class OIDTreeParser(object):
"""
Parse the oid.tre PAUP run file for the given Nexus Tree.
Uses the oid translation table to rename node taxon correctly.
@deprecated
"""
def __init__(self):
assert False, "Dummy, use the NEXUS parser"
TRANSLATION = "Translate"
NUMBER = "number"
TAXON = "taxon"
TREE = "tree"
name_line = Group(Word(nums).setResultsName(NUMBER)+
Word(alphanums+punctuation).setParseAction(lambda tokens:[tokens[0].replace(",","")]).setResultsName(TAXON)
)
tree = (Consume(Literal(";")).setResultsName(TREE)
)
translation = (OneOrMore(name_line).setResultsName(TRANSLATION)+
Literal(";")
)
expression = (Consume(Literal(TRANSLATION)).suppress()+
translation+
Consume(Literal("tree PAUP_1 = [&R]")).suppress()+
tree+
empty
)
def parse(self,handle):
ps = OIDTreeParser
result = OIDTreeParser.expression.parseFile(handle)
from Bio.Nexus.Trees import Tree
self.taxon = {}
runtime().debug("Found",len(result[ps.TRANSLATION]),"species")
print result
for translation in result[ps.TRANSLATION]:
print translation
num = translation[ps.NUMBER]
taxon = translation[ps.TAXON]
runtime().debug(num,taxon)
self.taxon[num] = taxon
self.tree = Tree(result[ps.TREE])
assert self.tree.count_terminals() == len(self.taxon.keys(),
"Translation count and # of tree terminals don't match")
for node in self.tree.get_terminals():
runtime().debug("Rename",node.get_data().taxon,"to",self.taxon[node.get_data().taxon])
node.get_data().taxon = self.taxon[node.get_data().taxon]
self.tree.no
return self
