def handle_click(xml, xpath, path=None):
from lxml import etree
xml_root = etree.fromstring(xml)
# Track back along xpath to find the source element where we're going to set the name
element = xml_root.xpath(xpath + "/string_value")
tree = element[0].text
if (path == None):
path = os.getcwd()
filter_names_and_patterns = {}
filter_names_and_patterns['Phylo files'] = [
"*.tre", "*nex", "*.nwk", "*.new", "*.tnt"
]
filename = dialogs.get_filename(
title="Choose tree file",
action=gtk.FILE_CHOOSER_ACTION_SAVE,
filter_names_and_patterns=filter_names_and_patterns,
folder_uri=path)
if filename == None:
return
# guess format based on ending, assuming matrix
new_output, ext = os.path.splitext(filename)
output_string = ""
if ext == ".tre":
# Nexus tree file
output_string = stk.permute_tree(tree, treefile="nexus")
elif ext == ".nex":
# Nexus matrix
output_string = stk.permute_tree(tree, matrix="nexus")
elif ext == ".tnt":
# tnt matrix
output_string = stk.permute_tree(tree, matrix="hennig")
elif ext == ".new" or ext == ".nwk":
# newick tree
output_string = stk.permute_tree(tree, treefile="newick")
else:
dialogs.error(
None,
"Error creating permuting trees. Unknown format. Did you use a file extension to indicate the format required?"
)
f = open(filename, 'w')
f.write(output_string)
f.close
return
def test_permute_tree_quoted(self):
"""Test an awkward tree to permute"""
tree = "(((Theatops_posticus, (Cryptops_spinipes, Scolopocryptops_sexspinosus)),((Rhysida_nuda, ((Alipes_crotalus, (Ethmostigmus_rubripes, (Ethmostigmus_sp1, Ethmostigmus_sp2))), (((Rhysida_sp, (Rhysida_lithobiodis, Rhysida_imarginata%1)), (Rhysida_imarginata%2, Rhysida_longipes%1)), (Rhysida_imarginata%3, (Rhysida_imarginata%4, (Rhysida_imarginata%5, Rhysida_longipes%2)))), (Digitipes_coonoorensis, Digitipes_sp1, Digitipes_barnabasi, Digitipes_sp2))), ((Cormocephalus_monthanii, (Cormocephalus_nigrificatus, (Cormocephalus_sp1, (Cormocephalus_nudipes, (Cormocephalus_sp2, Cormocephalus_westwoodi))))), (('Scolopendra cf. morsitans%1', 'Scolopendra cf. morsitans%2', ('Scolopendra cf. morsitans%3', Scolopendra_cf._amazonica)), (Asanada_agharkari, Asanada_brevicornis))))), (Craterostigmus_tasmanianus, Craterostigmus_crabilli), (Mecistocephalus_guildingii, ((Himantarium_gabrielis, Bothriogaster_signata), (Geophilus_electricus, (Strigamia_maritima, Pachymerium_ferrugineum)))));"
try:
trees = permute_tree(tree, treefile="nexus")
except:
self.assert_(False)
def test_permute_trees_3(self):
XML = etree.tostring(etree.parse('data/input/permute_trees.phyml',
parser),
pretty_print=True)
trees = obtain_trees(XML)
# contains quoted taxa too
output = permute_tree(trees['Hill_Davis_2011_2'], treefile="newick")
self.assert_(_trees_equal(output, "(A, (B, (C, D, E_E, F, G)));"))
def test_permute_trees_2(self):
XML = etree.tostring(etree.parse('data/input/permute_trees.phyml',
parser),
pretty_print=True)
trees = obtain_trees(XML)
output = permute_tree(trees['Davis_2011_1'], treefile="newick")
temp_file_handle, temp_file = tempfile.mkstemp(suffix=".new")
f = open(temp_file, "w")
f.write(output)
f.close()
output_trees = import_trees(temp_file)
expected_trees = import_trees("data/output/permute_trees_2.nex")
os.remove(temp_file)
self.assert_(len(output_trees) == len(expected_trees))
for i in range(0, len(output_trees)):
self.assert_(_trees_equal(output_trees[i], expected_trees[i]))
def test_collapse_with_quotes(self):
tree = "(Proteroiulus_fuscus, (Craterostigmus_tasmanianus, ((Scolopendra_viridis,(Lithobius_variegatus, (Paralamyctes_validus, Anopsobius_neozelanicus))),(Sphendononema_guildingii, ((Scutigerina_weberi%1, (Scutigerina_weberi%2,(Scutigerina_malagassa, Scutigerina_hova))), (Scutigera_coleoptrata,((Thereuopoda_longicornis, 'Thereuopodina, sp. nov.', (Thereuonema_tuberculata,Thereuonema_turkestana, Thereuopoda_clunifera)), (Allothereua_bidenticulata,Allothereua_serrulata, Parascutigera_festiva, Parascutigera_latericia))))))));"
output = permute_tree(tree, treefile="newick")
expected_tree = "(Proteroiulus_fuscus, (Craterostigmus_tasmanianus,((Scolopendra_viridis,(Lithobius_variegatus,(Paralamyctes_validus,Anopsobius_neozelanicus))),(Sphendononema_guildingii,((Scutigerina_weberi,(Scutigerina_malagassa, Scutigerina_hova)), (Scutigera_coleoptrata,((Thereuopoda_longicornis, 'Thereuopodina, sp. nov.', (Thereuonema_tuberculata,Thereuonema_turkestana, Thereuopoda_clunifera)), (Allothereua_bidenticulata,Allothereua_serrulata, Parascutigera_festiva, Parascutigera_latericia))))))));"
self.assert_(_trees_equal(output, expected_tree))