Add PharmGKB

src/datahandlers/pharmgkb.py

@@ -0,0 +1,38 @@
+from os import path
+from zipfile import ZipFile
+import requests
+from pathlib import Path
+
+from src.prefixes import GTOPDB
+from src.babel_utils import pull_via_urllib
+
+
+def download_and_unzip(url, filepath):
+    """
+    Given a `.zip` file, download it to a location, then uncompress it in the same folder.
+
+    :param url_prefix: The URL prefix, e.g. https://api.pharmgkb.org/v1/download/file/data/
+    :param filename: The filename to download and save, e.g. genes.zip
+    :param filepath: The location to write the file to.
+    """
+    with requests.get(url, stream=True) as r:
+        r.raise_for_status()
+        with open(filepath, 'wb') as f:
+            for chunk in r.iter_content(chunk_size=8192):
+                f.write(chunk)
+    bname = Path(filepath).stem
+    ddir = path.dirname(filepath)
+    with ZipFile(filepath, 'r') as zipObj:
+        zipObj.extractall(path.join(ddir, bname))
+
+
+def pull_pharmgkb(genes_zip_filepath, chemicals_zip_filepath, drugs_zip_filepath, phenotypes_zip_filepath, variants_zip_filepath):
+    """
+    Download the PharmaGKB files we need.
+    """
+    download_and_unzip('https://api.pharmgkb.org/v1/download/file/data/genes.zip', genes_zip_filepath)
+    download_and_unzip('https://api.pharmgkb.org/v1/download/file/data/chemicals.zip', chemicals_zip_filepath)
+    download_and_unzip('https://api.pharmgkb.org/v1/download/file/data/drugs.zip', drugs_zip_filepath)
+    download_and_unzip('https://api.pharmgkb.org/v1/download/file/data/phenotypes.zip', phenotypes_zip_filepath)
+    download_and_unzip('https://api.pharmgkb.org/v1/download/file/data/variants.zip', variants_zip_filepath)
+

src/snakefiles/datacollect.snakefile

@@ -29,6 +29,7 @@ import src.datahandlers.chebi as chebi
 import src.datahandlers.hgncfamily as hgncfamily
 import src.datahandlers.pantherfamily as pantherfamily
 import src.datahandlers.complexportal as complexportal
+import src.datahandlers.pharmgkb as pharmgkb
 
 import src.prefixes as prefixes
 
@@ -553,3 +554,26 @@ rule get_chebi:
         config['download_directory'] + '/CHEBI/database_accession.tsv',
     run:
         chebi.pull_chebi()
+
+# PharmaGKB
+
+rule get_pharmgkb:
+    output:
+        genes_zip_filepath = config['download_directory'] + '/PharmGKB/genes.zip',
+        genes_tsv_filepath = config['download_directory'] + '/PharmGKB/genes/genes.tsv',
+        chemicals_zip_filepath = config['download_directory'] + '/PharmGKB/chemicals.zip',
+        chemicals_tsv_filepath = config['download_directory'] + '/PharmGKB/chemicals/chemicals.tsv',
+        drugs_zip_filepath = config['download_directory'] + '/PharmGKB/drugs.zip',
+        drugs_tsv_filepath = config['download_directory'] + '/PharmGKB/drugs/drugs.tsv',
+        phenotypes_zip_filepath = config['download_directory'] + '/PharmGKB/phenotypes.zip',
+        phenotypes_tsv_filepath = config['download_directory'] + '/PharmGKB/phenotypes/phenotypes.tsv',
+        variants_zip_filepath = config['download_directory'] + '/PharmGKB/variants.zip',
+        variants_tsv_filepath = config['download_directory'] + '/PharmGKB/variants/variants.tsv',
+    run:
+        pharmgkb.pull_pharmgkb(
+            output.genes_zip_filepath,
+            output.chemicals_zip_filepath,
+            output.drugs_zip_filepath,
+            output.phenotypes_zip_filepath,
+            output.variants_zip_filepath,
+        )