def main():
args = read_params( argv )
ctree = CTree( args['intree'], args['warnings'] )
ctree.positions = args['positions']
ctree.draw(args['outimg'],
out_format=args['format'],
out_dpi=args['dpi'],
out_size=args['size'],
out_pad=args['pad'],
external_legends=args['external_legends'],
reorder_tree=args['avoid_reordering'])
default=False,
action='store_true',
help=
"specify whether the two external legends should be put in separate file or keep them "
"along with the image (default behavior)")
arg('--avoid_reordering',
default=True,
action='store_false',
help=
"specify whether the tree will be reorder or not (default the tree will be reordered)"
)
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'], args['warnings'])
ctree.positions = args['positions']
ctree.draw(args['outimg'],
out_format=args['format'],
out_dpi=args['dpi'],
out_size=args['size'],
out_pad=args['pad'],
external_legends=args['external_legends'],
reorder_tree=args['avoid_reordering'])
def main():
args = read_params(argv)
ctree = CTree(args['intree'])
ctree.annotate(args['annot'],
args['outtree'] if args['outtree'] else args['intree']) # ,
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'])