def main():
super_concat = False
options, args = interface()
xml = ElementTree().parse(options.input,
parser=XMLParser(target=MyTreeBuilder()))
# delete the older subs. models from the xml file
for node in [
'HKYModel', 'gtrModel', 'siteModel', 'patterns', 'treeLikelihood'
]:
xml = delete_node(xml, node, 1)
# delete the kappa and frequency parameters in 'operators'
delete = [
'kappa', 'frequencies', 'alpha', 'pInv', 'ac', 'ag', 'at', 'cg', 'gt'
]
xml = delete_children_from_node(xml, xml.find('operators'), delete)
xml = delete_children_from_node(
xml,
xml.find('mcmc').find('posterior').find('prior'), delete)
# there are 2 log tags, disambiguated w/ id params. delete elements from
# the one we want (fileLog)
xml = delete_children_from_node(xml, get_file_log_section(xml), delete)
# jettison some comments
xml = comment_remover(xml, [
'The general time reversible', 'HKY substitution model', 'site model',
'The unique patterns from 1 to end', 'npatterns='
])
# load our substitution model information
substitution_models = cPickle.load(open(options.subs))
snippets = ElementTree().parse(options.params,
parser=XMLParser(target=MyTreeBuilder()))
# insert patterns on a per locus basis
insert_position = get_position(xml, 'alignment')
xml = insert_patterns_for_locus(xml, substitution_models, insert_position,
snippets)
# insert substitution models on a per locus basis
insert_position = get_position(xml, 'strictClockBranchRates')
xml, insert_position = insert_models_for_locus(xml, substitution_models,
insert_position, snippets)
# insert site models on a per locus basis
xml, insert_position = insert_site_models_for_locus(
xml, substitution_models, insert_position, snippets)
# insert tree likelihoods on a per locus basis
xml, insert_position = insert_tree_likelihoods_for_locus(
xml, substitution_models, insert_position, snippets)
# insert operators
xml = insert_operators_for_locus(xml, substitution_models, snippets)
write(xml, options.output)
pdb.set_trace()
"""model_names, site_names = get_xml_model_names(set(sub_models_from_modeltest.values()))
def open_data_file(path):
with open(path, 'rb') as encoding_detect_file:
file_text = encoding_detect_file.read()
encoding = chardet.detect(file_text)['encoding']
parser = XMLParser(encoding=encoding)
tree = parse(path, parser=parser)
root = tree.getroot()
return root
def xml(self, cmd, **kwargs):
# NOTE: darcs is currently encoding agnostic and will print
# patch metadata byte-for-byte, even in the XML changelog.
etree = ElementTree()
# While we are decoding the XML as latin-1 to be as liberal as
# possible, etree will still raise an exception if any
# non-printable characters are in the XML changelog.
parser = XMLParser(encoding='latin-1')
fp = self._run(cmd, **kwargs)
etree.parse(fp, parser=parser)
self.checkexit(fp.close())
return etree.getroot()
def open(self):
register_namespace("mrng", "http://mremoteng.org")
xmlp = XMLParser(encoding="utf-8")
with open(self.filePath, 'r') as xml_file:
tree = ET.parse(xml_file, parser=xmlp)
self.root = tree.getroot()
def connect(self):
self.__parser = XMLParser(target=XmppHandler(self))
self.send((
'<?xml version=\'1.0\'?><stream:stream xmlns:stream="http://etherx.jabber.org/streams" xmlns="jabber:client" to="%s" version="1.0">'
% (_escape_attrib(self.__jid.domain()), )).encode(self.__encoding))
self.__stream_open = True
