Merge branch 'u/morriscb/codeOceanExecuteScript'

Author: morriscb

intro.md

@@ -58,6 +58,9 @@ Available notebooks:
   (Kimberly Siletti)**
 
 ## Release Notes
+* **[abc_atlas_access (v0.1.2)]**
+  * Added script for selecting genes from expression matrices for use on
+    CodeOcean.
 * **[abc_atlas_access (v0.1.1)]**
   * Fixed compatibility issue with read only local caches specifically for
     fuse style file mounts such as those used on CodeOcean.

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "abc_atlas_access"
-version = "0.1.1"
+version = "0.1.2"
 description = "A package for accessing/processing data from the ABC Atlas"
 dependencies = [
   "anndata",

scripts/create_gene_expression.py

@@ -0,0 +1,95 @@
+import argparse
+from pathlib import Path
+
+from abc_atlas_access.abc_atlas_cache.abc_project_cache import AbcProjectCache
+from abc_atlas_access.abc_atlas_cache.anndata_utils import get_gene_data
+
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser(
+        description="Load expression matrix data from the ABC Atlas and "
+                    "extract specific genes across multiple files and all "
+                    "cells."
+    )
+    parser.add_argument(
+        "--abc_atlas_cache_path",
+        type=str,
+        default="/root/capsule/data/abc_atlas",
+        help="Path to the ABC Atlas cache directory."
+    )
+    parser.add_argument(
+        "--manifest_version",
+        type=str,
+        default="releases/20240330/manifest.json",
+        help="The version of the ABC Atlas manifest to use."
+    )
+    parser.add_argument(
+        "--use_s3_cache",
+        action="store_true",
+        help="Use an S3 cache where the data is downloaded to disk instead of "
+             "a local cache already stored on disk."
+    )
+    parser.add_argument(
+        "--species",
+        help="Which data to load? `mouse` or `human`?",
+        choices=["human", "mouse"]
+    )
+    parser.add_argument(
+        "--use_raw",
+        action="store_true",
+        help="Use raw gene expression values instead of log2 values."
+    )
+    parser.add_argument(
+        "--output_file_path",
+        type=str,
+        help="Path to file to write to.",
+        default="~/capsule/results/gene_data.csv"
+    )
+    parser.add_argument(
+        '--genes',
+        type=str,
+        default="",
+        help="A comma-separated list of gene symbols to extract from the "
+             "expression matrix."
+    )
+    args = parser.parse_args()
+
+    genes = args.genes.split(",")
+    for idx, gene in enumerate(genes):
+        genes[idx] = gene.replace(" ", "")
+
+    print("Loading ABC Atlas cache from:", args.abc_atlas_cache_path)
+    cache_path = Path(args.abc_atlas_cache_path)
+    if args.use_s3_cache:
+        abc_cache = AbcProjectCache.from_s3_cache(cache_path)
+    else:
+        abc_cache = AbcProjectCache.from_local_cache(cache_path)
+    abc_cache.load_manifest(args.manifest_version)
+
+    if args.species == "human":
+        directory_name = "WHB-10Xv3"
+    elif args.species == "mouse":
+        directory_name = "WMB-10X"
+    else:
+        raise ValueError(f"Unknown species requested: {args.species}")
+
+    cell = abc_cache.get_metadata_dataframe(
+        directory=directory_name,
+        file_name='cell_metadata'
+    ).set_index('cell_label')
+    gene = abc_cache.get_metadata_dataframe(
+        directory=directory_name,
+        file_name='gene'
+    ).set_index('gene_identifier')
+
+    print("Processing genes:", genes)
+    gene_data = get_gene_data(
+        abc_atlas_cache=abc_cache,
+        all_cells=cell,
+        all_genes=gene,
+        selected_genes=genes,
+        data_type="raw" if args.use_raw else "log2"
+    )
+
+    print("Writing gene data to:", args.output_file_path)
+    gene_data.to_csv(args.output_file_path)