tweak to RheaParser.py for uniprot TrEMBL gzip during file fetch

ncats · Mar 7, 2024 · bf26a66 · bf26a66
1 parent 3bd34e6
commit bf26a66
Showing 1 changed file with 6 additions and 1 deletion.
diff --git a/src/parse/RheaParser.py b/src/parse/RheaParser.py
@@ -182,7 +182,12 @@ def getRheaFiles(self):
             rhea2UniprotUrl = uniprotToRheaConf.sourceURL
             rhea2UniprotRemoteFile = uniprotToRheaConf.sourceFileName
 
-            self.download_files(rhea2UniprotUrl, self.relDir + localDir + rhea2UniprotRemoteFile)            
+            self.download_files(rhea2UniprotUrl, self.relDir + localDir + rhea2UniprotRemoteFile)
+            swissProtLocalFileName = uniprotToRheaConf.extractFileName
+            # now gunzip
+            with gzip.open(self.relDir + localDir + rhea2UniprotRemoteFile, 'rb') as f_in:
+                with open(self.relDir + localDir + swissProtLocalFileName, 'wb') as f_out:
+                    shutil.copyfileobj(f_in, f_out)      
         else:
             print("Using cached Rhea Uniprot-to-Rhea file.")