diff --git a/AMULET.py b/AMULET.py index 35b25ee..8276b31 100644 --- a/AMULET.py +++ b/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 diff --git a/FragmentFileOverlapCounter.py b/FragmentFileOverlapCounter.py index d8e43ae..44ba203 100644 --- a/FragmentFileOverlapCounter.py +++ b/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(): diff --git a/peakoverlap.py b/peakoverlap.py index 87c04b9..f88d7e3 100644 --- a/peakoverlap.py +++ b/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)