update

sdomanskyi · Jun 24, 2020 · 3b11c0c · 3b11c0c
1 parent d3f7117
commit 3b11c0c
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Showing 7 changed files with 461 additions and 243 deletions.
diff --git a/ChangeLog.md b/ChangeLog.md
@@ -1,7 +1,9 @@
-- 1.3.4
+- 1.3.5
+   * Miscellaneous code improvements and bug fixes
+
+- 1.3.4.0-1.3.4.11
    * Integrated plotly offline figure saving (when orca is unavailable)
    * Added Quality Control pre-cut
-   * Minor code improvements
 
 - 1.3.2
    * Added Hopfield landscape visuzlization capability

diff --git a/DigitalCellSorter/GeneNameConverter.py b/DigitalCellSorter/GeneNameConverter.py
@@ -6,8 +6,11 @@
 
 class GeneNameConverter:
 
-    def __init__(self, dictDir = None, jumpStart = True, species = 'Human'):
+    def __init__(self, dictDir = None, jumpStart = True, species = 'Human', updateConversionDictFile = True, verbose = 1):
 
+        self.updateConversionDictFile = updateConversionDictFile
+
+        self.verbose = verbose
         self.species = species
 
         if self.species == 'Human':
@@ -26,7 +29,8 @@ def __init__(self, dictDir = None, jumpStart = True, species = 'Human'):
         try:
             self.conversionDict = read(self.dictDir)
         except Exception as exception:
-            print(exception)
+            if self.verbose >= 1:
+                print(exception)
 
             self.conversionDict = {'hugo': {'entrez': {}, 'ensembl': {}, 'alias': {}},
                                    'entrez': {'hugo': {}, 'ensembl': {}, 'retired': {}},
@@ -45,7 +49,8 @@ def __init__(self, dictDir = None, jumpStart = True, species = 'Human'):
                 except IOError: 
                     pass
             else:
-                write(self.conversionDict, self.dictDir)
+                if self.updateConversionDictFile:
+                    write(self.conversionDict, self.dictDir)
 
         return
 
@@ -260,7 +265,8 @@ def Fetch(self, genes, sourceType):
                 if targetGene is not None:
                     self.conversionDict['alias'][target][hugo] = targetGene
 
-        write(self.conversionDict,self.dictDir)
+        if self.updateConversionDictFile:
+            write(self.conversionDict,self.dictDir)
 
         return
 

diff --git a/DigitalCellSorter/GenericFunctions.py b/DigitalCellSorter/GenericFunctions.py
@@ -26,23 +26,28 @@ def write(data, fileName, compressed = False, jsonFormat = False):
         write(data, os.path.join('some dir 1', 'some dir 2', 'File with my data'))
     '''
 
-    if jsonFormat:
-        if not os.path.exists(os.path.basename(fileName)):
-            os.makedirs(os.path.basename(fileName))
+    try:
+        if jsonFormat:
+            if not os.path.exists(os.path.basename(fileName)):
+                os.makedirs(os.path.basename(fileName))
 
-        with gzip.GzipFile(fileName, 'w') as tempFile:
-            tempFile.write(json.dumps(data).encode('utf-8'))
+            with gzip.GzipFile(fileName, 'w') as tempFile:
+                tempFile.write(json.dumps(data).encode('utf-8'))
 
-        return
+            return
 
-    if compressed:
-        with gzip.open(fileName + '.pklz','wb') as temp_file:
+        if compressed:
+            with gzip.open(fileName + '.pklz','wb') as temp_file:
 
-            pickle.dump(data, temp_file, protocol=4)
-    else:
-        with open(fileName + '.pklz','wb') as temp_file:
+                pickle.dump(data, temp_file, protocol=4)
+        else:
+            with open(fileName + '.pklz','wb') as temp_file:
+
+                pickle.dump(data, temp_file, protocol=4)
+
+    except Exception as exception:
 
-            pickle.dump(data, temp_file, protocol=4)
+        print(exception)
 
     return None