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from __future__ import absolute_import
# #START_LICENSE###########################################################
#
#
# This file is part of the Environment for Tree Exploration program
# (ETE). http://etetoolkit.org
#
# ETE is free software: you can redistribute it and/or modify it
# under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# ETE is distributed in the hope that it will be useful, but WITHOUT
# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
# or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public
# License for more details.
#
# You should have received a copy of the GNU General Public License
# along with ETE. If not, see <http://www.gnu.org/licenses/>.
#
#
# ABOUT THE ETE PACKAGE
# =====================
#
# ETE is distributed under the GPL copyleft license (2008-2015).
#
# If you make use of ETE in published work, please cite:
#
# Jaime Huerta-Cepas, Joaquin Dopazo and Toni Gabaldon.
# ETE: a python Environment for Tree Exploration. Jaime BMC
# Bioinformatics 2010,:24doi:10.1186/1471-2105-11-24
#
# Note that extra references to the specific methods implemented in
# the toolkit may be available in the documentation.
#
# More info at http://etetoolkit.org. Contact: huerta@embl.de
#
#
# #END_LICENSE#############################################################
from .common import dump, src_tree_iterator
from six.moves import map
DESC = ""
def populate_args(annotate_args_p):
annotate_args = annotate_args_p.add_argument_group("TREE ANNOTATE OPTIONS")
annotate_args.add_argument("--ncbi", dest="ncbi", action="store_true",
help="annotate tree nodes using ncbi taxonomy database.")
annotate_args.add_argument("--taxid_attr", dest="taxid_attr", default='name',
help="attribute used as NCBI taxid number")
annotate_args.add_argument("--feature", dest="feature", nargs="+", action='append', default=[],
help="")
def run(args):
from .. import Tree, PhyloTree
features = set()
for nw in src_tree_iterator(args):
if args.ncbi:
tree = PhyloTree(nw)
features.update(["taxid", "name", "rank", "bgcolor", "sci_name",
"collapse_subspecies", "named_lineage", "lineage"])
tree.annotate_ncbi_taxa(args.taxid_attr)
else:
tree = Tree(nw)
type2cast = {"str":str, "int":int, "float":float, "set":set, "list":list}
for annotation in args.feature:
aname, asource, amultiple, acast = None, None, False, str
for field in annotation:
try:
key, value = [_f.strip() for _f in field.split(":")]
except Exception:
raise ValueError("Invalid feature option [%s]" %field )
if key == "name":
aname = value
elif key == "source":
asource = value
elif key == "multiple":
#append
amultiple = value
elif key == "type":
try:
acast = type2cast[value]
except KeyError:
raise ValueError("Invalid feature type [%s]" %field)
else:
raise ValueError("Unknown feature option [%s]" %field)
if not aname and not asource:
ValueError('name and source are required when annotating a new feature [%s]'
% annotation)
features.add(aname)
for line in open(asource, 'r'):
line = line.strip()
if not line or line.startswith('#'):
continue
nodenames, attr_value = [_ln.strip() for _ln in line.split('\t')]
nodenames = list(map(str.strip, nodenames.split(',')))
relaxed_grouping = True
if nodenames[0].startswith('!'):
relaxed_grouping = False
nodenames[0] = nodenames[0][1:]
if len(nodenames) > 1:
target_node = tree.get_common_ancestor(nodenames)
if not relaxed_grouping:
pass
# do something
else:
target_node = tree & nodenames[0]
if hasattr(target_node, aname):
log.warning('Overwriting annotation for node" [%s]"' %nodenames)
else:
target_node.add_feature(aname, acast(attr_value))
dump(tree, features=features)
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