Fix numpy error, outdated np.object > object

AMULET.py

@@ -99,7 +99,7 @@ def getDoublets(matrix, unionoverlaps, rcelliddict):
         doublets_probas.append([rcelliddict[index], doublet_probabilities[index], cur])
         index += 1
 
-    return np.array(doublets_probas, dtype=np.object)
+    return np.array(doublets_probas, dtype=object)
 
 
 
@@ -130,12 +130,12 @@ def getFilteredOverlaps(data, simplerepeats, expectedoverlap):
                 #Recalculate overlaps
 
                 #starts increment by 1
-                counts = np.ones((len(starts), 2), dtype=np.object)
+                counts = np.ones((len(starts), 2), dtype=object)
                 counts[:,0] = starts
                 counts
 
                 #ends decrement by 1
-                counts2 = -1*np.ones((len(starts), 2), dtype=np.object)
+                counts2 = -1*np.ones((len(starts), 2), dtype=object)
                 counts2[:,0] = ends
                 counts2
 

FragmentFileOverlapCounter.py

@@ -190,7 +190,7 @@ def writeOverlapSummary(filepath, overlapcounts, vreadspercell, readspercell):
                "Total Number of Reads"]
 
 
-    table = np.empty(shape=(len(overlapcounts),len(colnames)), dtype=np.object)
+    table = np.empty(shape=(len(overlapcounts),len(colnames)), dtype=object)
 
     rowindex = 0
     for curbarcode in overlapcounts.keys():

peakoverlap.py

@@ -355,6 +355,6 @@ def getUnionPeaks(datasets, chridx=0, startidx=1, endidx=2):
                 curloci[2] = max(curloci[2], nextloci[2])
 
         rv.append([curchr, curloci[1], curloci[2]])
-    return np.array(rv, dtype=np.object)
+    return np.array(rv, dtype=object)