tree_rename.py

#!/usr/bin/env python

import sys


try:
    import argparse as ap
except ImportError:
    sys.stderr.write( "argparse not found" )
    sys.exit(-1)

try:
    import pyphlan as ppa
except ImportError:
    sys.stderr.write( "pyphlan.py not found\n" )
    sys.exit(-1)

def read_params( args ):
    p = ap.ArgumentParser(description='Extract a subtree from a tree')

    p.add_argument( 'intree', nargs='?', default=None, type=str,
            help=   "the input tree [stdin if not present]")
    p.add_argument('outtree', nargs='?', default=None, type=str,
            help=   "the out file [stdout if not present]")
    p.add_argument('-f', default=None, type=str,
            help=   "file containing the list of clades for lca and ltcs " ) 
    p.add_argument('-n', default=None, type=str,
            help=   "name of the new root " )

    st = ['root_name','lca','ltcs']
    p.add_argument('-s', choices=st, default='root_name', type=str,
            help=  "set the strategy the select the root of the new tree")

    return vars( p.parse_args() )


if __name__ == "__main__":
    args = read_params( sys.argv )
    ctree = ppa.PpaTree( args['intree'] )
    if args['s'] in ['lca','ltcs']:
        with open( args['f'] ) as inp:
            for l in inp:
                line = l.strip().split('\t')
                ctree.rename( strategy = args['s'], n = line[0], terms = line[1:]  )
    else:
        ctree.rename( strategy = args['s'], n = args['n'] )
    ctree.export( args['outtree'] )