Code to run Colony2 from the command-line, bypassing the somewhat flaky R function which seems to mangle paths a lot of the time and does not deal real well with spaces/periods/etc. in filenames.

run_colony2.py

#!/usr/bin/env python
# encoding: utf-8

"""
run_colony2.py

Created by Brant Faircloth on 20 October 2010 13:55 PDT (-0700).
Copyright (c) 2010 Brant C. Faircloth. All rights reserved.

PURPOSE: to replace the flaky R function for running Colony2 from within R 
which seems to mangle paths a lot of the time and does not deal real well with
spaces/periods/etc. in filenames.

USAGE:  run_colony2 --bin ~/path/to/binary/colony2 --dat ~/path/to/my.DAT
"""

#import pdb
import os
import sys
import time
import shutil
import optparse

def interface():
    '''Command-line interface'''
    usage = "usage: %prog [options]"

    p = optparse.OptionParser(usage)

    p.add_option('--bin', dest = 'bin', action='store', 
type='string', default = None, help='The path to the configuration file.', 
metavar='FILE')
    p.add_option('--dat', dest = 'dat', action='store', 
type='string', default = None, help='The path to the configuration file.', 
metavar='FILE')

    (options,arg) = p.parse_args()
    options.bin = os.path.abspath(os.path.expanduser(options.bin))
    options.dat = os.path.abspath(os.path.expanduser(options.dat))
    if not options.bin:
        print "You must provide a valid path to colony2 binary."
        p.print_help()
        sys.exit(2)
    if not options.dat:
        print "You must provide a valid path to colony2 DAT file."
        p.print_help()
        sys.exit(2)
    return options, arg 


def main():
    start_time = time.time()
    print 'Started: ', time.strftime("%a %b %d, %Y  %H:%M:%S", time.localtime(start_time))
    options, args = interface()
    my_dir, my_file = os.path.split(options.dat)
    my_bin = os.path.split(options.bin)[1]
    #pdb.set_trace()
    os.chdir(my_dir)
    print 'Changing directory to {0}'.format(my_dir)
    # move a copy of the colony2 binary to the working directory
    if not os.path.isfile('colony2'):
        print 'Creating a copy of the Colony2 binary in {0}...'.format(my_dir)
        shutil.copyfile(options.bin, os.path.join(my_dir, my_bin))
        os.chmod(my_bin, 0755)
    # copy the data file to the name expected by colony2
    print 'Creating a copy of the INPUT file ({0}) with the appropriate name [Colony2.DAT]...'.format(my_file)
    shutil.copyfile(my_file, 'Colony2.DAT')
    print 'Setting parameters for Colony2 run...'
    os.system('export G95_MEM_SEGMENTS=0')
    print 'Running Colony2 (this may take some time)...'
    os.system('./Colony2 | tee temp.txt')
    print 'Unsetting environment variables...'
    os.system('unset $G95_MEM_SEGMENTS')
    print 'Cleaning up...'
    os.remove('colony2')
    os.remove('Colony2.DAT')
    end_time = time.time()
    print 'Ended: ', time.strftime("%a %b %d, %Y  %H:%M:%S", time.localtime(end_time))
    print '\nTime for execution: ', (end_time - start_time)/60, 'minutes'
    
if __name__ == '__main__':
    main()