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#!/usr/bin/env python
# #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 __future__ import absolute_import
from __future__ import print_function
import sys
import os
import errno
TOOLSPATH = os.path.realpath(os.path.split(os.path.realpath(__file__))[0])
#sys.path.insert(0, TOOLSPATH)
#sys.path.insert(1, TOOLSPATH.replace("ete3/tools", ''))
#print sys.path
import argparse
from . import (ete_split, ete_expand, ete_annotate, ete_ncbiquery, ete_view,
ete_generate, ete_mod, ete_extract, ete_compare, ete_evol,
ete_maptrees)
from . import common
from .common import log
from .utils import colorify, which
from subprocess import Popen, PIPE
"""
def ete_split(args):
# bydups, bydist, name, find clsuters
def ete_expand(args):
# polytomies
def ete_extract(args):
#dups, orthologs, partitions, edges, dist_matrix, ancestor,
def ete_convert(args):
# between newick formats, orthoxml, phyloxml
def ete_maptrees(args):
def ete_reconcile(args):
def ete_consense(args):
# all observed splits
def ete_fetch(args):
def ete_evol(args):
"""
def 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
elif not args.src_trees:
log.error("At least one tree is required as input (i.e --src_trees ) ")
sys.exit(-1)
for stree in args.src_trees:
# CHECK WHAT is needed before process the main command, allows mods before analyses
yield stree.strip()
def main():
_main(sys.argv)
def _main(arguments):
if len(arguments) > 1:
subcommand = arguments[1]
if subcommand == "version":
from .. import __version__
_version = __version__
try:
# If on a git repository and tags are available
# Use a tag based code (e.g. 3.1.1b2-8-gb2d12f4)
p = Popen(["git", "describe", "--tags"], stdout=PIPE, stderr=PIPE)
out, err = p.communicate()
except OSError as e:
if e.errno == errno.ENOENT:
# Git not installed
pass
else:
raise
else:
if p.returncode == 0:
_version += " (git-{})".format(bytes.decode(out).rstrip())
else:
# If tags were not available
# Use a short hash for the current commit (e.g. b2d12f4)
p = Popen(["git", "rev-parse", "--short", "HEAD"], stdout=PIPE, stderr=PIPE)
out, err = p.communicate()
if p.returncode == 0:
_version += " (git-{})".format(bytes.decode(out).rstrip())
_version += " Tools path: %s" %(TOOLSPATH)
print(_version)
return
elif subcommand == "upgrade-external-tools":
from . import ete_upgrade_tools
del arguments[1]
status = ete_upgrade_tools._main()
sys.exit(status)
elif subcommand == "build":
from . import ete_build
del arguments[1]
builtin_apps_path = None
ete3_path = which("ete3")
if ete3_path:
builtin_apps_path = os.path.join(os.path.split(ete3_path)[0], "ete3_apps/bin")
ete_build._main(arguments, builtin_apps_path)
return
# CREATE REUSABLE PARSER OPTIONS
# main args
main_args_p = argparse.ArgumentParser(add_help=False)
common.populate_main_args(main_args_p)
# source tree args
source_args_p = argparse.ArgumentParser(add_help=False)
common.populate_source_args(source_args_p)
# ref tree args
ref_args_p = argparse.ArgumentParser(add_help=False)
common.populate_ref_args(ref_args_p)
# mod
mod_args_p = argparse.ArgumentParser(add_help=False)
ete_mod.populate_args(mod_args_p)
# expand
expand_args_p = argparse.ArgumentParser(add_help=False)
ete_expand.populate_args(expand_args_p)
# extract
extract_args_p = argparse.ArgumentParser(add_help=False)
ete_extract.populate_args(extract_args_p)
# split
split_args_p = argparse.ArgumentParser(add_help=False)
ete_split.populate_args(split_args_p)
# ADD SUBPROGRAM TO THE MAIN PARSER
parser = argparse.ArgumentParser(description="",
formatter_class=argparse.RawDescriptionHelpFormatter)
subparser = parser.add_subparsers(title="AVAILABLE PROGRAMS")
# - MOD -
mod_args_pp = subparser.add_parser("mod", parents=[source_args_p, main_args_p, mod_args_p],
description=ete_mod.DESC,
formatter_class=argparse.RawDescriptionHelpFormatter)
mod_args_pp.set_defaults(func=ete_mod.run)
# - EXTRACT -
extract_args_pp = subparser.add_parser("extract", parents=[source_args_p, main_args_p, extract_args_p],
description=ete_extract.DESC,
formatter_class=argparse.RawDescriptionHelpFormatter)
extract_args_pp.set_defaults(func=ete_extract.run)
# - ANNOTATE -
annotate_args_p = subparser.add_parser("annotate", parents=[source_args_p, main_args_p],
description=ete_annotate.DESC,
formatter_class=argparse.RawDescriptionHelpFormatter)
annotate_args_p.set_defaults(func=ete_annotate.run)
ete_annotate.populate_args(annotate_args_p)
# - COMPARE -
compare_args_p = subparser.add_parser("compare", parents=[source_args_p, ref_args_p, main_args_p],
description=ete_compare.DESC,
formatter_class=argparse.RawDescriptionHelpFormatter)
compare_args_p.set_defaults(func=ete_compare.run)
ete_compare.populate_args(compare_args_p)
# - VIEW -
view_args_p = subparser.add_parser("view", parents=[source_args_p, main_args_p],
description=ete_view.DESC,
formatter_class=argparse.RawDescriptionHelpFormatter)
view_args_p.set_defaults(func=ete_view.run)
ete_view.populate_args(view_args_p)
# - NCBIQUERY -
ncbi_args_p = subparser.add_parser("ncbiquery", parents=[main_args_p],
description=ete_ncbiquery.DESC)
ncbi_args_p.set_defaults(func=ete_ncbiquery.run)
ete_ncbiquery.populate_args(ncbi_args_p)
# - GENERATE -
generate_args_p = subparser.add_parser("generate", parents=[source_args_p, main_args_p],
description=ete_generate.DESC,
formatter_class=argparse.RawDescriptionHelpFormatter)
generate_args_p.set_defaults(func=ete_generate.run)
ete_generate.populate_args(generate_args_p)
# - EVOL -
evol_args_p = subparser.add_parser("evol", parents=[source_args_p, main_args_p],
description=ete_evol.DESC)
evol_args_p.set_defaults(func=ete_evol.run)
ete_evol.populate_args(evol_args_p)
# - MAPTREES -
maptrees_args_p = subparser.add_parser("maptrees", parents=[source_args_p, ref_args_p, main_args_p],
description=ete_maptrees.DESC)
maptrees_args_p.set_defaults(func=ete_maptrees.run)
ete_maptrees.populate_args(maptrees_args_p)
# - build -
generate_args_p = subparser.add_parser("build")
# - helpers -
generate_args_p = subparser.add_parser("version")
generate_args_p = subparser.add_parser("upgrade-external-tools")
# ===================
# EXECUTE PROGRAM
# ===================
if len(arguments) == 1:
parser.print_usage()
return
args = parser.parse_args(arguments[1:])
LOG_LEVEL = args.verbosity
if hasattr(args, "src_trees"):
args.src_tree_iterator = tree_iterator(args)
elif args.func==ete_ncbiquery.run and not getattr(args, "search", None):
if not args.search and not sys.stdin.isatty():
log.debug("Reading taxa from standard input...")
args.search = sys.stdin
# Call main program
args.func(args)
if __name__=="__main__":
main()
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