Fixed incorrect reporting of number of marker genes/sets for taxonomi…

…c-specific marker sets.

checkm/VERSION

@@ -1 +1 @@
-1.0.6
+1.0.7

checkm/checkmData.py

@@ -174,7 +174,7 @@ def setRoot(self, path=None):
             return None
 
         # validate the supplied path or prompt for a new one
-	path = self.confirmPath(path=path)
+        path = self.confirmPath(path=path)
         if path is None:
             # The user is not interested
             return None
@@ -193,11 +193,11 @@ def confirmPath(self, path=None):
         minimal = False
         while not path_set:
             if not path:
-	    	if(minimal):
+                if(minimal):
                     path = raw_input("Please specify a location or type 'abort' to stop trying: \n")
-            	else:
+                else:
                     path = raw_input("Where should CheckM store it's data?\n" \
-                    	             "Please specify a location or type 'abort' to stop trying: \n")
+                                    "Please specify a location or type 'abort' to stop trying: \n")
 
             if path.upper() == "ABORT":
                 # user has given up
@@ -242,10 +242,3 @@ def checkPermissions(self):
             return False
 
         return True
-
-
-
-###############################################################################
-###############################################################################
-###############################################################################
-###############################################################################

checkm/markerSets.py

@@ -179,6 +179,17 @@ def getMarkerGenes(self):
                 markerGenes.add(marker)
 
         return markerGenes
+
+    def removeMarkers(self, markersToRemove):
+        """Remove specified markers from marker sets."""
+        newMarkerSet = []
+        for ms in self.markerSet:
+            newMS = ms - markersToRemove
+
+            if len(newMS) != 0:
+                newMarkerSet.append(newMS)
+
+        self.markerSet = newMarkerSet
 
     def genomeCheck(self, hits, bIndividualMarkers):
         """Calculate genome completeness and contamination."""

checkm/taxonParser.py

@@ -44,8 +44,11 @@ def readMarkerSets(self):
             lineage = lineSplit[2]
             numGenomes = int(lineSplit[3])
             markerSet = eval(lineSplit[6].rstrip())
+
+            ms = MarkerSet(ranksByLabel[rank], lineage, numGenomes, markerSet)
+            ms.removeMarkers(DefaultValues.MARKERS_TO_EXCLUDE)
 
-            taxonMarkerSets[rank][taxon] = MarkerSet(ranksByLabel[rank], lineage, numGenomes, markerSet)
+            taxonMarkerSets[rank][taxon] = ms
 
         return taxonMarkerSets