1 files changed, 181 insertions, 0 deletions
diff --git a/data_otol/namedTreeToJSON.py b/data_otol/namedTreeToJSON.py
new file mode 100755
index 0000000..30b8033
--- /dev/null
+++ b/data_otol/namedTreeToJSON.py
@@ -0,0 +1,181 @@
+#!/usr/bin/python3
+
+import sys, re, json
+
+usageInfo =  f"usage: {sys.argv[0]}\n"
+usageInfo += "Reads labelled_supertree_ottnames.tre & annotations.json (from an Open Tree of Life release), \n"
+usageInfo += "and prints a JSON object, which maps node names to objects of the form \n"
+usageInfo += "{\"children\": [name1, ...], \"parent\": name1, \"tips\": int1, \"pSupport\": bool1}, which holds \n"
+usageInfo += "child names, a parent name or null, descendant 'tips', and a phylogeny-support indicator\n"
+usageInfo += "\n"
+usageInfo += "This script was adapted to handle Open Tree of Life version 13.4.\n"
+usageInfo += "Link: https://tree.opentreeoflife.org/about/synthesis-release/v13.4\n"
+usageInfo += "\n"
+usageInfo += "labelled_supertree_ottnames.tre format:\n"
+usageInfo += "    Represents a tree-of-life in Newick format, roughly like (n1,n2,(n3,n4)n5)n6,\n"
+usageInfo += "    where root node is named n6, and has children n1, n2, and n5.\n"
+usageInfo += "    Name forms include Homo_sapiens_ott770315, mrcaott6ott22687, and 'Oxalis san-miguelii ott5748753'\n"
+usageInfo += "    Some names can be split up into a 'simple' name (like Homo_sapiens) and an id (like ott770315)\n"
+usageInfo += "annotations.json format:\n"
+usageInfo += "    JSON object holding information about the tree-of-life release.\n"
+usageInfo += "    The object's 'nodes' field maps node IDs to objects holding information about that node,\n"
+usageInfo += "    such as phylogenetic trees that support/conflict with it's placement.\n"
+
+if len(sys.argv) > 1:
+	print(usageInfo, file=sys.stderr)
+	sys.exit(1)
+
+nodeMap = {} # The JSON object to output
+idToName = {} # Maps node IDs to names
+
+# Parse labelled_supertree_ottnames.tre
+data = None
+with open("labelled_supertree_ottnames.tre") as file:
+	data = file.read()
+dataIdx = 0
+def parseNewick():
+	"""Parses a node using 'data' and 'dataIdx', updates nodeMap accordingly, and returns the node name or None"""
+	global dataIdx
+	# Check for EOF
+	if dataIdx == len(data):
+		print("ERROR: Unexpected EOF at index " + str(dataIdx), file=sys.stderr)
+		return None
+	# Check for inner-node start
+	if data[dataIdx] == "(":
+		dataIdx += 1
+		childNames = []
+		while True:
+			# Read child
+			childName = parseNewick()
+			if childName == None:
+				return None
+			childNames.append(childName)
+			if (dataIdx == len(data)):
+				print("ERROR: Unexpected EOF", file=sys.stderr)
+				return None
+			# Check for next child
+			if (data[dataIdx] == ","):
+				dataIdx += 1
+				continue
+			else:
+				# Get node name
+				dataIdx += 1 # Consume an expected ')'
+				[name, id] = parseNewickName()
+				idToName[id] = name
+				# Get child num-tips total
+				tips = 0
+				for childName in childNames:
+					tips += nodeMap[childName]["tips"]
+				# Add node to nodeMap
+				nodeMap[name] = {
+					"n": name, "id": id, "children": childNames, "parent": None, "tips": tips, "pSupport": False
+				}
+				# Update childrens' parent reference
+				for childName in childNames:
+					nodeMap[childName]["parent"] = name
+				return name
+	else:
+		[name, id] = parseNewickName()
+		idToName[id] = name
+		nodeMap[name] = {"n": name, "id": id, "children": [], "parent": None, "tips": 1, "pSupport": False}
+		return name
+def parseNewickName():
+	"""Helper that parses an input node name, and returns a [name,id] pair"""
+	global data, dataIdx
+	name = None
+	end = dataIdx
+	# Get name
+	if (end < len(data) and data[end] == "'"): # Check for quoted name
+		end += 1
+		inQuote = True
+		while end < len(data):
+			if (data[end] == "'"):
+				if end + 1 < len(data) and data[end+1] == "'": # Account for '' as escaped-quote
+					end += 2
+					continue
+				else:
+					end += 1
+					inQuote = False
+					break
+			end += 1
+		if inQuote:
+			raise Exception("ERROR: Unexpected EOF")
+		name = data[dataIdx:end]
+		dataIdx = end
+	else:
+		while end < len(data) and not re.match(r"[(),]", data[end]):
+			end += 1
+		if (end == dataIdx):
+			raise Exception("ERROR: Unexpected EOF")
+		name = data[dataIdx:end].rstrip()
+		if end == len(data): # Ignore trailing input semicolon
+			name = name[:-1]
+		dataIdx = end
+	# Convert to [name, id]
+	if name.startswith("mrca"):
+		return [name, name]
+	elif name[0] == "'":
+		match = re.fullmatch(r"'([^\\\"]+) (ott\d+)'", name)
+		if match == None:
+			raise Exception("ERROR: invalid name \"{}\"".format(name))
+		name = match.group(1).replace("''", "'")
+		return [name, match.group(2)]
+	else:
+		match = re.fullmatch(r"([^\\\"]+)_(ott\d+)", name)
+		if match == None:
+			raise Exception("ERROR: invalid name \"{}\"".format(name))
+		return [match.group(1).replace("_", " "), match.group(2)]
+rootName = parseNewick()
+
+# Parse annotations.json
+data = None
+with open("annotations.json") as file:
+	data = file.read()
+obj = json.loads(data)
+nodeAnnsMap = obj['nodes']
+
+# Do some more postprocessing on each node
+def convertMrcaName(name):
+	"""Given an mrca* name, returns an expanded version with the form [name1 + name2]"""
+	match = re.fullmatch(r"mrca(ott\d+)(ott\d+)", name)
+	if match == None:
+		print("ERROR: Invalid name \"{}\"".format(name), file=sys.stderr)
+	else:
+		subName1 = match.group(1)
+		subName2 = match.group(2)
+		if subName1 not in idToName:
+			print("ERROR: MRCA name \"{}\" sub-name \"{}\" not found".format(subName1), file=sys.stderr)
+		elif subName2 not in idToName:
+			print("ERROR: MRCA name \"{}\" sub-name \"{}\" not found".format(subName2), file=sys.stderr)
+		else:
+			return "[{} + {}]".format(idToName[subName1], idToName[subName2])
+namesToSwap = [] # Will hold [oldName, newName] pairs, for renaming nodes in nodeMap
+for node in nodeMap.values():
+	# Set has-support value using annotations
+	id = node["id"]
+	if id in nodeAnnsMap:
+		nodeAnns = nodeAnnsMap[id]
+		supportQty = len(nodeAnns["supported_by"]) if "supported_by" in nodeAnns else 0
+		conflictQty = len(nodeAnns["conflicts_with"]) if "conflicts_with" in nodeAnns else 0
+		node["pSupport"] = supportQty > 0 and conflictQty == 0
+	# Change mrca* names
+	name = node["n"]
+	if (name.startswith("mrca")):
+		namesToSwap.append([name, convertMrcaName(name)])
+	parentName = node["parent"]
+	if (parentName != None and parentName.startswith("mrca")):
+		node["parent"] = convertMrcaName(parentName)
+	childNames = node["children"]
+	for i in range(len(childNames)):
+		if (childNames[i].startswith("mrca")):
+			childNames[i] = convertMrcaName(childNames[i])
+	# Delete some no-longer-needed fields
+	del node["n"]
+	del node["id"]
+# Finish mrca* renamings
+for [oldName, newName] in namesToSwap:
+	nodeMap[newName] = nodeMap[oldName]
+	del nodeMap[oldName]
+
+# Output JSON
+print(json.dumps(nodeMap))