python 3

minimds.py

@@ -21,6 +21,8 @@ def infer_structure(contactMat, structure, alpha, num_threads, classical=False):
 	distMat = at.contactToDist(contactMat, alpha)
 	at.makeSymmetric(distMat)
 
+	distMat = distMat/np.mean(distMat)	#normalize
+
 	if classical:	#classical MDS
 		coords = la.cmds(distMat)
 	else:
@@ -76,11 +78,11 @@ def partitionedMDS(path, args):
 		high_substructures.append(high_substructure)
 		offset += len(high_substructure.points)	#update
 		offset -= 1
-	
+
 	highstructure.setstructures(high_substructures)
-	
+
 	infer_structure(low_contactMat, lowstructure, alpha, num_threads)
-	print "Low-resolution MDS complete"
+	print("Low-resolution MDS complete")
 
 	highSubstructures = pymp.shared.list(highstructure.structures)
 	lowSubstructures = pymp.shared.list(lowstructure.structures)
@@ -115,7 +117,7 @@ def partitionedMDS(path, args):
 				highSubstructure.transform(r, t)
 				highSubstructures[substructurenum] = highSubstructure
 
-				print "MDS performed on structure {} of {}".format(substructurenum + 1, numSubstructures)
+				print("MDS performed on structure {} of {}".format(substructurenum + 1, numSubstructures))
 
 	highstructure.setstructures(highSubstructures)
 

minimds_inter.py

@@ -43,7 +43,7 @@ def get_inter_mat(prefix, inter_res_string, intra_res_string, structures, offset
 				path = "{}_{}_{}.bed".format(prefix, names[i], intra_res_string)
 			else:
 				path = "{}_{}_{}_{}.bed".format(prefix, names[j], names[i], inter_res_string)
-			print "Reading {}".format(path)
+			print("Reading {}".format(path))
 			with open(path) as bed:
 				for line in bed:
 					line = line.strip().split()

tad.py

@@ -110,27 +110,3 @@ def substructuresFromTads(structure, tads):
 		points = structure.points[start-structure.offset:end-structure.offset]
 		structure.createSubstructure(points, offset)
 		offset = end	#update
-
-#def substructuresFromTads(high_structure, low_structure, low_tads):
-#	"""Create compatible substructures from TADs in high-res structure and low-res structure"""
-#	res_ratio = low_structure.chrom.res/high_structure.chrom.res
-#	high_tads = low_tads * res_ratio
- #       high_offset = 0
-#	low_offset = 0
- #       for high_tad, low_tad in zip(high_tads, low_tads):
-#		if high_tad[0] < len(high_structure.getPointNums()):
-#			high_start = high_structure.getPointNums()[high_tad[0]]	#convert from index to num
-#			high_end = high_structure.getPointNums()[min((high_tad[1], len(high_structure.getPoints()) - 1))]	#don't go out of bounds
-#			low_start = low_structure.getPointNums()[low_tad[0]]
-#			low_end = low_structure.getPointNums()[min((low_tad[1], len(low_structure.getPoints()) - 1))]	
-#		        high_points = high_structure.points[(high_start-high_structure.offset):(high_end-high_structure.offset)]
-#			low_points = low_structure.points[(low_start-low_structure.offset):(low_end-low_structure.offset)]
-#			high_nums = [high_point.num for high_point in high_points if high_point != 0]
-#			inferred_low_nums = np.array(high_nums)/res_ratio
-#			true_low_nums = [low_point.num for low_point in low_points if low_point != 0]
-#			intersection = [num for num in true_low_nums if num in inferred_low_nums]
-#			if len(intersection) > 0:	#compatible
-#		        	high_structure.createSubstructure(high_points, high_offset)
-#				low_structure.createSubstructure(low_points, low_offset)
-#		        high_offset = high_end
-#			low_offset = low_end