def main_cli():
description = "%s %s %s" % (_program_name, _program_version, _program_subtitle)
parser = argparse.ArgumentParser(version =_program_version, description=description)
parser.add_argument(
"sources",
metavar="TREEFILE",
nargs="+")
parser.add_argument("-t","--target",
dest="target_tree_filepath",
default=None,
help="path to file with tree (Newick or NEXUS format) "
+ "to which labels will be written")
parser.add_argument("--preserve-target-labels",
action="store_true",
dest="preserve_target_labels",
default=False,
help="keep any existing labels on target tree (by default, these will be cleared before writing the new labels)")
parser.add_argument("--rooted",
action="store_true",
dest="rooted_trees",
default=None,
help="treat trees as rooted")
parser.add_argument("--unrooted",
action="store_false",
dest="rooted_trees",
default=None,
help="treat trees as unrooted")
parser.add_argument("--ignore-missing-source",
action="store_true",
dest="ignore_missing_source",
default=False,
help="ignore missing source tree files (at least one must exist!)")
parser.add_argument("-o","--output",
dest="output_filepath",
default=None,
help="path to output file (if not given, will print to standard output)")
parser.add_argument("-s","--separator",
dest="separator",
default="/",
help="string to use to separate labels from different source trees (default='%(default)s')")
parser.add_argument("--no-taxa-block",
action="store_false",
dest="include_taxa_block",
default=True,
help="do not include a taxa block in the output treefile (otherwise will create taxa block by default)")
parser.add_argument("-c", "--additional-comments",
action="store",
dest="additional_comments",
default=None,
help="additional comments to be added to the summary file")
parser.add_argument("--to-newick",
action="store_true",
dest="to_newick_format",
default=False,
help="save results in NEWICK (PHYLIP) format (default is to save in NEXUS format)")
parser.add_argument("--to-phylip",
action="store_true",
dest="to_newick_format",
default=False,
help="same as --to-newick")
parser.add_argument("-r", "--replace",
action="store_true",
dest="replace",
default=False,
help="replace/overwrite output file without asking if it already exists ")
parser.add_argument("-q", "--quiet",
action="store_true",
dest="quiet",
default=False,
help="suppress ALL logging, progress and feedback messages")
args = parser.parse_args()
if args.quiet:
messaging_level = ConsoleMessenger.ERROR_MESSAGING_LEVEL
else:
messaging_level = ConsoleMessenger.INFO_MESSAGING_LEVEL
messenger = ConsoleMessenger(name="SumLabels", messaging_level=messaging_level)
# splash
if not args.quiet:
show_splash(prog_name=_program_name,
prog_subtitle=_program_subtitle,
prog_version=_program_version,
prog_author=_program_author,
prog_copyright=_program_copyright,
dest=sys.stderr,
)
###################################################
# Source file idiot checking
source_filepaths = []
if len(args.sources) > 0:
for fpath in args.sources:
fpath = os.path.expanduser(os.path.expandvars(fpath))
if not os.path.exists(fpath):
if args.ignore_missing_source:
messenger.send_warning("Source file not found: '%s'" % fpath)
else:
messenger.error("Terminating due to missing source files. "
+ "Use the '--ignore-missing-source' option to continue even "
+ "if some files are missing.")
sys.exit(1)
else:
source_filepaths.append(fpath)
if len(source_filepaths) == 0:
messenger.error("No valid sources of input trees specified. "
+ "Please provide the path to at least one (valid and existing) file "
+ "containing trees")
sys.exit(1)
else:
messenger.info("No sources of input trees specified. "
+ "Please provide the path to at least one (valid and existing) file "
+ "containing tree samples to summarize. See '--help' for other options.")
sys.exit(1)
###################################################
# Lots of other idiot-checking ...
# target tree
if args.target_tree_filepath is not None:
target_tree_filepath = os.path.expanduser(os.path.expandvars(args.target_tree_filepath))
if not os.path.exists(target_tree_filepath):
messenger.error("Target tree file not found: '%s'" % target_tree_filepath)
sys.exit(1)
else:
messenger.error("Target tree file not specified: use the '-t' or '--target' option to provide path to target tree")
sys.exit(1)
# output
if args.output_filepath is None:
output_dest = sys.stdout
else:
output_fpath = os.path.expanduser(os.path.expandvars(args.output_filepath))
if confirm_overwrite(filepath=output_fpath, replace_without_asking=args.replace):
output_dest = open(output_fpath, "w")
else:
sys.exit(1)
# taxon set to handle target trees
master_taxon_namespace = dendropy.TaxonNamespace()
is_rooted = args.rooted_trees
messenger.info("Reading target tree: '%s'" % target_tree_filepath)
target_tree = None
if is_rooted:
rooting = "force-rooted"
else:
rooting = None
for tree in dendropy.Tree.yield_from_files(
[target_tree_filepath, "rU",],
schema='nexus/newick',
taxon_namespace=master_taxon_namespace,
rooting=rooting):
target_tree = tree
break
bipartition_labels = {}
for src_fpath in source_filepaths:
messenger.info("Reading source tree(s) from: '%s'" % src_fpath)
for tree in dendropy.Tree.yield_from_files(
[src_fpath,],
schema='nexus/newick',
taxon_namespace=master_taxon_namespace,
rooting=rooting):
tree.encode_bipartitions()
for bipartition, edge in tree.bipartition_edge_map.items():
label = edge.head_node.label
if not label:
continue
try:
bipartition_labels[bipartition].append(label)
except KeyError:
bipartition_labels[bipartition] = [label]
messenger.info("Mapping labels")
target_tree.encode_bipartitions()
for bipartition, edge in target_tree.bipartition_edge_map.items():
label = []
if args.preserve_target_labels and edge.head_node.label:
label.append(edge.head_node.label)
elif not args.preserve_target_labels:
edge.head_node.label = None
if bipartition in bipartition_labels:
label.extend(bipartition_labels[bipartition])
else:
pass
# messenger.send_warning("Split on target tree not found in source trees: ignoring")
if label:
edge.head_node.label = args.separator.join(label)
output_dataset = dendropy.DataSet()
tree_list = output_dataset.new_tree_list(taxon_namespace=master_taxon_namespace)
tree_list.append(target_tree)
if args.to_newick_format:
output_dataset.write(
file=output_dest,
schema="newick",
suppress_rooting=False,
suppress_edge_lengths=False,
unquoted_underscores=False,
preserve_spaces=False,
store_tree_weights=False,
suppress_annotations=False,
annotations_as_nhx=False,
suppress_item_comments=False,
suppress_leaf_taxon_labels=False,
suppress_leaf_node_labels=True,
suppress_internal_taxon_labels=False,
suppress_internal_node_labels=False,
node_label_element_separator=' ',
)
else:
if args.include_taxa_block:
simple = False
else:
simple = True
comment = []
try:
username = getpass.getuser()
except:
username = "******"
comment.append("%s %s by %s." % (_program_name, _program_version, _program_author))
comment.append("Using DendroPy Version %s by Jeet Sukumaran and Mark T. Holder."
% dendropy.__version__)
python_version = sys.version.replace("\n", "").replace("[", "(").replace("]",")")
comment.append("Running under Python %s on %s." % (python_version, sys.platform))
comment.append("Executed on %s by %s@%s." % (platform.node(), username, socket.gethostname()))
if args.additional_comments:
comment.append("\n")
comment.append(args.additional_comments)
output_dataset.write(
file=output_dest,
schema="nexus",
simple=simple,
file_comments=comment,
suppress_rooting=False,
unquoted_underscores=False,
preserve_spaces=False,
store_tree_weights=False,
suppress_annotations=False,
annotations_as_nhx=False,
suppress_item_comments=False,
suppress_leaf_taxon_labels=False,
suppress_leaf_node_labels=True,
suppress_internal_taxon_labels=False,
suppress_internal_node_labels=False,
node_label_element_separator=' ',
)
if not args.output_filepath:
pass
else:
messenger.info("Results written to: '%s'." % (output_fpath))
def main_cli():
description = "%s %s %s" % (_program_name, _program_version,
_program_subtitle)
parser = argparse.ArgumentParser(version=_program_version,
description=description)
parser.add_argument("sources", metavar="TREEFILE", nargs="+")
parser.add_argument(
"-t",
"--target",
dest="target_tree_filepath",
default=None,
help="path to file with tree (Newick or NEXUS format) " +
"to which labels will be written")
parser.add_argument(
"--preserve-target-labels",
action="store_true",
dest="preserve_target_labels",
default=False,
help=
"keep any existing labels on target tree (by default, these will be cleared before writing the new labels)"
)
parser.add_argument("--rooted",
action="store_true",
dest="rooted_trees",
default=None,
help="treat trees as rooted")
parser.add_argument("--unrooted",
action="store_false",
dest="rooted_trees",
default=None,
help="treat trees as unrooted")
parser.add_argument(
"--ignore-missing-source",
action="store_true",
dest="ignore_missing_source",
default=False,
help="ignore missing source tree files (at least one must exist!)")
parser.add_argument(
"-o",
"--output",
dest="output_filepath",
default=None,
help="path to output file (if not given, will print to standard output)"
)
parser.add_argument(
"-s",
"--separator",
dest="separator",
default="/",
help=
"string to use to separate labels from different source trees (default='%(default)s')"
)
parser.add_argument(
"--no-taxa-block",
action="store_false",
dest="include_taxa_block",
default=True,
help=
"do not include a taxa block in the output treefile (otherwise will create taxa block by default)"
)
parser.add_argument(
"-c",
"--additional-comments",
action="store",
dest="additional_comments",
default=None,
help="additional comments to be added to the summary file")
parser.add_argument(
"--to-newick",
action="store_true",
dest="to_newick_format",
default=False,
help=
"save results in NEWICK (PHYLIP) format (default is to save in NEXUS format)"
)
parser.add_argument("--to-phylip",
action="store_true",
dest="to_newick_format",
default=False,
help="same as --to-newick")
parser.add_argument(
"-r",
"--replace",
action="store_true",
dest="replace",
default=False,
help=
"replace/overwrite output file without asking if it already exists ")
parser.add_argument(
"-q",
"--quiet",
action="store_true",
dest="quiet",
default=False,
help="suppress ALL logging, progress and feedback messages")
args = parser.parse_args()
if args.quiet:
messaging_level = ConsoleMessenger.ERROR_MESSAGING_LEVEL
else:
messaging_level = ConsoleMessenger.INFO_MESSAGING_LEVEL
messenger = ConsoleMessenger(name="SumLabels",
messaging_level=messaging_level)
# splash
if not args.quiet:
show_splash(
prog_name=_program_name,
prog_subtitle=_program_subtitle,
prog_version=_program_version,
prog_author=_program_author,
prog_copyright=_program_copyright,
dest=sys.stderr,
)
###################################################
# Source file idiot checking
source_filepaths = []
if len(args.sources) > 0:
for fpath in args.sources:
fpath = os.path.expanduser(os.path.expandvars(fpath))
if not os.path.exists(fpath):
if args.ignore_missing_source:
messenger.send_warning("Source file not found: '%s'" %
fpath)
else:
messenger.error(
"Terminating due to missing source files. " +
"Use the '--ignore-missing-source' option to continue even "
+ "if some files are missing.")
sys.exit(1)
else:
source_filepaths.append(fpath)
if len(source_filepaths) == 0:
messenger.error(
"No valid sources of input trees specified. " +
"Please provide the path to at least one (valid and existing) file "
+ "containing trees")
sys.exit(1)
else:
messenger.info(
"No sources of input trees specified. " +
"Please provide the path to at least one (valid and existing) file "
+
"containing tree samples to summarize. See '--help' for other options."
)
sys.exit(1)
###################################################
# Lots of other idiot-checking ...
# target tree
if args.target_tree_filepath is not None:
target_tree_filepath = os.path.expanduser(
os.path.expandvars(args.target_tree_filepath))
if not os.path.exists(target_tree_filepath):
messenger.error("Target tree file not found: '%s'" %
target_tree_filepath)
sys.exit(1)
else:
messenger.error(
"Target tree file not specified: use the '-t' or '--target' option to provide path to target tree"
)
sys.exit(1)
# output
if args.output_filepath is None:
output_dest = sys.stdout
else:
output_fpath = os.path.expanduser(
os.path.expandvars(args.output_filepath))
if confirm_overwrite(filepath=output_fpath,
replace_without_asking=args.replace):
output_dest = open(output_fpath, "w")
else:
sys.exit(1)
# taxon set to handle target trees
master_taxon_namespace = dendropy.TaxonNamespace()
is_rooted = args.rooted_trees
messenger.info("Reading target tree: '%s'" % target_tree_filepath)
target_tree = None
if is_rooted:
rooting = "force-rooted"
else:
rooting = None
for tree in dendropy.Tree.yield_from_files(
[
target_tree_filepath,
"rU",
],
schema='nexus/newick',
taxon_namespace=master_taxon_namespace,
rooting=rooting):
target_tree = tree
break
bipartition_labels = {}
for src_fpath in source_filepaths:
messenger.info("Reading source tree(s) from: '%s'" % src_fpath)
for tree in dendropy.Tree.yield_from_files(
[
src_fpath,
],
schema='nexus/newick',
taxon_namespace=master_taxon_namespace,
rooting=rooting):
tree.encode_bipartitions()
for bipartition, edge in tree.bipartition_edge_map.items():
label = edge.head_node.label
if not label:
continue
try:
bipartition_labels[bipartition].append(label)
except KeyError:
bipartition_labels[bipartition] = [label]
messenger.info("Mapping labels")
target_tree.encode_bipartitions()
for bipartition, edge in target_tree.bipartition_edge_map.items():
label = []
if args.preserve_target_labels and edge.head_node.label:
label.append(edge.head_node.label)
elif not args.preserve_target_labels:
edge.head_node.label = None
if bipartition in bipartition_labels:
label.extend(bipartition_labels[bipartition])
else:
pass
# messenger.send_warning("Split on target tree not found in source trees: ignoring")
if label:
edge.head_node.label = args.separator.join(label)
output_dataset = dendropy.DataSet()
tree_list = output_dataset.new_tree_list(
taxon_namespace=master_taxon_namespace)
tree_list.append(target_tree)
if args.to_newick_format:
output_dataset.write(
file=output_dest,
schema="newick",
suppress_rooting=False,
suppress_edge_lengths=False,
unquoted_underscores=False,
preserve_spaces=False,
store_tree_weights=False,
suppress_annotations=False,
annotations_as_nhx=False,
suppress_item_comments=False,
suppress_leaf_taxon_labels=False,
suppress_leaf_node_labels=True,
suppress_internal_taxon_labels=False,
suppress_internal_node_labels=False,
node_label_element_separator=' ',
)
else:
if args.include_taxa_block:
simple = False
else:
simple = True
comment = []
try:
username = getpass.getuser()
except:
username = "******"
comment.append("%s %s by %s." %
(_program_name, _program_version, _program_author))
comment.append(
"Using DendroPy Version %s by Jeet Sukumaran and Mark T. Holder." %
dendropy.__version__)
python_version = sys.version.replace("\n", "").replace("[",
"(").replace(
"]", ")")
comment.append("Running under Python %s on %s." %
(python_version, sys.platform))
comment.append("Executed on %s by %s@%s." %
(platform.node(), username, socket.gethostname()))
if args.additional_comments:
comment.append("\n")
comment.append(args.additional_comments)
output_dataset.write(
file=output_dest,
schema="nexus",
simple=simple,
file_comments=comment,
suppress_rooting=False,
unquoted_underscores=False,
preserve_spaces=False,
store_tree_weights=False,
suppress_annotations=False,
annotations_as_nhx=False,
suppress_item_comments=False,
suppress_leaf_taxon_labels=False,
suppress_leaf_node_labels=True,
suppress_internal_taxon_labels=False,
suppress_internal_node_labels=False,
node_label_element_separator=' ',
)
if not args.output_filepath:
pass
else:
messenger.info("Results written to: '%s'." % (output_fpath))
