label: dmmmhiv_060
-    node_files: ["processed_prize_060.txt"]
+    node_files: ["processed_prizes_060.txt"]
     edge_files: ["../raw/phosphosite-irefindex13.0-uniprot.txt"]
     other_files: []
     data_dir: "datasets/hiv/processed"
   - label: dmmmhiv_05
-    node_files: ["processed_prize_05.txt"]
+    node_files: ["processed_prizes_05.txt"]
     edge_files: ["../raw/phosphosite-irefindex13.0-uniprot.txt"]
     other_files: []
     data_dir: "datasets/hiv/processed"

datasets/hiv/.gitignore

@@ -1 +1,4 @@
-processed
+/processed
+/pickles
+/raw
+/intermediate

datasets/hiv/README.md

@@ -0,0 +1,30 @@
+# HIV dataset
+
+This folder contains data pertaining to following paper: **[HIV-1 virological synapse formation enhances infection spread by dysregulating Aurora Kinase B](https://doi.org/10.1371/journal.ppat.1011492)** - Bruce JW, Park E et al. (2023)
+
+The study examines human immune cells responding to viral infection as well as the changes that take place inside the already infected cells, which is the focus here.
+The data is from protein abundance and phosphorylation experiments, which will be the input to pathway reconstruction.
+
+**Overarching goal:** Recreate published biological case study on HIV data using SPRAS. This will help in identifying nodes i.e. proteins that are relevant to the disease.
+
+## Raw files
+
+Follow the `Snakemake` directive to find the fetched URLs for these.
+
+- `prize_05.tsv`: Prizes files from HIV expressing Jurkat cells grown for 5 minutes, from the original paper above.
+- `prize_060.tsv`: Prizes files from growing for 60 minutes.
+- `ko03250.xml`: KEGG Orthology Pathway ID 03250 (currently unused - was used previously for an attempt at gold standard generation.)
+- `HUMAN_9606_idmapping.tsv`: File provided by UniProt, used for mapping UniProt identifiers for  `name_mapping.py`.
+- `phosphosite-irefindex13.0-uniprot.txt`: The background interactome from the now-gone iRefIndex.
+
+## File organization
+
+See `Snakefile` for the way that all of the IO files are connected.
+
+1. `prepare.py` - This cleans up the prize files in `raw`; specifically to remove duplicates, and to prepare the list of UniProt nodes to be mapped by `name_mapping.py`
+1. `name_mapping.py` - Converts from UniProt KB-ACID to UniProt KB to meet in the middle with `kegg_ortholog.py`, and to match with the proteins for the iRefIndex interactome. We chose UniProt KB for its generality. We also remove identifiers with an `-N` suffix and remove duplicates, to make sure isoforms aren't considered as distinct during pathway reconstruction.
+1. `spras_formatting.py` - Formats the input files into the universal SPRAS format.
+
+> [!NOTE]
+> This dataset does not have a gold standard. There was a prior attempt [see original](../README.md) to use KEGG as the gold standard,
+> but there was very little overlap between the nodes generated from this paper and the current KEGG HIV pathway.