from __future__ import division
import sys

def pminf(array):
    x = 1
    pmin_list = []
    N = len(array)
    for index in range(N):
        if array[index] < x:
            pmin_list.insert(index, array[index])
        else:
            pmin_list.insert(index, x)
    return pmin_list
#end function

def cumminf(array):
    cummin = []
    cumulative_min = array[0]
    for p in array:
        if p < cumulative_min:
            cumulative_min = p
        cummin.append(cumulative_min)
    return cummin
#end

def cummaxf(array):
    cummax = []
    cumulative_max = array[0]
    for e in array:
        if e > cumulative_max:
            cumulative_max = e
        cummax.append(cumulative_max)
    return cummax
#end

def order(*args):
    if len(args) > 1:
        if args[1].lower() == 'false':# if ($string1 eq $string2) {
            return sorted(range(len(args[0])), key = lambda k: args[0][k])
        elif list(args[1].lower()) == list('true'):
            return sorted(range(len(args[0])), key = lambda k: args[0][k], reverse = True)
        else:
            print "%s isn't a recognized parameter" % args[1]
            sys.exit()
    elif len(args) == 1:
        return sorted(range(len(args[0])), key = lambda k: args[0][k])
#end

def p_adjust(*args):
    method = "bh"
    pvalues = args[0]
    if len(args) > 1:
        methods = {"bh", "fdr", "by", "holm", "hommel", "bonferroni", "hochberg"}
        metharg = arg[1].lower()
        if metharg in methods:
            method = metharg
    lp = len(pvalues)
    n = lp
    qvalues = []

    if method == 'hochberg':#already all lower case
        o = order(pvalues, 'TRUE')
        cummin_input = []
        for index in range(n):
            cummin_input.insert(index, (index+1)*pvalues[o[index]])
        cummin = cumminf(cummin_input)
        pmin = pminf(cummin)
        ro = order(o)
        qvalues = [pmin[i] for i in ro]
    elif method == 'bh':
        o = order(pvalues, 'TRUE')
        cummin_input = []
        for index in range(n):
            cummin_input.insert(index, (n/(n-index))* pvalues[o[index]])
        ro = order(o)
        cummin = cumminf(cummin_input)
        pmin = pminf(cummin)
        qvalues = [pmin[i] for i in ro]
    elif method == 'by':
        q = 0.0
        o = order(pvalues, 'TRUE')
        ro = order(o)
        for index in range(1, n+1):
            q += 1.0 / index;
        cummin_input = []
        for index in range(n):
            cummin_input.insert(index, q * (n/(n-index)) * pvalues[o[index]])
        cummin = cumminf(cummin_input)
        pmin = pminf(cummin)
        qvalues = [pmin[i] for i in ro]
    elif method == 'bonferroni':
        for index in range(n):
            q = pvalues[index] * n
            if (0 <= q) and (q < 1):
                qvalues.insert(index, q)
            elif q >= 1:
                qvalues.insert(index, 1)
            else:
                print '%g won\'t give a Bonferroni adjusted p' % q
                sys.exit()
    elif method == 'holm':
        o = order(pvalues)
        cummax_input = []
        for index in range(n):
            cummax_input.insert(index, (n - index) * pvalues[o[index]])
        ro = order(o)
        cummax = cummaxf(cummax_input)
        pmin = pminf(cummax)
        qvalues = [pmin[i] for i in ro]
    elif method == 'hommel':
        i = range(1,n+1)
        o = order(pvalues)
        p = [pvalues[index] for index in o]
        ro = order(o)
        pa = []
        q = []
        smin = n*p[0]
        for index in range(n):
            temp = n*p[index] / (index + 1)
            if temp < smin:
                smin = temp
        for index in range(n):
            pa.insert(index, smin)
            q.insert(index, smin)
        for j in range(n-1,1,-1):
            ij = range(1,n-j+2)
            for x in range(len(ij)):
                ij[x] -= 1
            I2_LENGTH = j - 1
            i2 = []
            for index in range(I2_LENGTH+1):
                i2.insert(index, n - j + 2 + index - 1)
            q1 = j * p[i2[0]] / 2.0
            for index in range(1,I2_LENGTH):
                TEMP_Q1 = j * p[i2[index]] / (2.0 + index)
                if TEMP_Q1 < q1:
                    q1 = TEMP_Q1
            for index in range(n - j + 1):
                q[ij[index]] = min(j * p[ij[index]], q1)
            for index in range(I2_LENGTH):
                q[i2[index]] = q[n-j]
            for index in range(n):
                if pa[index] < q[index]:
                    pa[index] = q[index]
            qvalues = [pa[index] for index in ro]
    else:
        print "method %s isn't defined." % method
        sys.exit()
    return qvalues

pvalues = [4.533744e-01, 7.296024e-01, 9.936026e-02, 9.079658e-02, 1.801962e-01,
8.752257e-01, 2.922222e-01, 9.115421e-01, 4.355806e-01, 5.324867e-01,
4.926798e-01, 5.802978e-01, 3.485442e-01, 7.883130e-01, 2.729308e-01,
8.502518e-01, 4.268138e-01, 6.442008e-01, 3.030266e-01, 5.001555e-02,
3.194810e-01, 7.892933e-01, 9.991834e-01, 1.745691e-01, 9.037516e-01,
1.198578e-01, 3.966083e-01, 1.403837e-02, 7.328671e-01, 6.793476e-02,
4.040730e-03, 3.033349e-04, 1.125147e-02, 2.375072e-02, 5.818542e-04,
3.075482e-04, 8.251272e-03, 1.356534e-03, 1.360696e-02, 3.764588e-04,
1.801145e-05, 2.504456e-07, 3.310253e-02, 9.427839e-03, 8.791153e-04,
2.177831e-04, 9.693054e-04, 6.610250e-05, 2.900813e-02, 5.735490e-03]

correct_answers = {}

correct_answers['bh'] = [6.126681e-01, 8.521710e-01, 1.987205e-01, 1.891595e-01, 3.217789e-01,
9.301450e-01, 4.870370e-01, 9.301450e-01, 6.049731e-01, 6.826753e-01,
6.482629e-01, 7.253722e-01, 5.280973e-01, 8.769926e-01, 4.705703e-01,
9.241867e-01, 6.049731e-01, 7.856107e-01, 4.887526e-01, 1.136717e-01,
4.991891e-01, 8.769926e-01, 9.991834e-01, 3.217789e-01, 9.301450e-01,
2.304958e-01, 5.832475e-01, 3.899547e-02, 8.521710e-01, 1.476843e-01,
1.683638e-02, 2.562902e-03, 3.516084e-02, 6.250189e-02, 3.636589e-03,
2.562902e-03, 2.946883e-02, 6.166064e-03, 3.899547e-02, 2.688991e-03,
4.502862e-04, 1.252228e-05, 7.881555e-02, 3.142613e-02, 4.846527e-03,
2.562902e-03, 4.846527e-03, 1.101708e-03, 7.252032e-02, 2.205958e-02]

correct_answers['by'] = [1.000000e+00, 1.000000e+00, 8.940844e-01, 8.510676e-01, 1.000000e+00,
1.000000e+00, 1.000000e+00, 1.000000e+00, 1.000000e+00, 1.000000e+00,
1.000000e+00, 1.000000e+00, 1.000000e+00, 1.000000e+00, 1.000000e+00,
1.000000e+00, 1.000000e+00, 1.000000e+00, 1.000000e+00, 5.114323e-01,
1.000000e+00, 1.000000e+00, 1.000000e+00, 1.000000e+00, 1.000000e+00,
1.000000e+00, 1.000000e+00, 1.754486e-01, 1.000000e+00, 6.644618e-01,
7.575031e-02, 1.153102e-02, 1.581959e-01, 2.812089e-01, 1.636176e-02,
1.153102e-02, 1.325863e-01, 2.774239e-02, 1.754486e-01, 1.209832e-02,
2.025930e-03, 5.634031e-05, 3.546073e-01, 1.413926e-01, 2.180552e-02,
1.153102e-02, 2.180552e-02, 4.956812e-03, 3.262838e-01, 9.925057e-02]

correct_answers['bonferroni'] = [1.000000e+00, 1.000000e+00, 1.000000e+00, 1.000000e+00, 1.000000e+00,
1.000000e+00, 1.000000e+00, 1.000000e+00, 1.000000e+00, 1.000000e+00,
1.000000e+00, 1.000000e+00, 1.000000e+00, 1.000000e+00, 1.000000e+00,
1.000000e+00, 1.000000e+00, 1.000000e+00, 1.000000e+00, 1.000000e+00,
1.000000e+00, 1.000000e+00, 1.000000e+00, 1.000000e+00, 1.000000e+00,
1.000000e+00, 1.000000e+00, 7.019185e-01, 1.000000e+00, 1.000000e+00,
2.020365e-01, 1.516674e-02, 5.625735e-01, 1.000000e+00, 2.909271e-02,
1.537741e-02, 4.125636e-01, 6.782670e-02, 6.803480e-01, 1.882294e-02,
9.005725e-04, 1.252228e-05, 1.000000e+00, 4.713920e-01, 4.395577e-02,
1.088915e-02, 4.846527e-02, 3.305125e-03, 1.000000e+00, 2.867745e-01]

correct_answers['hochberg'] = [9.991834e-01, 9.991834e-01, 9.991834e-01, 9.991834e-01, 9.991834e-01,
9.991834e-01, 9.991834e-01, 9.991834e-01, 9.991834e-01, 9.991834e-01,
9.991834e-01, 9.991834e-01, 9.991834e-01, 9.991834e-01, 9.991834e-01,
9.991834e-01, 9.991834e-01, 9.991834e-01, 9.991834e-01, 9.991834e-01,
9.991834e-01, 9.991834e-01, 9.991834e-01, 9.991834e-01, 9.991834e-01,
9.991834e-01, 9.991834e-01, 4.632662e-01, 9.991834e-01, 9.991834e-01,
1.575885e-01, 1.383967e-02, 3.938014e-01, 7.600230e-01, 2.501973e-02,
1.383967e-02, 3.052971e-01, 5.426136e-02, 4.626366e-01, 1.656419e-02,
8.825610e-04, 1.252228e-05, 9.930759e-01, 3.394022e-01, 3.692284e-02,
1.023581e-02, 3.974152e-02, 3.172920e-03, 8.992520e-01, 2.179486e-01]

correct_answers['holm'] = [1.000000e+00, 1.000000e+00, 1.000000e+00, 1.000000e+00, 1.000000e+00,
1.000000e+00, 1.000000e+00, 1.000000e+00, 1.000000e+00, 1.000000e+00,
1.000000e+00, 1.000000e+00, 1.000000e+00, 1.000000e+00, 1.000000e+00,
1.000000e+00, 1.000000e+00, 1.000000e+00, 1.000000e+00, 1.000000e+00,
1.000000e+00, 1.000000e+00, 1.000000e+00, 1.000000e+00, 1.000000e+00,
1.000000e+00, 1.000000e+00, 4.632662e-01, 1.000000e+00, 1.000000e+00,
1.575885e-01, 1.395341e-02, 3.938014e-01, 7.600230e-01, 2.501973e-02,
1.395341e-02, 3.052971e-01, 5.426136e-02, 4.626366e-01, 1.656419e-02,
8.825610e-04, 1.252228e-05, 9.930759e-01, 3.394022e-01, 3.692284e-02,
1.023581e-02, 3.974152e-02, 3.172920e-03, 8.992520e-01, 2.179486e-01]

correct_answers['hommel'] = [9.991834e-01, 9.991834e-01, 9.991834e-01, 9.987624e-01, 9.991834e-01,
9.991834e-01, 9.991834e-01, 9.991834e-01, 9.991834e-01, 9.991834e-01,
9.991834e-01, 9.991834e-01, 9.991834e-01, 9.991834e-01, 9.991834e-01,
9.991834e-01, 9.991834e-01, 9.991834e-01, 9.991834e-01, 9.595180e-01,
9.991834e-01, 9.991834e-01, 9.991834e-01, 9.991834e-01, 9.991834e-01,
9.991834e-01, 9.991834e-01, 4.351895e-01, 9.991834e-01, 9.766522e-01,
1.414256e-01, 1.304340e-02, 3.530937e-01, 6.887709e-01, 2.385602e-02,
1.322457e-02, 2.722920e-01, 5.426136e-02, 4.218158e-01, 1.581127e-02,
8.825610e-04, 1.252228e-05, 8.743649e-01, 3.016908e-01, 3.516461e-02,
9.582456e-03, 3.877222e-02, 3.172920e-03, 8.122276e-01, 1.950067e-01]

for key in correct_answers.keys():
    error = 0.0
    q = p_adjust(pvalues, key)
    for i in range(len(q)):
        error += abs(q[i] - correct_answers[key][i])
    print '%s error = %g' % (key.upper(), error)