class Wrapper(object):
'''
This class contains wrappers for all the tools used in this project
'''
def __init__(self, workDir, resultsFile, inFile, coreId, seqType, seedNum, bootNum, method, interLeaved):
'''
Data Fields:
work_dir = temproray directory
inFile = data file,
id = core id (int),
seqType = d (dna); p (protein); r (rna),
bootNum = number of replicates,
seedNum = Random number seed between 1 and 32767
method =b (Bootstrap) Default,
j (Jackknife)
c (Permute species for each character)
o (Permute character order)
s (Permute within species)
r (Rewrite data)),
interLeaved=True if sequence data is interleaved otherwise False
'''
self.work_dir = workDir
self.resultsFile = resultsFile
self.inFile = inFile
self.coreId = coreId
self.seqType = seqType
self.seedNum = seedNum
self.bootNum = bootNum
self.method = method
self.n = bootNum
self.nt = False
self.interLeaved = interLeaved
self.outFile = "bootstrap_"+str(coreId)+".out"
self.newSpeciesTree = Tree()
self.leafLabelStree = []
self.internalExRootSpeceLabels= []
if self.seqType in ['r', 'd']:
self.nt = True
def getSpeciesTree(self):
return self.newSpeciesTree
def setSpeceistree(self, stree):
self.newSpeciesTree= stree
def writeSpeciesTree(self):
self.newSpeciesTree.write_to_path(self.resultsFile+'.speciestree.'+str(self.coreId), 'newick', suppress_internal_node_labels=False,annotations_as_nhx=True, extract_comment_metadata=True , suppress_annotations=False)
def allLeafLabels(self, myTree):
'''
returns the list containing all the leaf nodes' label of this tree and the internal nodes without the root label
'''
leafLabels=[]
internalLabelsExRoot=[]
for i in myTree.leaf_nodes():
leafLabels.append(i.get_node_str().replace("'", ""))
for i in myTree.internal_nodes():
if i.level() != 0:
internalLabelsExRoot.append(i.label)
return leafLabels, internalLabelsExRoot
def onlyLeafLabels(self, myTree):
'''
returns the list containing labels of leaf nodes for this tree
'''
leafLabels=[]
for i in myTree.leaf_nodes():
leafLabels.append(i.get_node_str().replace("'", ""))
return leafLabels
def readTreeFromFile(self, treePath):
'''
input: path to the file containing newick tree
return Tree object
'''
print treePath
myTree= Tree()
myTree= Tree.get_from_path(treePath, 'newick', suppress_edge_lengths=False, annotations_as_nhx=True, extract_comment_metadata=True , suppress_annotations=False)
return myTree
def readTreeFromString(self, treeString):
'''
input: string containing newick tree
return Tree object
'''
myTree= Tree()
myTree= Tree.get_from_string( treeString, 'newick', annotations_as_nhx=True, extract_comment_metadata=True , suppress_annotations=False)
return myTree
def checkExe(self, exePath):
return os.path.isfile(exePath) and os.access(exePath, os.X_OK)
def Where(self, program):
'''
input: name of executable
output: path to executable
'''
fpath, fname = os.path.split(program)
if fpath:
if self.checkExe(program):
return program
else:
for path in os.environ["PATH"].split(os.pathsep):
path = path.strip('"')
pathToProgram = os.path.join(path, program)
if self.checkExe(pathToProgram):
return pathToProgram
return None
def checkNotung(self, program):
for path in os.environ["PATH"].split(os.pathsep):
path = path.strip('"')
pathToProgram = os.path.join(path, program)
if os.path.isfile(pathToProgram):
return pathToProgram
return None
def WrapFseqboot(self):
'''
WrapFseqboot() function is a wrapper over the fseqboot tool.
input: inFile = data file,
id = core id (int),
seqType = d (dna); p (protein); r (rna),
bootNum = number of replicates,
seedNum = Random number seed between 1 and 32767
method = b (Bootstrap) Default,
j (Jackknife)
c (Permute species for each character)
o (Permute character order)
s (Permute within species)
r (Rewrite data)),
output: bootstrap alignments to bootstrap_(id).out
'''
# check if path exists
cmd= self.Where('fseqboot')
if cmd != None:
bootSeqOutFile= os.path.join(self.work_dir, self.outFile)
print "bootSeqOutFile: %s" % bootSeqOutFile
null = open("/dev/null")
print "--> Bootstrap begins..."
try:
cline = FSeqBootCommandline(sequence = self.inFile, outfile = bootSeqOutFile, seqtype = self.seqType, test= self.method, seed= self.seedNum, reps = self.bootNum, filter = True)
stdout, stderr= cline()
except IOError, e:
print ("Class: Wrapper, Function: WrapFseqboot(): %s " % e)
print "--> Bootstrap done..."
else:
