Merge pull request #4527 from thehyve/mouse_validator

Allow gene symbols starting with numbers for mouse studies
cBioPortal · Feb 8, 2019 · 2324d12 · 2324d12
2 parents 8a137b1 + 7f41ce2
commit 2324d12
Showing 1 changed file with 18 additions and 17 deletions.
diff --git a/core/src/main/scripts/importer/validateData.py b/core/src/main/scripts/importer/validateData.py
@@ -677,23 +677,24 @@ def checkGeneIdentification(self, gene_symbol=None, entrez_id=None):
         # set to upper, as both maps contain symbols in upper
         if gene_symbol is not None:
             gene_symbol = gene_symbol.upper()
-            # Check in case gene symbol is not null if it starts with an integer
-            if gene_symbol is not '':
-                # Check if the gene_symbol starts with a number
-                if gene_symbol[0] in ['0', '1', '2', '3', '4', '5', '6', '7', '8', '9']:
-                    # In case portal properties are defined check if the gene symbol that starts
-                    # with an integer is in the alias table, if not report an error
-                    if self.portal.hugo_entrez_map is not None and self.portal.alias_entrez_map is not None:
-                        if gene_symbol not in self.portal.hugo_entrez_map and \
-                                gene_symbol not in self.portal.alias_entrez_map:
-                            self.logger.error('Hugo Symbol is not in gene or alias table and starts with a '
-                                              'number. This can be caused by unintentional gene conversion in Excel.',
-                                              extra={'line_number': self.line_number, 'cause': gene_symbol})
-                    # If alias table cannot be checked report warning that hugo symbols normally do not start
-                    # with a number
-                    else:
-                        self.logger.warning('Hugo Symbol should not start with a number.',
-                                            extra={'line_number': self.line_number, 'cause': gene_symbol})
+            if self.portal.species == "human":
+                # Check in case gene symbol is not null if it starts with an integer
+                if gene_symbol is not '':
+                    # Check if the gene_symbol starts with a number
+                    if gene_symbol[0] in ['0', '1', '2', '3', '4', '5', '6', '7', '8', '9']:
+                        # In case portal properties are defined check if the gene symbol that starts
+                        # with an integer is in the alias table, if not report an error
+                        if self.portal.hugo_entrez_map is not None and self.portal.alias_entrez_map is not None:
+                            if gene_symbol not in self.portal.hugo_entrez_map and \
+                                    gene_symbol not in self.portal.alias_entrez_map:
+                                self.logger.error('Hugo Symbol is not in gene or alias table and starts with a '
+                                'number. This can be caused by unintentional gene conversion in Excel.',
+                                                    extra={'line_number': self.line_number, 'cause': gene_symbol})
+                        # If alias table cannot be checked report warning that hugo symbols normally do not start
+                        # with a number
+                        else:
+                            self.logger.warning('Hugo Symbol should not start with a number.',
+                                                extra={'line_number': self.line_number, 'cause': gene_symbol})
 
         if entrez_id is not None:
             try: