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#!/usr/bin/python3
#------------------------------------------------------------------------------
# NAME: graphlan_annotate.py
# DESCRIPTION: TBA
#
# Author: Nicola Segata
# email: nsegata@hsph.harvard.edu
#
#
#------------------------------------------------------------------------------
__author__ = 'Nicola Segata (nsegata@hsph.harvard.edu)'
__version__ = '1.1.3'
__date__ = '5 June 2018'
import sys
#if sys.version_info[0] > 2:
# raise Exception("GraPhlAn requires Python 2, your current Python version is {}.{}.{}"
# .format(sys.version_info[0], sys.version_info[1], sys.version_info[2]))
from sys import argv
from argparse import ArgumentParser
from src.graphlan_lib import CircTree as CTree
def read_params(args):
parser = ArgumentParser(
description="GraPhlAn annotate module "+__version__+" ("+__date__+") "
"AUTHORS: "+__author__)
arg = parser.add_argument
arg('intree', type=str, metavar='input_tree',
help = "the input tree in Newick, Nexus, PhyloXML or "
"plain text format" )
arg('outtree', type=str, metavar='output_tree', nargs='?',
default = None,
help = "the output tree in PhyloXML format containing the newly "
"added annotations. If not specified, the input tree file "
"will be overwritten")
arg('--annot', default=None, metavar="annotation_file", type=str,
help = "specify the annotation file" )
#arg('-c', type=str, metavar='clade_name', default=None,
# help = "For command line annotation specifies the clade to be "
# "annotated (\* means global setting)")
#arg('-p', type=str, metavar='property_name', default=None,
# help = "For command line annotation specifies the property to be "
# "annotated")
#arg('-v', type=str, metavar='property_name', default=None,
# help = "For command line annotation specifies the value to be "
# "annotated")
arg( '-v','--version', action='version', version="GraPhlAn version "+__version__+" ("+__date__+")",
help="Prints the current GraPhlAn version and exit" )
return vars(parser.parse_args())
if __name__ == "__main__":
args = read_params( argv )
ctree = CTree( args['intree'] )
ctree.annotate( args['annot'], args['outtree'] if args['outtree'] else args['intree'] ) # ,
# c = args['c'], p = args['p'], v = args['v'])
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