# #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 . # # # 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 __future__ import absolute_import from __future__ import print_function import sys import operator import re from six.moves import map __CITATION__ = '''# ** If you use this software for a published work, please cite: ** # # Jaime Huerta-Cepas, Joaquin Dopazo and Toni Gabaldon. ETE: a python Environment # for Tree Exploration. BMC Bioinformatics 2010, 11:24. doi: 10.1186/1471-2105-11-24.''' LOG_LEVEL = 2 class ArgError(ValueError): def __init__(self, value): self.value = value def __str__(self): # return repr(self.value) return self.value pass class Logger(object): def __init__(self, buff): self.out = buff def error(self, *args): if LOG_LEVEL >=1: print("ERROR - ", ' '.join(map(str, args)), file=self.out) def warn(self, *args): if LOG_LEVEL >=2: print("WARN - ", ' '.join(map(str, args)), file=self.out) def info(self, *args): if LOG_LEVEL >=3: print("INFO - ", ' '.join(map(str, args)), file=self.out) def debug(self, *args): if LOG_LEVEL >=4: print("DEBUG - ", ' '.join(map(str, args)), file=self.out) log = Logger(sys.stderr) def itertrees(trees, treefile): if trees: for nw in trees: yield nw if treefile: for line in open(treefile): line = line.strip() if not line or line.startswith('#'): continue else: yield line def node_matcher(node, filters): if not filters: return True for f in filters: node_v = getattr(node, f[0], None) if node_v: try: node_v = type(f[2])(node_v) except ValueError: pass if OPFUNC[f[1]](node_v, f[2]): return True # else: # print f, node_v, type(node_v) return False def _re(q, exp): if re.search(exp, q): return True return False POSNAMES = { "b-right":"branch-right", "b-top":"branch-top", "b-bottom":"branch-bottom", "float":"float", "float-behind":"float-behind", "aligned":"aligned", } OPFUNC = { "<":operator.lt, ">":operator.gt, "=":operator.eq, "==":operator.eq, "!=":operator.ne, ">=":operator.ge, "<-":operator.le, "~=":_re, } def as_str(v): if isinstance(v, float): return '%0.2f' %v else: return str(v) def shorten_str(string, l, reverse=False): if len(string) > l: if reverse: return "(..)%s" % string[l+4:] else: return "%s(..)" % string[:l-4] else: return string def parse_value(fvalue): func_match = re.search("(\w+)\(([^)]*)\)", fvalue) if func_match: func_name = func_match.groups()[0] func_arg = func_match.groups()[1] #RETURN SOMETHING def dump(t, features=None): #if getattr(args, "output", None): # t.write(format=0, features=features) #else: print(t.write(format=0, features=features)) def populate_main_args(main_args_p): main_args = main_args_p.add_argument_group('GENERAL OPTIONS') main_args.add_argument("-o", dest="output", type=str, help="""Base output file name""") #main_args.add_argument('--features', dest='output_features', type=str, nargs="+", default=[]) #main_args.add_argument("--nocolor", dest="nocolor", # action="store_true", # help="If enabled, it will NOT use colors when logging") main_args.add_argument("-v", dest="verbosity", type=int, choices= [0, 1, 2, 3, 4], default=2, help=("Verbosity level: 0=totally quite, 1=errors only," " 2=warning+errors, 3=info+warnings+errors 4=debug ")) def populate_source_args(source_args_p): source_args = source_args_p.add_argument_group('SOURCE TREES') source_args.add_argument("-t", dest='src_trees', type=str, nargs="*", help=("a list of trees in newick format (filenames or" " quoted strings)")) source_args.add_argument("--src_tree_list", dest="src_tree_list", type=str, help=("path to a file containing many source trees, one per line")) source_args.add_argument("--src_tree_attr", dest="src_tree_attr", type=str, default="name", help=("attribute in source tree used as leaf name")) source_args.add_argument("--src_attr_parser", dest="src_attr_parser", type=str, help=("Perl regular expression wrapping the portion of the target attribute that should be used.")) source_args.add_argument('--src_tree_format', dest='src_newick_format', type=int, default=0) def populate_ref_args(ref_args_p): ref_args = ref_args_p.add_argument_group('REFERENCE TREES') ref_args.add_argument("-r", dest="ref_trees", type=str, nargs="*", help=("One or more reference trees in newick format (filename" " or quoted string")) ref_args.add_argument("--ref_tree_list", dest="ref_tree_list", type=str, help="path to a file containing many ref trees, one per line") ref_args.add_argument("--ref_tree_attr", dest="ref_tree_attr", type=str, default="name", help=("attribute in ref tree used as leaf name")) ref_args.add_argument("--ref_attr_parser", dest="ref_attr_parser", type=str, help=("Perl regular expression wrapping the portion of the target attribute that should be used.")) ref_args.add_argument('--ref_tree_format', dest='ref_newick_format', type=int, default=0) def src_tree_iterator(args): if not args.src_trees and not sys.stdin.isatty(): log.debug("Reading trees from standard input...") args.src_trees = sys.stdin if args.src_trees: for stree in args.src_trees: yield stree.strip() elif args.src_tree_list: for line in open(args.src_tree_list): line = line.strip() if line: yield line def ref_tree_iterator(args): if args.ref_trees: for stree in args.ref_trees: yield stree elif args.ref_tree_list: for line in open(args.ref_tree_list): line = line.strip() if line: yield line