Merge remote-tracking branch 'origin/no-pandas' into no-pandas

Author: pbashyal-nmdp

pyard/loader/allele_list.py

@@ -0,0 +1,59 @@
+from urllib.request import urlopen
+from urllib.error import URLError
+import csv
+import sys
+from ..simple_table import Table
+from ..loader import IMGT_HLA_URL
+
+
+def load_allele_list(imgt_version):
+    """
+    The format of the AlleleList file has a 6-line header with a header
+    on the 7th line
+    ```
+    # file: Allelelist.3290.txt
+    # date: 2017-07-10
+    # version: IPD-IMGT/HLA 3.29.0
+    # origin: https://github.com/ANHIG/IMGTHLA/Allelelist.3290.txt
+    # repository: https://raw.githubusercontent.com/ANHIG/IMGTHLA/Latest/allelelist/Allelelist.3290.txt
+    # author: WHO, Steven G. E. Marsh ([email protected])
+    AlleleID,Allele
+    HLA00001,A*01:01:01:01
+    HLA02169,A*01:01:01:02N
+    HLA14798,A*01:01:01:03
+    HLA15760,A*01:01:01:04
+    HLA16415,A*01:01:01:05
+    HLA16417,A*01:01:01:06
+    HLA16436,A*01:01:01:07
+    ```
+
+    Returns a Table object with AlleleID and Allele columns
+
+    :param imgt_version: IMGT database version
+    :return: Table object with AlleleID and Allele data
+    """
+
+    if imgt_version == "Latest":
+        allele_list_url = f"{IMGT_HLA_URL}Latest/Allelelist.txt"
+    else:
+        if imgt_version == "3130":
+            # 3130 was renamed to 3131 for Allelelist file only 🤷🏾
+            imgt_version = "3131"
+        allele_list_url = (
+            f"{IMGT_HLA_URL}Latest/allelelist/Allelelist.{imgt_version}.txt"
+        )
+
+    try:
+        response = urlopen(allele_list_url)
+        lines = [line.decode("utf-8").strip() for line in response]
+
+        # Skip first 6 header lines
+        data_lines = lines[6:]
+
+        reader = csv.DictReader(data_lines)
+        columns = ["AlleleID", "Allele"]
+
+        return Table(reader, columns)
+    except URLError as e:
+        print(f"Error downloading {allele_list_url}", e, file=sys.stderr)
+        sys.exit(1)