#!/usr/bin/env python2.7
import sys, argparse
import logging
from subprocess import PIPE, Popen

def runFisher(indat, alt):
    rstr = '''print.matrix <- function(m) write.table(format(m, justify="right"), row.names=F, col.names=F, quote=F); xdat = matrix({0}, 2, 2, byrow = 1); print(xdat); print(fisher.test(xdat, alternative = '{1}'))'''.\
        format('c(' + ','.join([eval(repr(i.replace(",", ""))) for i in indat]) + ')',
               alt)
    tc = Popen(["R", '--slave', '--vanilla'], stdin = PIPE, stdout = PIPE, stderr = PIPE)
    out, error = tc.communicate(rstr)
    return out 


def iniLogger(args):
    if args.verbosity > 1:
        logging.basicConfig(level = logging.DEBUG, format = '%(asctime)s\n%(message)s')
    else:
        logging.basicConfig(level = logging.ERROR, format = '%(asctime)s\n%(message)s')
    return
    
def testTwosided(args):
    iniLogger(args)
    print runFisher(args.inData, 'two.sided')
    return
def testGreater(args):
    iniLogger(args)
    print runFisher(args.inData, 'greater')
    return
def testLess(args):
    iniLogger(args)
    print runFisher(args.inData, 'less')
    return

def getTestArguments(parser):
    parser.add_argument('inData',
                        metavar = 'DATA',
                        nargs = 4,
                        help='''Input data. MUST be length of 4 AND in the order of [a11, a12, a21, a22] (by row)''')
    parser.add_argument('-v', '--verbosity',
                        action='store',
                        default = 0,
                        help='''Verbisity argument. 0 for only p-value, 1 for more output''')

if __name__ == '__main__':
    #
    master_parser = argparse.ArgumentParser(
        description = '''Fisher's exact test on 2X2 tables | Gao Wang (c) 2011''',
        prog = 'gw-fisher',
        fromfile_prefix_chars = '@',  
        epilog = '''Quickly run Fisher's test in R on a 2X2 table''')
    master_parser.add_argument('--version', action='version', version='%(prog)s 1.0')
    subparsers = master_parser.add_subparsers()
    
    # two-sided test
    parser = subparsers.add_parser('two', help='Calculate a two-sided p-value')
    getTestArguments(parser)
    parser.set_defaults(func=testTwosided)

    # one-sided test, greater
    parser = subparsers.add_parser('greater', help='Calculate a one-sided p-value for alternative \'greater\'')
    getTestArguments(parser)
    parser.set_defaults(func=testGreater)
    
    # two-sided test
    parser = subparsers.add_parser('less', help='Calculate a one-sided p-value for alternative \'less\'')
    getTestArguments(parser)
    parser.set_defaults(func=testLess)
    
    # getting args
    args = master_parser.parse_args()
    # calling the associated functions
    args.func(args)