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#!/usr/bin/python3
#------------------------------------------------------------------------------
# NAME: graphlan.py
# DESCRIPTION: GraPhlAn is a python program for creating images of circular
# cladogram starting from a tree given in PhyloXML format. The
# PhyloXML input tree can be formatted and annotated using the
# graphlan_annotate.py script.
#
# 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 "+__version__+" ("+__date__+") "
"AUTHORS: "+__author__)
arg = parser.add_argument
arg('intree', type=str, default = None, metavar='input_tree',
help = "the input tree in PhyloXML format " )
arg('outimg', type=str, default = None, metavar='output_image',
help = "the output image, the format is guessed from the extension "
"unless --format is given. Available file formats are: png, "
"pdf, ps, eps, svg" )
arg('--format', choices=['png','pdf','ps','eps','svg'], default=None,
type = str, metavar=['output_image_format'],
help = "set the format of the output image (default none meaning that "
"the format is guessed from the output file extension)")
arg('--warnings', default=1, type=int,
help = "set whether warning messages should be reported or not (default 1)")
arg('--positions', default=0, type=int,
help = "set whether the absolute position of the points should be reported on "
"the standard output. The two cohordinates are r and theta")
arg('--dpi', default=72, type=int, metavar='image_dpi',
help = "the dpi of the output image for non vectorial formats")
arg('--size', default=7.0, type=float, metavar='image_size',
help = "the size of the output image (in inches, default 7.0)")
arg('--pad', default=0.5, type=float, metavar='pad_in',
help = "the distance between the most external graphical element and "
"the border of the image")
arg('--external_legends', 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'])
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