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 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():
if len(sys.argv) > 1 and sys.argv[1] == "version":
import ete3
print(ete3.__version__)
return
elif len(sys.argv) > 1 and sys.argv[1] == "build":
from . import phylobuild
del sys.argv[1]
phylobuild._main()
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)
# - build -
generate_args_p = subparser.add_parser("build")
generate_args_p = subparser.add_parser("version")
# ===================
# EXECUTE PROGRAM
# ===================
args = parser.parse_args()
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)
def main():
if len(sys.argv) > 1 and sys.argv[1] == "version":
import ete3
print(ete3.__version__)
return
elif len(sys.argv) > 1 and sys.argv[1] == "build":
from . import phylobuild
del sys.argv[1]
phylobuild._main()
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)
# - build -
generate_args_p = subparser.add_parser("build")
generate_args_p = subparser.add_parser("version")
# ===================
# EXECUTE PROGRAM
# ===================
args = parser.parse_args()
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)