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scripts/netCountAttributeConnections.py

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+#!/usr/bin/env python3
+
+import argparse
+import re
+
+parser = argparse.ArgumentParser(description="")
+
+# Add the arguments to the parser
+requiredArgs = parser.add_argument_group('required arguments')
+
+requiredArgs.add_argument("-f", "--file", dest="net", required=True,
+                    help="Net file. A file with at least two columns: origin node and destination node. The rest of the columns will be ignored.")
+
+requiredArgs.add_argument("-a", "--attributes", dest="attributes", required=True,
+                    help="A tab separated table with at least two columns: the nodes and the chosen attribute corresponding to the node (with no spaces in the attribute names). The rest of the columns will be ignored.")
+
+parser.add_argument("-c", "--compressed", dest="compress", required=False, action="store_true",
+                    help="Reads a gzip compressed net file.")
+
+args = parser.parse_args()
+
+print("  Reading attributes file")
+attributes = {}
+for line in open(args.attributes):
+	line = line.split("\t")
+	key = line[0]
+	value = line[1]
+	value = re.sub("\n", "", value)
+	attributes[key] = value
+
+print("  Counting network connections")
+
+with open(args.net, 'r') as tmp:
+	for lines, line in enumerate(tmp):
+		pass
+tmp.close()
+lines = lines + 1
+l = 0
+count = {}
+errors = set()
+for line in open(args.net):
+	l += 1
+	i = round(l/lines*100)
+	if l == 1:
+		I = i
+	if i != I:
+		I = i
+		print("\r  Counting network connections ", i, "%", sep="", end="")
+	line = line.split("\t")
+	source = line[0]
+	satt = attributes.get(source)
+	target = line[1]
+	target = re.sub("\n", "", target)
+	tatt = attributes.get(target)
+	if satt is None or tatt is None:
+		if satt is None:
+			errors.add(source)
+		if tatt is None:
+			errors.add(target)
+	else:
+		edge = sorted((satt, tatt))
+		edge = ' '.join(edge)
+		if edge in count.keys():
+			count[edge] += 1
+		else:
+			count[edge] = 0
+
+print("\n")
+
+if len(errors) > 0:
+	if len(errors) < 20:
+		print("  Warning!! The following", len(errors), "nodes didn't have a match in the attributes file:")
+		for e in errors:
+			print("  -", e)
+	if len(errors) > 19:
+		import re
+		tmp = re.sub("\\.[^\\.]+$", "_countAttributeConnections_errorReport.log", args.net)
+		print("  Warning!!", len(errors), "nodes didn't have a match in the attributes file.")
+		print("  Please check: '", tmp, "' for further details on which nodes.", sep="")
+		with open(tmp, "w") as TMP:
+			for e in errors:
+				print(e, file=TMP)
+
+print("\nAttribute1\tAttribute2\tConnections")
+for key, value in count.items():
+	key = key.split(" ")
+	key1 = key[0]
+	key2 = key[1]
+	print(key1, "\t", key2, "\t", value)
+
+print("\nDone")