def main():
usage = "%prog [options] <TREES FILE> [<TREES FILE> [<TREES FILE> [...]]"
parser = OptionParser(usage=usage, add_help_option=True)
parser.add_option('-s',
'--schema',
action='store',
dest='schema',
default="nexus/newick",
help="file format of trees (default = '%s')")
parser.add_option('-v',
'--verbose',
action='store_true',
dest='verbose',
default=False,
help="suppress progress messages")
(opts, args) = parser.parse_args()
support_filepaths = []
missing = False
for fpath in args:
fpath = os.path.expanduser(os.path.expandvars(fpath))
if not os.path.exists(fpath):
sys.stderr.write('File not found: "%s".\n' % fpath)
missing = True
else:
support_filepaths.append(fpath)
if len(support_filepaths) == 0:
sys.stderr.write("No valid tree files specified or found.\n")
sys.exit(1)
start_time = datetime.datetime.now()
total_trees_read = 0
for t in multi_tree_source_iter(support_filepaths, schema=opts.schema):
total_trees_read += 1
end_time = datetime.datetime.now()
parse_time = end_time - start_time
hours, mins, secs = str(end_time - start_time).split(":")
parse_seconds = float(hours * 3600) + float(mins * 60) + float(secs)
if not not opts.verbose:
sys.stderr.write("---\n\n")
sys.stdout.write("%s\t%s\n" %
((", ".join(support_filepaths)), parse_seconds))
if not not opts.verbose:
sys.stderr.write("\nTotal trees parsed: %d\n" % total_trees_read)
sys.stderr.write(" Began at: %s.\n" %
(start_time.isoformat(' ')))
sys.stderr.write(" Ended at: %s.\n" %
(end_time.isoformat(' ')))
sys.stderr.write(
" Parse time: %s hour(s), %s minute(s), %s second(s).\n" %
(hours, mins, secs))
sys.stderr.write(" [= %s seconds]\n" % parse_seconds)
def testMixedNexusAndNewickSameTaxa(self):
filenames = [datagen.reference_trees_filename(schema="newick"),
datagen.reference_trees_filename(schema="nexus"),
datagen.reference_trees_filename(schema="newick"),
datagen.reference_trees_filename(schema="nexus")]
filepaths = [pathmap.tree_source_path(f) for f in filenames]
taxon_set = self.ref_tree_list.taxon_set
for idx, test_tree in enumerate(dataio.multi_tree_source_iter(filepaths, schema="nexus/newick", taxon_set=taxon_set)):
self.assertDistinctButEqualTree(self.next_ref_tree(), test_tree, distinct_taxa=False, ignore_taxon_order=True)
self.assertEqual(idx, 43)
def main():
usage = "%prog [options] <TREES FILE> [<TREES FILE> [<TREES FILE> [...]]"
parser = OptionParser(usage=usage, add_help_option=True)
parser.add_option('-s', '--schema',
action='store',
dest='schema',
default="nexus/newick",
help="file format of trees (default = '%s')")
parser.add_option('-v', '--verbose',
action='store_true',
dest='verbose',
default=False,
help="suppress progress messages")
(opts, args) = parser.parse_args()
support_filepaths = []
missing = False
for fpath in args:
fpath = os.path.expanduser(os.path.expandvars(fpath))
if not os.path.exists(fpath):
sys.stderr.write('File not found: "%s".\n' % fpath)
missing = True
else:
support_filepaths.append(fpath)
if len(support_filepaths) == 0:
sys.stderr.write("No valid tree files specified or found.\n")
sys.exit(1)
start_time = datetime.datetime.now()
total_trees_read = 0
for t in multi_tree_source_iter(support_filepaths, schema=opts.schema):
total_trees_read += 1
end_time = datetime.datetime.now()
parse_time = end_time-start_time
hours, mins, secs = str(end_time-start_time).split(":")
parse_seconds = float(hours * 3600) + float(mins * 60) + float(secs)
if not not opts.verbose:
sys.stderr.write("---\n\n")
sys.stdout.write("%s\t%s\n" % ((", ".join(support_filepaths)), parse_seconds))
if not not opts.verbose:
sys.stderr.write("\nTotal trees parsed: %d\n" % total_trees_read)
sys.stderr.write(" Began at: %s.\n" % (start_time.isoformat(' ')))
sys.stderr.write(" Ended at: %s.\n" % (end_time.isoformat(' ')))
sys.stderr.write(" Parse time: %s hour(s), %s minute(s), %s second(s).\n" % (hours, mins, secs))
sys.stderr.write(" [= %s seconds]\n" % parse_seconds)
def testBurnIn(self):
filenames = [datagen.reference_trees_filename(schema="newick"),
datagen.reference_trees_filename(schema="nexus"),
datagen.reference_trees_filename(schema="newick"),
datagen.reference_trees_filename(schema="nexus")]
filepaths = [pathmap.tree_source_path(f) for f in filenames]
taxon_set = self.ref_tree_list.taxon_set
self.ref_index = 5
for idx, test_tree in enumerate(dataio.multi_tree_source_iter(filepaths,
schema="nexus/newick",
taxon_set=taxon_set,
tree_offset=5)):
check_tree = self.next_ref_tree(restart_index=5)
self.assertDistinctButEqualTree(check_tree, test_tree, distinct_taxa=False, ignore_taxon_order=True)
self.assertEqual(idx, 23)
def testMixedNexusAndNewickSameTaxa(self):
filenames = [
datagen.reference_trees_filename(schema="newick"),
datagen.reference_trees_filename(schema="nexus"),
datagen.reference_trees_filename(schema="newick"),
datagen.reference_trees_filename(schema="nexus")
]
filepaths = [pathmap.tree_source_path(f) for f in filenames]
taxon_set = self.ref_tree_list.taxon_set
for idx, test_tree in enumerate(
dataio.multi_tree_source_iter(filepaths,
schema="nexus/newick",
taxon_set=taxon_set)):
self.assertDistinctButEqualTree(self.next_ref_tree(),
test_tree,
distinct_taxa=False,
ignore_taxon_order=True)
self.assertEqual(idx, 43)
def testBurnIn(self):
filenames = [
datagen.reference_trees_filename(schema="newick"),
datagen.reference_trees_filename(schema="nexus"),
datagen.reference_trees_filename(schema="newick"),
datagen.reference_trees_filename(schema="nexus")
]
filepaths = [pathmap.tree_source_path(f) for f in filenames]
taxon_set = self.ref_tree_list.taxon_set
self.ref_index = 5
for idx, test_tree in enumerate(
dataio.multi_tree_source_iter(filepaths,
schema="nexus/newick",
taxon_set=taxon_set,
tree_offset=5)):
check_tree = self.next_ref_tree(restart_index=5)
self.assertDistinctButEqualTree(check_tree,
test_tree,
distinct_taxa=False,
ignore_taxon_order=True)
self.assertEqual(idx, 23)
