Merge pull request #10 from moka-guys/panelapp_gene_query

Panelapp gene query script added (#10)

.gitignore

@@ -0,0 +1 @@
+okd_qc_commands.py

README.md

@@ -62,3 +62,27 @@ If run with the name of a TSO related project in DNA nexus as an argument, this
 ```bash tso_upload.sh 002_240216_A01229_0290_AHNL5GDMXY_TSO24006```
 
 The resulting command will be sent to std out with just the APP_ID and MOKAGUYS_AUTH_TOKEN needing to be added to each line, this can be done using find & replace.  IMPORTANT: HD200 and NTC samples (HD200 or 00000_00000 in sample name) should have their lines removed manually as these should not be uploaded.
+
+## panelapp_gene_query.py
+
+Generates a list of all signed-off gene/panel relations using the PanelApp API.
+
+Confidence scores:
+
+- Score 3 (lime green) - High level of evidence for this gene-disease association. Demonstrates confidence that this gene should be used for genome interpretation.
+- Score 2 (amber) - Moderate evidence for this gene-disease association. This gene should not be used for genomic interpretation.
+- Score 0 or 1 (red) - Not enough evidence for this gene-disease association. This gene should not be used for genomic interpretation.
+
+### Usage:
+```
+python3 panelapp_gene_query.py
+```
+
+### Output:
+CSV within the current working directory (```panelapp_gene_data.csv```). Data contains the following columns: gene_symbol, hgnc_id, panel_name, confidence_level and panel_id
+
+### Testing:
+Spotcheck of output CSV to ensure both:
+
+- Results and confidence scores are reflected on the live PanelApp website
+- All results pertain to signed-off panels

panelapp_gene_query.py

@@ -0,0 +1,97 @@
+'''
+Created by the bioinformatics team @ Synnovis
+Guy's & St. Thomas' NHS Trust
+
+Simple script to generate CSV containing all current gene/panel relations using PanelApp API
+Includes data only from signed-off panels
+Stores gene_symbol, hgnc_id, panel[name], confidence_level and panel_id
+
+Usage: python3 panelapp_gene_query.py
+panelapp_gene_data.csv will be saved in the current working directory
+'''
+
+import csv
+import requests
+
+def fetch_data(url):
+    """Call the API"""
+    response = requests.get(url)
+    if response.status_code == 200:
+        return response.json()
+    else:
+        print(f"Failed to retrieve data from the API. Status code: {response.status_code}")
+        return None
+
+def check_panel_signed(panel_id, signed_panels_cache, invalid_panels_cache):
+    """Check if the panel is signed off using the signed_off panels endpoint"""
+
+    # If panel_id already checked, skip check to avoid extra API calls
+    if panel_id in signed_panels_cache:
+        # Already checked and signed-off
+        return True
+    if panel_id in invalid_panels_cache:
+        # Already checked and not signed-off
+        return False
+
+    # New panel_id found, use API to check status and cache results
+    url = f"https://panelapp.genomicsengland.co.uk/api/v1/panels/signedoff/{panel_id}"
+    response = requests.get(url)
+    if response.status_code == 200 and "detail" not in response.json():
+        print(f"Panel {panel_id} is signed off. Caching as signed-off.")
+        signed_panels_cache.add(panel_id)
+        return True
+    else:
+        print(f"Panel {panel_id} is not a signed-off panel or does not exist. Caching as invalid.")
+        invalid_panels_cache.add(panel_id)
+        return False
+
+def write_data_to_csv(data, file_path, signed_panels_cache, invalid_panels_cache):
+    """Write to CSV"""
+    with open(file_path, mode="w", newline='') as file:
+        writer = csv.writer(file)
+        writer.writerow(["Gene Symbol", "HGNC ID", "Panel Name", "Confidence Level", "Panel ID"])
+        write_rows(writer, data, signed_panels_cache, invalid_panels_cache)
+
+def write_rows(writer, data, signed_panels_cache, invalid_panels_cache):
+    """Helper function to write rows in CSV"""
+    for result in data["results"]:
+        gene_data = result["gene_data"]
+        gene_symbol = gene_data["gene_symbol"]
+        hgnc_id = gene_data["hgnc_id"]
+        panel_name = result["panel"]["name"]
+        panel_id = result["panel"]["id"]
+        confidence_level = result["confidence_level"]
+
+        # Check if the panel is present in the signed-off panel list before adding to list
+        if check_panel_signed(panel_id, signed_panels_cache, invalid_panels_cache):
+            writer.writerow([gene_symbol, hgnc_id, panel_name, confidence_level, panel_id])
+
+def handle_pagination(data, writer, signed_panels_cache, invalid_panels_cache):
+    """Handle pagination"""
+    while data["next"]:
+        data = fetch_data(data["next"])
+        if data:
+            write_rows(writer, data, signed_panels_cache, invalid_panels_cache)
+        else:
+            break
+
+def main():
+    url = "https://panelapp.genomicsengland.co.uk/api/v1/genes/"
+    output_file = "panelapp_gene_data.csv"
+    signed_panels_cache = set()
+    invalid_panels_cache = set()
+
+    # Initial data fetch
+    initial_data = fetch_data(url)
+    if initial_data:
+        write_data_to_csv(initial_data, output_file, signed_panels_cache, invalid_panels_cache)
+
+        # Handle rest of pages
+        with open(output_file, mode="a", newline='') as file:
+            writer = csv.writer(file)
+            handle_pagination(initial_data, writer, signed_panels_cache, invalid_panels_cache)
+
+        print(f"Gene data saved to {output_file}")
+
+if __name__ == "__main__":
+    main()

settings.json

@@ -0,0 +1,37 @@
+{
+    "python.testing.pytestArgs": [
+        "."
+    ],
+    "python.testing.unittestEnabled": false,
+    "python.testing.pytestEnabled": true,
+    "python.envFile": "${workspaceFolder}/.venv",
+    "python.analysis.extraPaths": [
+    ],
+    "editor.formatOnSaveMode": "file",
+    "editor.formatOnSave": true,
+    "editor.codeActionsOnSave": {
+        "source.organizeImports": "explicit"
+    },
+    "[python]": {
+        "editor.defaultFormatter": "ms-python.black-formatter",
+        "editor.formatOnSave": true,
+        "editor.codeActionsOnSave": {
+            "source.organizeImports": "explicit"
+        }
+    },
+    "isort.args": [
+        "--profile",
+        "black"
+    ],
+    "flake8.args": [
+        "--max-line-length=120"
+    ],
+    "pylint.args": [
+        "--max-line-length=120"
+    ],
+    "black-formatter.args": [
+        "--line-length",
+        "120"
+    ],
+    "python.analysis.typeCheckingMode": "basic"
+}