added UniprotEnzymeParser.py for expacy level 4 ec annotations

src/parse/UniprotEnzymeParser.py

@@ -0,0 +1,145 @@
+'''
+Created on Mar 15, 2024
+
+@author: braistedjc
+'''
+import sys, os
+from os.path import exists
+
+from parse.MetabolomicsData import MetabolomicsData
+from rampConfig.RampConfig import RampConfig
+from rampConfig.SourceConfig import SourceConfig
+
+class UniprotEnzymeParser(MetabolomicsData):
+    '''
+    classdocs
+    '''
+
+    def __init__(self, resConfig):
+
+                # relative dir, use '../' for testing, use "" for production calls
+        self.relDir = ""
+
+        self.resourceConfig = resConfig
+
+        self.keyFields = ['ID', "DE"]
+
+        self.ecToDescription = dict()
+
+
+
+    def parseEnzyme(self):
+
+        # need to load uniprot TrEMBL and SwissProt human
+
+        # TrEMBL
+        enzymeConfig = self.resourceConfig.getConfig("expasy_enzyme_dat")
+        file_proteins = enzymeConfig.sourceFileName
+        proteins_url = enzymeConfig.sourceURL        
+        localDir = enzymeConfig.localDir
+        extractFile = enzymeConfig.extractFileName 
+        remoteFile = enzymeConfig.sourceFileName
+
+
+        # make the data dir if needed...
+        if not exists(self.relDir + localDir):
+            os.mkdir(self.relDir + localDir)
+
+        if not exists(self.relDir + localDir + extractFile):
+
+            self.download_files(proteins_url, self.relDir + localDir + remoteFile)
+
+        else:
+            print("Uniprot/Expasy enzyme.dat exists. Using cached copy.")
+
+
+
+        print("starting to parse uniprot expasy enzyme.dat")
+
+        self.parseEnzymeDatFile(self.relDir + localDir + extractFile)
+
+        print("number of ec records")
+        ecCount = len(self.ecToDescription)
+        print(str(ecCount))
+
+        # now add SwissProt human
+
+
+
+    def parseEnzymeDatFile(self, filePath):
+        enzymeDB = open(filePath, 'r+', encoding="utf-8")
+
+        protein = None
+
+        start = 1
+
+        while True:
+
+            line = enzymeDB.readline()
+
+            if start == 1:
+                ec = ""
+                description = ""
+
+            if len(line) == 0:
+                print("line is none...")
+                break    
+
+            prefix = line[0:2]
+
+            if prefix in self.keyFields:
+
+                start = 2
+
+                line = line.strip()
+
+                print(line)
+
+                if prefix == 'ID':
+                    splitLine = line.split(" ")
+                    ec = [s for s in splitLine if s][1]
+                if prefix == 'DE':
+                    if description == "":
+                        description = line.replace('DE   ', '')
+                        description = description.strip()
+
+
+
+            if(prefix == "//"):
+
+                # check transfered entry condition
+                if description.find('Transferred entry') == -1:                
+                    if ec != "":
+                        self.ecToDescription[ec] = description
+                start = 1
+
+        return self.ecToDescription
+
+
+# testing code
+
+# config = RampConfig()
+# source = SourceConfig()
+# 
+# source.resourceName = "expasy_enzyme_dat"        
+# source.sourceFetchMethod = "http"
+#         
+# source.sourceURL = "https://ftp.expasy.org/databases/enzyme/enzyme.dat"
+#         
+# source.sourceFileName = "enzyme.dat"
+#         
+# source.compressType = "None"
+# 
+# source.extractFileName = "enzyme.dat"
+#                 
+# source.localDir = "C:/Users/braistedjc/Downloads/"
+#         
+# source.resourceType = "enzyme info"
+# 
+# config.configDict['expasy_enzyme_dat'] = source
+# 
+# uep = UniprotEnzymeParser(config)
+# uep.parseEnzyme()
+# 
+# print(uep.ecToDescription['7.6.2.9'])
+