def test_import_combined(self):
test_file = "data/input/processed_tree.tre"
tree = import_tree(test_file)
expected_tree = "(Mimodes_graysoni, (Mimus_gilvus, Mimus_polyglottos), ((Mimus_gundlachii, (Nesomimus_macdonaldi, Nesomimus_melanotis, Nesomimus_parvulus, Nesomimus_trifasciatus)), ((Mimus_longicaudatus, ((Mimus_patagonicus, Mimus_thenca), (Mimus_saturninus, Mimus_triurus))), (Oreoscoptes_montanus, (Toxostoma_curvirostre, Toxostoma_rufum)))));"
self.assert_(expected_tree == tree)
test_file = "data/input/processed_tree_translate.tre"
tree = import_tree(test_file)
expected_tree = "(Cettia_fortipes, ((((Garrulax_squamatus, Minla_ignotincta), ((Stachyris_chrysaea, Stachyris_ruficeps), Stachyris_nigriceps)), (((((Stachyris_whiteheadi, ((Zosterops_erythropleurus, Zosterops_japonicus), Zosterops_palpebrosus)), ((Yuhina_bakeri, Yuhina_flavicollis), (Yuhina_gularis, Yuhina_occipitalis))), (Yuhina_castaniceps, Yuhina_everetti)), (Yuhina_brunneiceps, Yuhina_nigrimenta)), Yuhina_diademata)), Yuhina_zantholeuca));"
self.assert_(expected_tree == tree)
def test_import_trees(self):
""" Test reading all trees from a file """
test_file = "data/input/multiple_trees.tre"
tree = import_tree(test_file, tree_no=0)
expected_tree = "(Coracias_caudata, (Gallus_gallus, Apus_affinis), (Acanthisitta_chloris, ((Formicarius_colma, Thamnophilus_nigrocinereus, Furnarius_rufus), (Tyrannus_tyrannus, (Pipra_coronata, Rupicola_rupicola)), (Pitta_guajana, (Smithornis_rufolateralis, (Philepitta_castanea, Psarisomus_dalhousiae)))), (Menura_novaehollandiae, (Climacteris_picumnus, Ptilonorhynchus_violaceus), (Aegithalos_iouschensis, Callaeas_cinerea, Notiomystis_cincta, Tregellasia_leucops, Troglodytes_aedon, Regulus_calendula, Sitta_pygmaea, Pycnonotus_barbatus, Picathartes_gymnocephalus, Parus_inornatus, Orthonyx_spaldingii, Petrochelidon_pyrrhonota, Cisticola_anonymus, Certhia_familiaris, Bombycilla_garrulus, Alauda_arvensis, (Ficedula_strophiata, Turdus_falklandii), (Meliphaga_analoga, Pardalotus_striatus), (Malurus_melanocephalus, Pomatostomus_isidorei), (Dicaeum_melanoxanthum, Nectarinia_olivacea), (Toxorhamphus_novaeguineae, (Melanocharis_nigra, Oedistoma_iliolophum)), (Sylvia_nana, (Garrulax_milleti, Zosterops_senegalensis)), (Cinclus_cinclus, (Mimus_patagonicus, Sturnus_vulgaris)), (Chloropsis_cochinchinensis, Irena_cyanogaster, (Cardinalis_cardinalis, Passer_montanus, Fringilla_montifringilla, (Motacilla_cinerea, Ploceus_cucullatus, Prunella_collaris), (Emberiza_schoeniclus, Thraupis_cyanocephala, Parula_americana, Icterus_parisorum))), ((Artamus_leucorynchus, (Aegithina_tiphia, Vanga_curvirostris)), ((Oriolus_larvatus, (Pachycephala_soror, Vireo_philadelphicus)), (Corvus_corone, Paradisaea_raggiana, (Monarcha_axillaris, Dicrurus_adsimilis), (Coracina_lineata, Lanius_ludovicianus))))))));"
self.assert_(expected_tree == tree)
tree = import_tree(test_file, tree_no=1)
expected_tree2 = "(Coracias_caudata, Gallus_gallus, Apus_affinis, (Acanthisitta_chloris, ((Formicarius_colma, Thamnophilus_nigrocinereus, Furnarius_rufus), (Tyrannus_tyrannus, (Pipra_coronata, Rupicola_rupicola)), (Pitta_guajana, (Smithornis_rufolateralis, (Philepitta_castanea, Psarisomus_dalhousiae)))), (Menura_novaehollandiae, (Climacteris_picumnus, Ptilonorhynchus_violaceus), (Aegithalos_iouschensis, Callaeas_cinerea, Notiomystis_cincta, Tregellasia_leucops, Troglodytes_aedon, Regulus_calendula, Sitta_pygmaea, Pycnonotus_barbatus, Picathartes_gymnocephalus, Parus_inornatus, Orthonyx_spaldingii, Petrochelidon_pyrrhonota, Cisticola_anonymus, Certhia_familiaris, Bombycilla_garrulus, Alauda_arvensis, (Ficedula_strophiata, Turdus_falklandii), (Meliphaga_analoga, Pardalotus_striatus), (Malurus_melanocephalus, Pomatostomus_isidorei), (Dicaeum_melanoxanthum, Nectarinia_olivacea), (Toxorhamphus_novaeguineae, (Melanocharis_nigra, Oedistoma_iliolophum)), (Sylvia_nana, (Garrulax_milleti, Zosterops_senegalensis)), (Cinclus_cinclus, (Mimus_patagonicus, Sturnus_vulgaris)), (Chloropsis_cochinchinensis, Irena_cyanogaster, (Cardinalis_cardinalis, Passer_montanus, Fringilla_montifringilla, (Motacilla_cinerea, Ploceus_cucullatus, Prunella_collaris), (Emberiza_schoeniclus, Thraupis_cyanocephala, Parula_americana, Icterus_parisorum))), ((Artamus_leucorynchus, (Aegithina_tiphia, Vanga_curvirostris)), ((Oriolus_larvatus, (Pachycephala_soror, Vireo_philadelphicus)), (Corvus_corone, Paradisaea_raggiana, (Monarcha_axillaris, Dicrurus_adsimilis), (Coracina_lineata, Lanius_ludovicianus))))))));"
self.assert_(expected_tree2 == tree)
trees = import_trees(test_file)
self.assert_(expected_tree == trees[0])
self.assert_(expected_tree2 == trees[1])
def test_create_tnt_matrix_with_taxonomy(self):
XML = etree.tostring(etree.parse('data/input/create_matrix.phyml',
parser),
pretty_print=True)
taxonomy = import_tree('data/input/paup_tree.tre')
matrix = create_matrix(XML, taxonomy=taxonomy)
self.assertRegexpMatches(matrix, 'Mimus_gilvus')
def handle_click(xml, xpath, path=None):
from lxml import etree
xml_root = etree.fromstring(xml)
if (path == None):
path = os.getcwd()
filter_names_and_patterns = {}
filter_names_and_patterns['Trees'] = ["*.tre","*nex","*.nwk","*.tnt"]
filename = dialogs.get_filename(title = "Choose tree file", action = gtk.FILE_CHOOSER_ACTION_OPEN,
filter_names_and_patterns = filter_names_and_patterns,
folder_uri = path)
if filename == None:
return
# Track back along xpath to find the source element where we're going to set the name
element = xml_root.xpath(xpath+"/string_value")
try:
tree = stk.import_tree(filename,gui=True)
except TreeParseError as detail:
msg = "Failed to import tree - can't parse tree.\n"+detail.msg
dialogs.error(self.main_window,msg)
source_tree_ele = element[0].getparent().getparent().getparent()
tree_name = stk.create_tree_name(xml,source_tree_ele)
print tree_name
element[0].text = tree
source_tree_ele.attrib['name'] = tree_name
stk_gui.interface.plugin_xml = etree.tostring(xml_root)
stk_gui.interface.pluginSender.emit('plugin_changed_xml')
return
def main():
# do stuff
parser = argparse.ArgumentParser(
prog="supertree_support",
description="Add supertree support measures to your supertree.",
)
parser.add_argument('-v',
'--verbose',
action='store_true',
help="Verbose output: mainly progress reports.",
default=False)
parser.add_argument(
'--measure',
choices=['v', 'v+', 'v-', 'wv', 'wv+', 'wv-'],
default='v+',
help=
"Choose measure to add to the supertree output. The w version weight against the length of the source tree."
)
parser.add_argument('input_file',
metavar='input_file',
nargs=1,
help="Your Phyml")
parser.add_argument('input_supertree',
metavar='input_supertree',
nargs=1,
help="Your supertree")
parser.add_argument(
'output_file',
metavar='output_file',
nargs=1,
help="The output stub for all the various output files")
args = parser.parse_args()
verbose = args.verbose
measure = args.measure
input_file = args.input_file[0]
input_supertree = args.input_supertree[0]
output_stub = args.output_file[0]
if measure == 'wv+':
measure = 10
elif measure == 'wv':
measure = 9
elif measure == 'wv-':
measure = 11
elif measure == 'v+':
measure = 7
elif measure == 'v':
measure = 6
elif measure == 'v-':
measure = 8
else:
print "Unknown metric"
sys.exit(-1)
# see p4.SuperTreeSupport for indices.
# if non stadard decoration, what metric to use
# [S, P, R, Q, WS, WP, V, V+, V-, wV, wV+,wV-]
# 0 1 2 3 4 5 6 7 8 9 10 11
# grab taxa in dataset
if (verbose):
print "Parsing PHYML"
XML = stk.load_phyml(input_file)
taxa = stk.get_all_taxa(XML)
# load supertree
supertree_data = stk.import_tree(input_supertree)
supertree = stk._parse_tree(supertree_data)
terminals = supertree.getAllLeafNames(supertree.root)
if (not len(taxa) == len(terminals)):
# this happens if the supertree has been pruned to remove dodgy taxa
if (verbose):
print "Warning: supertree contains different number of taxa to your input data. Pruning input data"
taxa.sort()
terminals.sort()
delete_me = []
# create subs file
for t in taxa:
if not t in terminals:
delete_me.append(t)
# strip from phyml
if (verbose):
print "Deleting: " + str(len(delete_me)) + " from original " + str(
len(taxa))
try:
XML = stk.substitute_taxa(XML, delete_me, ignoreWarnings=True)
# do we need a clean data to check for non-informative trees here?
except TreeParseError as detail:
msg = "***Error: failed to parse a tree in your data set.\n" + detail.msg
print msg
return
# get all trees from phyml
input_trees = stk.obtain_trees(XML)
source_trees = []
for t in input_trees:
source_trees.append(stk._parse_tree(input_trees[t]))
sts = SuperTreeSupport(input_supertree, source_trees)
sts.doSaveDecoratedTree = True
sts.doStandardDecoration = False
sts.decorationMetric = measure
sts.decoratedFilename = output_stub + '_dec_st.nex'
sts.doSaveIndexTree = True
sts.indexFilename = output_stub + '_index.nex'
sts.csvFilename = output_stub + '_index.csv'
sts.doDrawTree = False
sts.verbose = 1
sts.superTreeSupport()
def test_import_paup(self):
test_file = "data/input/paup_tree.tre"
tree = import_tree(test_file)
expected_tree = "(Mimodes_graysoni, (Mimus_gilvus, Mimus_polyglottos), ((Mimus_gundlachii, (Nesomimus_macdonaldi, Nesomimus_melanotis, Nesomimus_parvulus, Nesomimus_trifasciatus)), ((Mimus_longicaudatus, ((Mimus_patagonicus, Mimus_thenca), (Mimus_saturninus, Mimus_triurus))), (Oreoscoptes_montanus, (Toxostoma_curvirostre, Toxostoma_rufum)))));"
self.assert_(_trees_equal(expected_tree, tree))
def test_import_macclade(self):
test_file = "data/input/macclade_test.tre"
tree = import_tree(test_file)
expected_tree = "((Taxon_c, (Taxon_a, Taxon_b)), (Taxon_d, Taxon_e));"
self.assert_(_trees_equal(expected_tree, tree))
def test_import_dendroscope(self):
test_file = "data/input/dendroscope_test.tre"
tree = import_tree(test_file)
expected_tree = "((Taxon_c:1, (Taxon_a:1, Taxon_b:1):0):0, (Taxon_d:1, Taxon_e:1):0);"
self.assert_(_trees_equal(expected_tree, tree))
def test_import_mesquite(self):
test_file = "data/input/mesquite_test.tre"
expected_tree = "((Taxon_c, (Taxon_a, Taxon_b)), (Taxon_d, Taxon_e));"
tree = import_tree(test_file)
self.assert_(expected_tree == tree)
def test_import_tutorial_tree(self):
test_file = "../../doc/tutorial/5.3_DataEntry/HallThatje_2009.tre"
e_tree = "((Aegla_sp., (Pagurus_bernhardus, Pagurus_hirsutiusculus)), (((Cryptolithodes_sitchensis, Cryptolithodes_typicus), (Phyllolithodes_papillosus, (Lopholithodes_mandtii, (Glyptolithodes_cristatipes, (Paralomis_formosa, Paralomis_spinosissima))), (Neolithodes_brodiei, (Paralithodes_camtschaticus, Paralithodes_brevipes), (Lithodes_confundens, Lithodes_ferox)))), (Oedignathus_inermis, (Hapalogaster_dentata, Hapalogaster_mertensii))));"
tree = import_tree(test_file)
self.assert_(e_tree == tree)
def test_import_quoted_tree(self):
test_file = "data/input/quoted_taxa.tre"
e_tree = "(('Taxon (c)', (Taxon_a, Taxon_b)), (Taxon_d, Taxon_e));"
tree = import_tree(test_file)
self.assert_(e_tree == tree)