def test_params_merge(self):
t = LoadTree(treestring='((((a,b)ab,c)abc),d)')
for (label, length, beta) in [('a',1, 20),('b',3,2.0),('ab',4,5.0),]:
t.getNodeMatchingName(label).params = {'length':length, 'beta':beta}
t = t.getSubTree(['b', 'c', 'd'])
self.assertEqual(t.getNodeMatchingName('b').params,
{'length':7, 'beta':float(2*3+4*5)/(3+4)})
self.assertRaises(ValueError, t.getSubTree, ['b','c','xxx'])
self.assertEqual(str(t.getSubTree(['b','c','xxx'],ignore_missing=True)),
'(b:7,c)root;')
def test_getsetParamValue(self):
"""test getting, setting of param values"""
t = LoadTree(treestring='((((a:.2,b:.3)ab:.1,c:.3)abc:.4),d:.6)')
self.assertEqual(t.getParamValue('length', 'ab'), 0.1, 2)
t.setParamValue('zz', 'ab', 4.321)
node = t.getNodeMatchingName('ab')
self.assertEqual(4.321, node.params['zz'], 4)
def MatchNodes(self):
#print "YAY"
self.correctForFastMLNameChanges() #performs the correction on the output string if necessary
#print "NAY"
TerminiStringToNodeName_D = {}
#a termini string is prepared for each internal node, that is, all termini under the internal node sorted an placed into a single string
for NodeKey in self.UpperKey_L:
TerminiStringToNodeName_D['-'.join(sorted(self.Nodes_D[NodeKey]['terminal']))] = NodeKey
#prepares a cogent tree object for the fastML output
FH = getInputTempFile(self.FastMLOutputTreeString)
FastMLCogentTree = LoadTree(FH.name)
self.FastMLToOriginalMatchedNodes_D = {}
#for each cogent node in the FastML cogent tree
for FastMLCogentNodeKey in FastMLCogentTree.getNodeNames():
#a termini string is prepared for the fastML node
FastMLCogentNode = FastMLCogentTree.getNodeMatchingName(FastMLCogentNodeKey)
FastMLTermini_L = [tip.Name for tip in FastMLCogentNode.iterTips()]
#if it has more than 0 termini under the node
if len(FastMLTermini_L) > 0:
#A fastML termini string is prepared, and this termini string will be the same termini string as the equivalent cogent node
FastMLTerminiString = '-'.join(sorted(FastMLTermini_L))
self.FastMLToOriginalMatchedNodes_D[FastMLCogentNodeKey] = TerminiStringToNodeName_D[FastMLTerminiString]
#if it has no termini under it, then the node itself is a terminus and has the same name in FastML and Cogent
else:
self.FastMLToOriginalMatchedNodes_D[FastMLCogentNodeKey] = FastMLCogentNodeKey
def test_getsetParamValue(self):
"""test getting, setting of param values"""
t = LoadTree(treestring='((((a:.2,b:.3)ab:.1,c:.3)abc:.4),d:.6)')
self.assertEqual(t.getParamValue('length', 'ab'), 0.1, 2)
t.setParamValue('zz', 'ab', 4.321)
node = t.getNodeMatchingName('ab')
self.assertEqual(4.321, node.params['zz'], 4)
def test_params_merge(self):
t = LoadTree(treestring='((((a,b)ab,c)abc),d)')
for (label, length, beta) in [
('a', 1, 20),
('b', 3, 2.0),
('ab', 4, 5.0),
]:
t.getNodeMatchingName(label).params = {
'length': length,
'beta': beta
}
t = t.getSubTree(['b', 'c', 'd'])
self.assertEqual(
t.getNodeMatchingName('b').params, {
'length': 7,
'beta': float(2 * 3 + 4 * 5) / (3 + 4)
})
self.assertRaises(ValueError, t.getSubTree, ['b', 'c', 'xxx'])
self.assertEqual(
str(t.getSubTree(['b', 'c', 'xxx'], ignore_missing=True)),
'(b:7,c)root;')
def MatchNodes(self):
#print "YAY"
self.correctForFastMLNameChanges(
) #performs the correction on the output string if necessary
#print "NAY"
TerminiStringToNodeName_D = {}
#a termini string is prepared for each internal node, that is, all termini under the internal node sorted an placed into a single string
for NodeKey in self.UpperKey_L:
TerminiStringToNodeName_D['-'.join(
sorted(self.Nodes_D[NodeKey]['terminal']))] = NodeKey
#prepares a cogent tree object for the fastML output
FH = getInputTempFile(self.FastMLOutputTreeString)
FastMLCogentTree = LoadTree(FH.name)
self.FastMLToOriginalMatchedNodes_D = {}
#for each cogent node in the FastML cogent tree
for FastMLCogentNodeKey in FastMLCogentTree.getNodeNames():
#a termini string is prepared for the fastML node
FastMLCogentNode = FastMLCogentTree.getNodeMatchingName(
FastMLCogentNodeKey)
FastMLTermini_L = [tip.Name for tip in FastMLCogentNode.iterTips()]
#if it has more than 0 termini under the node
if len(FastMLTermini_L) > 0:
#A fastML termini string is prepared, and this termini string will be the same termini string as the equivalent cogent node
FastMLTerminiString = '-'.join(sorted(FastMLTermini_L))
self.FastMLToOriginalMatchedNodes_D[
FastMLCogentNodeKey] = TerminiStringToNodeName_D[
FastMLTerminiString]
#if it has no termini under it, then the node itself is a terminus and has the same name in FastML and Cogent
else:
self.FastMLToOriginalMatchedNodes_D[
FastMLCogentNodeKey] = FastMLCogentNodeKey
class FastMLTree:
"""
Class attributes:
Parsed (Bool): an indication of whether or not the user-defined tree was successfully parsed, if it was not, then the rest of the analysis is not performed
TreePath (String): absolute path to tree file
NeedsToBeCogentModded (Bool): whether or not placeholder names for the internal nodes need to be created
CogentTree (Object LoadTree): pyCogent Class object containing parsed newick syntax tree
FastMLInputTreeString (String): representation of tree in newick with internal node names removed
FastMLOutputTreeString (String): representation of tree in newick with internal nodes named according to FastML naming convention
FastMLToOriginalMatchedNodes_D (Dict): Key is the node name in the cogent convention, value is the node name in the FastML convention
NodeKey_L (List): List of all node name keys
LeafKey_L (List): List of all terminal node name keys
UpperKey_L (List): List of all internal (non-terminal) node name keys
TopKey (String): root node name key
BranchKey_L (List): List of all paths (from ancestral to immediate derived) along the tree
Nodes_D (Dict): Key is the node name, value is a sub-dict containing immediate derived nodes and terminal nodes under the node
"""
"CONSTRUCTOR"
def __init__(self, TreePath, NeedsToBeCogentModded):
self.Parsed = True #used to determine if the full analysis can be conducted
try:
self.TreePath = TreePath
self.NeedsToBeCogentModded = NeedsToBeCogentModded
self.CogentTree = None
#if the internal nodes need to be renamed, then it is done according to the "FixUpFileForCogent" method
if self.NeedsToBeCogentModded:
cogentFixUp = fixUpFileForCogent(self.TreePath)
self.CogentTreeFile = cogentFixUp[0]
self.CogentInputTreeString = cogentFixUp[1]
self.CogentTree = LoadTree(self.CogentTreeFile.name)
else:
self.CogentTree = LoadTree(self.TreePath)
#prepares an input string for FastML
self.FastMLInputTreeString = self.FixUpFileForFastML(
self.CogentTree)
#executes method to fully parse tree, then sets all returned variables as class variables
CogentNodesLeavesBranches = completeNodesLeavesBranches(
self.CogentTree)
self.NodeKey_L = CogentNodesLeavesBranches['NodeKey_L']
self.LeafKey_L = CogentNodesLeavesBranches['LeafKey_L']
self.UpperKey_L = CogentNodesLeavesBranches['UpperKey_L']
self.TopKey = CogentNodesLeavesBranches['TopKey']
self.BranchKey_L = CogentNodesLeavesBranches['BranchKey_L']
self.Nodes_D = CogentNodesLeavesBranches['Nodes_D']
#print self.LeafKey_L
#executes quick run of FastML to get FastML's naming convention of internal nodes
self.FastMLOutputTreeString = executeFastML(
self.getTempFASTAFile(), self.FastMLInputTreeString, True)
#prepares the FastMLToOriginalMatchedNodes_D
self.MatchNodes()
except Exception as e:
self.Parsed = False
"Removes internal node names so that FastML adds its own naming convention"
def FixUpFileForFastML(self, CogentTree):
#gets the tree string for the cogent object
TreeString = CogentTree.getNewick(with_distances=True).replace("'", "")
i = 0
NotThroughTheString = True
#while loop moves one space along tree string until it gets to the end
while NotThroughTheString:
#when a close bracket is found, it signifies the end of an internal node
if TreeString[i] == ")":
if TreeString[i + 1] == ";":
pass
else:
#tree string replaces the name of the internal node with nothing
lengthToColon = len(
re.compile("^(.+?)[:;]").search(
TreeString[i:]).group(1)) - 1
TreeString = TreeString[:i +
1] + TreeString[i + lengthToColon +
1:]
#check to end while loop
if i == len(TreeString) - 1:
NotThroughTheString = False
i += 1
return TreeString
"Prepares simple FastaFile to be given to FastML"
def getTempFASTAFile(self):
retString_L = []
#FastaFile will have the sequence "GREAT" for each terminal sequence
for LeafKey in self.LeafKey_L:
retString_L.append(">" + LeafKey)
retString_L.append("GREAT")
return '\n'.join(retString_L)
"Corrects for instances where FastML anomalously renames terminal nodes"
def correctForFastMLNameChanges(self):
#gets lists of terminal names in the FastML input and output strings (in the same order)
FastMLInputNames = [
re.compile("^(.+?):").search(TaxString).group(1) for TaxString in
re.findall("[A-Za-z0-9_./]+:[.0-9]+", self.FastMLInputTreeString)
]
#print FastMLInputNames
FastMLOutputNames = [
re.compile("^(.+?):").search(TaxString).group(1) for TaxString in
re.findall("[A-Za-z0-9_./]+:[.0-9]+", self.FastMLOutputTreeString)
]
FastMLOutputNames = [
Name for Name in FastMLOutputNames
if re.compile("^N[0-9]+$").search(Name) == None
]
#when equivalent node names are not the same, then the output string node name is renamed according to the input string node name
for i in range(0, len(FastMLInputNames)):
if FastMLInputNames[i] != FastMLOutputNames[i]:
self.FastMLOutputTreeString = re.sub(
"([,\(\)])%s:" % (FastMLOutputNames[i]),
r"\1%s:" % (FastMLInputNames[i]),
self.FastMLOutputTreeString)
"Matches original (cogent) node names with how the nodes are named in FastML"
def MatchNodes(self):
#print "YAY"
self.correctForFastMLNameChanges(
) #performs the correction on the output string if necessary
#print "NAY"
TerminiStringToNodeName_D = {}
#a termini string is prepared for each internal node, that is, all termini under the internal node sorted an placed into a single string
for NodeKey in self.UpperKey_L:
TerminiStringToNodeName_D['-'.join(
sorted(self.Nodes_D[NodeKey]['terminal']))] = NodeKey
#prepares a cogent tree object for the fastML output
FH = getInputTempFile(self.FastMLOutputTreeString)
FastMLCogentTree = LoadTree(FH.name)
self.FastMLToOriginalMatchedNodes_D = {}
#for each cogent node in the FastML cogent tree
for FastMLCogentNodeKey in FastMLCogentTree.getNodeNames():
#a termini string is prepared for the fastML node
FastMLCogentNode = FastMLCogentTree.getNodeMatchingName(
FastMLCogentNodeKey)
FastMLTermini_L = [tip.Name for tip in FastMLCogentNode.iterTips()]
#if it has more than 0 termini under the node
if len(FastMLTermini_L) > 0:
#A fastML termini string is prepared, and this termini string will be the same termini string as the equivalent cogent node
FastMLTerminiString = '-'.join(sorted(FastMLTermini_L))
self.FastMLToOriginalMatchedNodes_D[
FastMLCogentNodeKey] = TerminiStringToNodeName_D[
FastMLTerminiString]
#if it has no termini under it, then the node itself is a terminus and has the same name in FastML and Cogent
else:
self.FastMLToOriginalMatchedNodes_D[
FastMLCogentNodeKey] = FastMLCogentNodeKey
"Sets branch lengths of each node"
def setBranchLengths(self):
self.BranchLength_D = {}
#gets the distance between a node and its immediate ancestor
for NodeNameKey in self.NodeKey_L:
HigherNode = self.CogentTree.getNodeMatchingName(NodeNameKey)
for ImmediateNeighbourNodeNameKey in self.Nodes_D[NodeNameKey][
'immediate']:
LowerNode = self.CogentTree.getNodeMatchingName(
ImmediateNeighbourNodeNameKey)
self.BranchLength_D[
ImmediateNeighbourNodeNameKey] = HigherNode.distance(
LowerNode)
class FastMLTree:
"""
Class attributes:
Parsed (Bool): an indication of whether or not the user-defined tree was successfully parsed, if it was not, then the rest of the analysis is not performed
TreePath (String): absolute path to tree file
NeedsToBeCogentModded (Bool): whether or not placeholder names for the internal nodes need to be created
CogentTree (Object LoadTree): pyCogent Class object containing parsed newick syntax tree
FastMLInputTreeString (String): representation of tree in newick with internal node names removed
FastMLOutputTreeString (String): representation of tree in newick with internal nodes named according to FastML naming convention
FastMLToOriginalMatchedNodes_D (Dict): Key is the node name in the cogent convention, value is the node name in the FastML convention
NodeKey_L (List): List of all node name keys
LeafKey_L (List): List of all terminal node name keys
UpperKey_L (List): List of all internal (non-terminal) node name keys
TopKey (String): root node name key
BranchKey_L (List): List of all paths (from ancestral to immediate derived) along the tree
Nodes_D (Dict): Key is the node name, value is a sub-dict containing immediate derived nodes and terminal nodes under the node
"""
"CONSTRUCTOR"
def __init__(self, TreePath , NeedsToBeCogentModded):
self.Parsed = True #used to determine if the full analysis can be conducted
try:
self.TreePath = TreePath
self.NeedsToBeCogentModded = NeedsToBeCogentModded
self.CogentTree = None
#if the internal nodes need to be renamed, then it is done according to the "FixUpFileForCogent" method
if self.NeedsToBeCogentModded:
cogentFixUp = fixUpFileForCogent(self.TreePath)
self.CogentTreeFile = cogentFixUp[0]
self.CogentInputTreeString = cogentFixUp[1]
self.CogentTree = LoadTree(self.CogentTreeFile.name)
else:
self.CogentTree = LoadTree(self.TreePath)
#prepares an input string for FastML
self.FastMLInputTreeString = self.FixUpFileForFastML(self.CogentTree)
#executes method to fully parse tree, then sets all returned variables as class variables
CogentNodesLeavesBranches = completeNodesLeavesBranches(self.CogentTree)
self.NodeKey_L = CogentNodesLeavesBranches['NodeKey_L']
self.LeafKey_L = CogentNodesLeavesBranches['LeafKey_L']
self.UpperKey_L = CogentNodesLeavesBranches['UpperKey_L']
self.TopKey = CogentNodesLeavesBranches['TopKey']
self.BranchKey_L = CogentNodesLeavesBranches['BranchKey_L']
self.Nodes_D = CogentNodesLeavesBranches['Nodes_D']
#print self.LeafKey_L
#executes quick run of FastML to get FastML's naming convention of internal nodes
self.FastMLOutputTreeString = executeFastML(self.getTempFASTAFile() , self.FastMLInputTreeString , True)
#prepares the FastMLToOriginalMatchedNodes_D
self.MatchNodes()
except Exception as e:
self.Parsed = False
"Removes internal node names so that FastML adds its own naming convention"
def FixUpFileForFastML(self, CogentTree):
#gets the tree string for the cogent object
TreeString = CogentTree.getNewick(with_distances=True).replace("'","")
i = 0
NotThroughTheString = True
#while loop moves one space along tree string until it gets to the end
while NotThroughTheString:
#when a close bracket is found, it signifies the end of an internal node
if TreeString[i] == ")":
if TreeString[i+1] == ";":
pass
else:
#tree string replaces the name of the internal node with nothing
lengthToColon = len(re.compile("^(.+?)[:;]").search(TreeString[i:]).group(1)) - 1
TreeString = TreeString[:i+1]+ TreeString[i+lengthToColon+1:]
#check to end while loop
if i == len(TreeString) - 1:
NotThroughTheString = False
i += 1
return TreeString
"Prepares simple FastaFile to be given to FastML"
def getTempFASTAFile(self):
retString_L = []
#FastaFile will have the sequence "GREAT" for each terminal sequence
for LeafKey in self.LeafKey_L:
retString_L.append(">"+LeafKey)
retString_L.append("GREAT")
return '\n'.join(retString_L)
"Corrects for instances where FastML anomalously renames terminal nodes"
def correctForFastMLNameChanges(self):
#gets lists of terminal names in the FastML input and output strings (in the same order)
FastMLInputNames = [re.compile("^(.+?):").search(TaxString).group(1) for TaxString in re.findall("[A-Za-z0-9_./]+:[.0-9]+",self.FastMLInputTreeString)]
#print FastMLInputNames
FastMLOutputNames = [re.compile("^(.+?):").search(TaxString).group(1) for TaxString in re.findall("[A-Za-z0-9_./]+:[.0-9]+",self.FastMLOutputTreeString)]
FastMLOutputNames = [Name for Name in FastMLOutputNames if re.compile("^N[0-9]+$").search(Name) == None]
#when equivalent node names are not the same, then the output string node name is renamed according to the input string node name
for i in range(0,len(FastMLInputNames)):
if FastMLInputNames[i] != FastMLOutputNames[i]:
self.FastMLOutputTreeString = re.sub("([,\(\)])%s:" % (FastMLOutputNames[i]) , r"\1%s:" % (FastMLInputNames[i]) , self.FastMLOutputTreeString)
"Matches original (cogent) node names with how the nodes are named in FastML"
def MatchNodes(self):
#print "YAY"
self.correctForFastMLNameChanges() #performs the correction on the output string if necessary
#print "NAY"
TerminiStringToNodeName_D = {}
#a termini string is prepared for each internal node, that is, all termini under the internal node sorted an placed into a single string
for NodeKey in self.UpperKey_L:
TerminiStringToNodeName_D['-'.join(sorted(self.Nodes_D[NodeKey]['terminal']))] = NodeKey
#prepares a cogent tree object for the fastML output
FH = getInputTempFile(self.FastMLOutputTreeString)
FastMLCogentTree = LoadTree(FH.name)
self.FastMLToOriginalMatchedNodes_D = {}
#for each cogent node in the FastML cogent tree
for FastMLCogentNodeKey in FastMLCogentTree.getNodeNames():
#a termini string is prepared for the fastML node
FastMLCogentNode = FastMLCogentTree.getNodeMatchingName(FastMLCogentNodeKey)
FastMLTermini_L = [tip.Name for tip in FastMLCogentNode.iterTips()]
#if it has more than 0 termini under the node
if len(FastMLTermini_L) > 0:
#A fastML termini string is prepared, and this termini string will be the same termini string as the equivalent cogent node
FastMLTerminiString = '-'.join(sorted(FastMLTermini_L))
self.FastMLToOriginalMatchedNodes_D[FastMLCogentNodeKey] = TerminiStringToNodeName_D[FastMLTerminiString]
#if it has no termini under it, then the node itself is a terminus and has the same name in FastML and Cogent
else:
self.FastMLToOriginalMatchedNodes_D[FastMLCogentNodeKey] = FastMLCogentNodeKey
"Sets branch lengths of each node"
def setBranchLengths(self):
self.BranchLength_D = {}
#gets the distance between a node and its immediate ancestor
for NodeNameKey in self.NodeKey_L:
HigherNode = self.CogentTree.getNodeMatchingName(NodeNameKey)
for ImmediateNeighbourNodeNameKey in self.Nodes_D[NodeNameKey]['immediate']:
LowerNode = self.CogentTree.getNodeMatchingName(ImmediateNeighbourNodeNameKey)
self.BranchLength_D[ImmediateNeighbourNodeNameKey] = HigherNode.distance(LowerNode)