ea8777d868c3941788a164aba71ade478cb1c8e9
max
  Wed Jun 25 02:55:18 2025 -0700
no output anymore if quickgenes is read and we have no symbol map, refs #29459

diff --git src/cbPyLib/cellbrowser/cellbrowser.py src/cbPyLib/cellbrowser/cellbrowser.py
index ebd6d0a..512a4f5 100755
--- src/cbPyLib/cellbrowser/cellbrowser.py
+++ src/cbPyLib/cellbrowser/cellbrowser.py
@@ -3613,32 +3613,34 @@
 
         # case 2: matrix has only symbols and user provides symbol. This is our legacy format for old datasets.
         # store only the symbol. We could look up the geneId but that's data inference, 
         # which we try not to do. The lookup could be wrong.
         elif matrixSyms is not None and geneOrSym in matrixSyms:
             geneStr = geneOrSym
             if geneStr not in matrixGeneIds:
                 logging.info("case 2: geneId %s in quickgenes file is not in expression matrix" % repr(geneStr))
                 continue
 
         # case 3: matrix has geneIds and user provides a geneId. add the symbol from our mapping
         # that's data inference, but that should be OK
         elif geneOrSym in matrixGeneIds:
             geneId = geneOrSym
             if not geneToSym:
-                logging.info("quick gene %s has a geneId but we have no geneId/symbol table. You can use "
-                        "the format geneId|symbol in the quick genes file to manually assign a label" % repr(geneId))
+                #logging.info("Quick gene %s but we have no geneId/symbol table. You can use "
+                        #"the format geneId|symbol in the quick genes file to manually assign a label" % repr(geneId))
+                # when geneToSym is None, that means that we have symbols in the matrix. So just pass through the
+                # symbol. example dataset: ams-supercluster
                 geneStr = geneId
             else:
                 if geneId in geneToSym:
                     geneStr = geneId+"|"+geneToSym[geneId]
                 else:
                     logging.info("GeneId %s from marker file was not found in gene symbol table." % geneId)
                     geneStr = geneId
 
         # case 4: matrix has geneIds and user provides geneId or symbol. Store both.
         elif geneToSym:
             # if we have a gene symbol mapping, we can resolve the symbols to geneIds
             # one can provide either geneIDs or symbols in the quick genes file
             if geneOrSym in geneToSym:
                 geneId = geneOrSym
                 sym = geneToSym[geneId]