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#!/usr/bin/python3
import sys, re, os
import json, sqlite3
usageInfo = f"""
Usage: {sys.argv[0]}
Reads files describing a tree-of-life from an 'Open Tree of Life' release,
and stores tree information in a database.
Reads a labelled_supertree_ottnames.tre file, which is assumed to have this format:
The tree-of-life is represented in Newick format, which looks like: (n1,n2,(n3,n4)n5)n6
The root node is named n6, and has children n1, n2, and n5.
Name examples include: Homo_sapiens_ott770315, mrcaott6ott22687, 'Oxalis san-miguelii ott5748753',
'ott770315' and 'mrcaott6ott22687' are node IDs. The latter is for a 'compound node'.
The node with ID 'ott770315' will get the name 'homo sapiens'.
A compound node will get a name composed from it's sub-nodes (eg: [name1 + name2]).
It is possible for multiple nodes to have the same name.
In these cases, extra nodes will be named sequentially, as 'name1 [2]', 'name1 [3]', etc.
Reads an annotations.json file, which is assumed to have this format:
Holds a JSON object, whose 'nodes' property maps node IDs to objects holding information about that node,
such as the properties 'supported_by' and 'conflicts_with', which list phylogenetic trees that
support/conflict with the node's placement.
Reads from a picked-names file, if present, which specifies name and node ID pairs.
These help resolve cases where multiple nodes share the same name.
"""
if len(sys.argv) > 1:
print(usageInfo, file=sys.stderr)
sys.exit(1)
treeFile = "otol/labelled_supertree_ottnames.tre" # Had about 2.5e9 nodes
annFile = "otol/annotations.json"
dbFile = "data.db"
nodeMap = {} # Maps node IDs to node objects
nameToFirstId = {} # Maps node names to first found ID (names might have multiple IDs)
dupNameToIds = {} # Maps names of nodes with multiple IDs to those IDs
pickedNamesFile = "pickedOtolNames.txt"
class Node:
" Represents a tree-of-life node "
def __init__(self, name, childIds, parentId, tips, pSupport):
self.name = name
self.childIds = childIds
self.parentId = parentId
self.tips = tips
self.pSupport = pSupport
print("Parsing tree file")
# Read file
data = None
with open(treeFile) as file:
data = file.read()
dataIdx = 0
# Parse content
iterNum = 0
def parseNewick():
" Parses a node using 'data' and 'dataIdx', updates nodeMap accordingly, and returns the node's ID "
global data, dataIdx, iterNum
iterNum += 1
if iterNum % 1e5 == 0:
print(f"At iteration {iterNum}")
# Check for EOF
if dataIdx == len(data):
raise Exception(f"ERROR: Unexpected EOF at index {dataIdx}")
# Check for node
if data[dataIdx] == "(": # parse inner node
dataIdx += 1
childIds = []
while True:
# Read child
childId = parseNewick()
childIds.append(childId)
if (dataIdx == len(data)):
raise Exception(f"ERROR: Unexpected EOF at index {dataIdx}")
# Check for next child
if (data[dataIdx] == ","):
dataIdx += 1
continue
else:
# Get node name and id
dataIdx += 1 # Consume an expected ')'
name, id = parseNewickName()
updateNameMaps(name, id)
# Get child num-tips total
tips = 0
for childId in childIds:
tips += nodeMap[childId].tips
# Add node to nodeMap
nodeMap[id] = Node(name, childIds, None, tips, False)
# Update childrens' parent reference
for childId in childIds:
nodeMap[childId].parentId = id
return id
else: # Parse node name
name, id = parseNewickName()
updateNameMaps(name, id)
nodeMap[id] = Node(name, [], None, 1, False)
return id
def parseNewickName():
" Parses a node name using 'data' and 'dataIdx', 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(f"ERROR: Unexpected EOF at index {dataIdx}")
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(f"ERROR: Unexpected EOF at index {dataIdx}")
name = data[dataIdx:end].rstrip()
if end == len(data): # Ignore trailing input semicolon
name = name[:-1]
dataIdx = end
# Convert to (name, id)
name = name.lower()
if name.startswith("mrca"):
return (name, name)
elif name[0] == "'":
match = re.fullmatch(r"'([^\\\"]+) (ott\d+)'", name)
if match == None:
raise Exception(f"ERROR: invalid name \"{name}\"")
name = match.group(1).replace("''", "'")
return (name, match.group(2))
else:
match = re.fullmatch(r"([^\\\"]+)_(ott\d+)", name)
if match == None:
raise Exception(f"ERROR: invalid name \"{name}\"")
return (match.group(1).replace("_", " "), match.group(2))
def updateNameMaps(name, id):
global nameToFirstId, dupNameToIds
if name not in nameToFirstId:
nameToFirstId[name] = id
else:
if name not in dupNameToIds:
dupNameToIds[name] = [nameToFirstId[name], id]
else:
dupNameToIds[name].append(id)
rootId = parseNewick()
print("Resolving duplicate names")
# Read picked-names file
nameToPickedId = {}
if os.path.exists(pickedNamesFile):
with open(pickedNamesFile) as file:
for line in file:
(name, _, otolId) = line.rstrip().partition("|")
nameToPickedId[name] = otolId
# Resolve duplicates
for (dupName, ids) in dupNameToIds.items():
# Check for picked id
if dupName in nameToPickedId:
idToUse = nameToPickedId[dupName]
else:
# Get conflicting node with most tips
tipNums = [nodeMap[id].tips for id in ids]
maxIdx = tipNums.index(max(tipNums))
idToUse = ids[maxIdx]
# Adjust name of other conflicting nodes
counter = 2
for id in ids:
if id != idToUse:
nodeMap[id].name += f" [{counter}]"
counter += 1
print("Changing mrca* names")
def convertMrcaName(id):
node = nodeMap[id]
name = node.name
childIds = node.childIds
if len(childIds) < 2:
print(f"WARNING: MRCA node \"{name}\" has less than 2 children")
return
# Get 2 children with most tips
childTips = [nodeMap[id].tips for id in childIds]
maxIdx1 = childTips.index(max(childTips))
childTips[maxIdx1] = 0
maxIdx2 = childTips.index(max(childTips))
childId1 = childIds[maxIdx1]
childId2 = childIds[maxIdx2]
childName1 = nodeMap[childId1].name
childName2 = nodeMap[childId2].name
# Check for mrca* child names
if childName1.startswith("mrca"):
childName1 = convertMrcaName(childId1)
if childName2.startswith("mrca"):
childName2 = convertMrcaName(childId2)
# Check for composite names
match = re.fullmatch(r"\[(.+) \+ (.+)]", childName1)
if match != None:
childName1 = match.group(1)
match = re.fullmatch(r"\[(.+) \+ (.+)]", childName2)
if match != None:
childName2 = match.group(1)
# Create composite name
node.name = f"[{childName1} + {childName2}]"
return childName1
for (id, node) in nodeMap.items():
if node.name.startswith("mrca"):
convertMrcaName(id)
print("Parsing annotations file")
# Read file
data = None
with open(annFile) as file:
data = file.read()
obj = json.loads(data)
nodeAnnsMap = obj["nodes"]
# Find relevant annotations
for (id, node) in nodeMap.items():
# Set has-support value using annotations
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
print("Creating nodes and edges tables")
dbCon = sqlite3.connect(dbFile)
dbCur = dbCon.cursor()
dbCur.execute("CREATE TABLE nodes (name TEXT PRIMARY KEY, id TEXT UNIQUE, tips INT)")
dbCur.execute("CREATE INDEX nodes_idx_nc ON nodes(name COLLATE NOCASE)")
dbCur.execute("CREATE TABLE edges (parent TEXT, child TEXT, p_support INT, PRIMARY KEY (parent, child))")
dbCur.execute("CREATE INDEX edges_child_idx ON edges(child)")
for (otolId, node) in nodeMap.items():
dbCur.execute("INSERT INTO nodes VALUES (?, ?, ?)", (node.name, otolId, node.tips))
for childId in node.childIds:
childNode = nodeMap[childId]
dbCur.execute("INSERT INTO edges VALUES (?, ?, ?)",
(node.name, childNode.name, 1 if childNode.pSupport else 0))
print("Closing database")
dbCon.commit()
dbCon.close()
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