Try to build FASTA indexes again on startup

FHIR · Aug 31, 2023 · 5e376b2 · 5e376b2
1 parent 11b450c
commit 5e376b2
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Showing 2 changed files with 7 additions and 3 deletions.
diff --git a/app/fasta.py b/app/fasta.py
@@ -1,5 +1,6 @@
 from pathlib import Path
 from urllib.request import urlretrieve
+from utilities.SPDI_Normalization import init_fasta
 
 
 def download_fasta():
@@ -16,8 +17,6 @@ def download_fasta():
                 urlretrieve('https://ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/annotation/' + build + '_latest/refseq_identifiers/' + filename, filepath)
 
             # Build indexes
-            # Disable this for now
-            # if not Path(filepath + '.fxi').is_file():
-            #     Fasta(filepath)
+            init_fasta()
     except Exception as error:
         print(error)
diff --git a/utilities/SPDI_Normalization.py b/utilities/SPDI_Normalization.py
@@ -22,6 +22,11 @@ def get_fasta(file):
         return fasta_cache[file]
 
 
+def init_fasta():
+    get_fasta(BUILD37_FILE)
+    get_fasta(BUILD38_FILE)
+
+
 def get_normalized_spdi(ref_seq, pos, ref, alt, build):
     if build == 'GRCh37':
         GRCh37_ref_seq_fasta = get_fasta(BUILD37_FILE)