f6bebb8752bbd5f6f40713cc4ee93ed6c0804325
angie
  Mon May 11 16:06:38 2020 -0700
Removed the warning about amino acid changes that don't match regex because they have added changes to '-' (as they did before for SNVs).  refs #25188

diff --git src/hg/utils/otto/nextstrainNcov/nextstrain.py src/hg/utils/otto/nextstrainNcov/nextstrain.py
index 44344a8..3012d76 100755
--- src/hg/utils/otto/nextstrainNcov/nextstrain.py
+++ src/hg/utils/otto/nextstrainNcov/nextstrain.py
@@ -155,32 +155,30 @@
                     aaM = snvAaRe.match(change)
                     if (aaM):
                         aaRef, aaPos, aaAlt = aaM.groups()
                         varStartMin = (int(aaPos) - 1) * 3
                         if (genePos.get(geneName)):
                             cdsStart = genePos.get(geneName)
                             varStartMin += cdsStart
                             varStartMax = varStartMin + 2
                             for varName in localVariants:
                                 ref, pos, alt = snvRe.match(varName).groups()
                                 pos = int(pos) - 1
                                 if (pos >= varStartMin and pos <= varStartMax):
                                     variantAaChanges[varName] = geneName + ':' + change
                         else:
                             warn("Can't find start for gene " + geneName)
-                    else:
-                        warn("Can't match amino acid change" + change)
     # Inherit parent variants
     branchVariants = parentVariants.copy()
     # Add variants specific to this branch (if any)
     for varName in localVariants:
         branchVariants[varName] = 1
     # Make an ordered variant string as David requested: semicolons between nodes,
     # comma-separated within a node:
     branchVarStr = ''
     for varName in localVariants:
         if (len(branchVarStr)):
             branchVarStr += ', '
         branchVarStr += varName
         aaVar = variantAaChanges.get(varName)
         if (aaVar):
             branchVarStr += ' (' + aaVar + ')'