Merge pull request #138 from pbashyal-nmdp/0.6.x-fix-imgt-url

IMGT URL fix for 0.6.x release

Author: mmaiers-nmdp

pyard/__init__.py

@@ -24,4 +24,4 @@
 from .pyard import ARD
 
 __author__ = """NMDP Bioinformatics"""
-__version__ = '0.6.10'
+__version__ = '0.6.11'

pyard/data_repository.py

@@ -192,7 +192,7 @@ def generate_alleles_and_xx_codes_and_who(db_connection: sqlite3.Connection, img
     # 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.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
@@ -228,7 +228,7 @@ def generate_alleles_and_xx_codes_and_who(db_connection: sqlite3.Connection, img
     if imgt_version == "Latest":
         allele_list_url = f'{IMGT_HLA_URL}Latest/Allelelist.txt'
     else:
-        allele_list_url = f'{IMGT_HLA_URL}Latest/Allelelist.{imgt_version}.txt'
+        allele_list_url = f'{IMGT_HLA_URL}Latest/allelelist/Allelelist.{imgt_version}.txt'
     allele_df = pd.read_csv(allele_list_url, header=6, usecols=['Allele'])
 
     # Create a set of valid alleles

scripts/pyard-reduce-csv

@@ -176,13 +176,14 @@ if __name__ == '__main__':
     verbose = ard_config["verbose_log"]
     white_space_regex = re.compile(r"\s+")
 
-    try:
-        import openpyxl
-    except ImportError:
-        print("For Excel output, openpyxl library needs to be installed. "
-              "Install with:")
-        print("  pip install openpyxl")
-        sys.exit(1)
+    if ard_config["output_file_format"] == 'xlsx':
+        try:
+            import openpyxl
+        except ImportError:
+            print("For Excel output, openpyxl library needs to be installed. "
+                  "Install with:")
+            print("  pip install openpyxl")
+            sys.exit(1)
 
     # Instantiate py-ard object with the latest
     ard = pyard.ARD()

setup.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.6.10
+current_version = 0.6.11
 commit = True
 tag = True
 

setup.py

@@ -42,7 +42,7 @@
 
 setup(
     name='py-ard',
-    version='0.6.10',
+    version='0.6.11',
     description="ARD reduction for HLA with Python",
     long_description=readme + '\n\n' + history,
     author="CIBMTR",