Merge pull request #1 from genenetwork/testing

Updating my testing branch

1 files changed, 4 insertions, 921 deletions

diff --git a/wqflask/utility/webqtlUtil.py b/wqflask/utility/webqtlUtil.py
index 4fc978f5..53661ae4 100644
--- a/wqflask/utility/webqtlUtil.py
+++ b/wqflask/utility/webqtlUtil.py
@@ -30,13 +30,8 @@ import re
 import math
 from math import *
 
-from htmlgen import HTMLgen2 as HT
-
 from base import webqtlConfig
 
-
-
-
 # NL, 07/27/2010. moved from webqtlForm.py
 #Dict of Parents and F1 information, In the order of [F1, Mat, Pat]
 ParInfo ={
@@ -57,180 +52,18 @@ ParInfo ={
 'AXB':['ABF1', 'BAF1', 'C57BL/6J', 'A/J'],
 'BXA':['BAF1', 'ABF1', 'C57BL/6J', 'A/J'],
 'LXS':['LSF1', 'SLF1', 'ISS', 'ILS'],
-'HXBBXH':['HSRBNF1', 'BNHSRF1', 'BN', 'HSR'],
+'HXBBXH':['SHR_BNF1', 'BN_SHRF1', 'BN-Lx/Cub', 'SHR/OlaIpcv'],
 'BayXSha':['BayXShaF1', 'ShaXBayF1', 'Bay-0','Shahdara'],
 'ColXBur':['ColXBurF1', 'BurXColF1', 'Col-0','Bur-0'],
 'ColXCvi':['ColXCviF1', 'CviXColF1', 'Col-0','Cvi'],
-'SXM':['SMF1', 'MSF1', 'Steptoe','Morex']
+'SXM':['SMF1', 'MSF1', 'Steptoe','Morex'],
+'HRDP':['SHR_BNF1', 'BN_SHRF1', 'BN-Lx/Cub', 'SHR/OlaIpcv']
 }
 
-
-# NL, 07/27/2010. moved from template.py
-IMGSTEP1 = HT.Image('/images/step1.gif', alt='STEP 1',border=0) #XZ, Only be used in inputPage.py
-IMGSTEP2 = HT.Image('/images/step2.gif', alt='STEP 2',border=0) #XZ, Only be used in inputPage.py
-IMGSTEP3 = HT.Image('/images/step3.gif', alt='STEP 3',border=0) #XZ, Only be used in inputPage.py
-IMGNEXT = HT.Image('/images/arrowdown.gif', alt='NEXT',border=0) #XZ, Only be used in inputPage.py
-
-IMGASC = HT.Image("/images/sortup.gif", border=0)
-IMGASCON = HT.Image("/images/sortupon.gif", border=0)
-IMGDESC = HT.Image("/images/sortdown.gif", border=0)
-IMGDESCON = HT.Image("/images/sortdownon.gif", border=0)
-
-"""
-IMGASC = HT.Image("/images/sortup_icon.gif", border=0)
-IMGASCON = HT.Image("/images/sortupon.gif", border=0)
-IMGDESC = HT.Image("/images/sortdown_icon.gif", border=0)
-IMGDESCON = HT.Image("/images/sortdownon.gif", border=0)
-IMG_UNSORTED = HT.Image("/images/unsorted_icon.gif", border=0)
-"""
-
-PROGRESSBAR = HT.Image('/images/waitAnima2.gif', alt='checkblue',align="middle",border=0)
-
 #########################################
 #      Accessory Functions
 #########################################
 
-def inverseCumul(p):
-    #Coefficients in rational approximations.
-    a = [-3.969683028665376e+01,2.209460984245205e+02,-2.759285104469687e+02,1.383577518672690e+02,-3.066479806614716e+01,2.506628277459239e+00]
-
-    b = [-5.447609879822406e+01,1.615858368580409e+02,-1.556989798598866e+02,6.680131188771972e+01,-1.328068155288572e+01]
-
-    c = [-7.784894002430293e-03,-3.223964580411365e-01,-2.400758277161838e+00,-2.549732539343734e+00,4.374664141464968e+00,2.938163982698783e+00]
-
-    d =  [7.784695709041462e-03,3.224671290700398e-01,2.445134137142996e+00,3.754408661907416e+00]
-
-    #Define break-points.
-
-    p_low  = 0.02425
-    p_high = 1 - p_low
-
-    #Rational approximation for lower region.
-
-    if p > 0 and p < p_low:
-        q = sqrt(-2*log(p))
-        x = (((((c[0]*q+c[1])*q+c[2])*q+c[3])*q+c[4])*q+c[5]) / ((((d[0]*q+d[1])*q+d[2])*q+d[3])*q+1)
-
-
-    #Rational approximation for central region.
-
-    elif p>= p_low and p <= p_high:
-        q = p - 0.5
-        r = q*q
-        x = (((((a[0]*r+a[1])*r+a[2])*r+a[3])*r+a[4])*r+a[5])*q /(((((b[0]*r+b[1])*r+b[2])*r+b[3])*r+b[4])*r+1)
-
-    #Rational approximation for upper region.
-
-    elif p>p_high and  p < 1:
-        q = sqrt(-2*log(1-p))
-        x = -(((((c[0]*q+c[1])*q+c[2])*q+c[3])*q+c[4])*q+c[5]) /((((d[0]*q+d[1])*q+d[2])*q+d[3])*q+1)
-
-    else:
-        return None
-
-    if p>0 and p < 1:
-        e = 0.5 * erfcc(-x/sqrt(2)) - p
-        u = e * sqrt(2*pi) * exp(x*x/2)
-        x = x - u/(1 + x*u/2)
-        return x
-    else:
-        return None
-
-def erfcc(x):
-	z=abs(x)
-	t=1.0/(1.0+0.5*z)
-	ans=t*exp(-z*z-1.26551223+t*(1.00002368+t*(0.37409196+t*(0.09678418+t*(-0.18628806+t*(0.27886807+t*(-1.13520398+t*(1.48851587+t*(-0.82215223+t*0.17087277)))))))))
-	if x>=0.0:
-		return ans
-	else:
-		return 2.0-ans
-
-def U(n):
-	x=pow(0.5,1.0/n)
-	m=[1-x]
-	for i in range(2,n):
-		a=(i-0.3175)/(n+0.365)
-		m.append(a)
-	m.append(x)
-	return m
-
-def decodeEscape(str):
-    a = str
-    pattern = re.compile('(%[0-9A-Fa-f][0-9A-Fa-f])')
-    match = pattern.findall(a)
-    matched = []
-    for item in match:
-        if item not in matched:
-            a = a.replace(item, '%c' % eval("0x"+item[-2:]))
-        matched.append(item)
-    return a
-
-def exportData(hddn, tdata, NP = None):
-    for key in tdata.keys():
-        _val, _var, _N = tdata[key].val, tdata[key].var, tdata[key].N
-        if _val != None:
-            hddn[key] = _val
-            if _var != None:
-                hddn['V'+key] = _var
-            if NP and _N != None:
-                hddn['N'+key] = _N
-
-def genShortStrainName(RISet='', input_strainName=''):
-    #aliasStrainDict = {'C57BL/6J':'B6','DBA/2J':'D2'}
-    strainName = input_strainName
-    if RISet != 'AXBXA':
-        if RISet == 'BXD300':
-            this_RISet = 'BXD'
-        elif RISet == 'BDF2-2005':
-            this_RISet = 'CASE05_'
-        else:
-            this_RISet = RISet
-        strainName = string.replace(strainName,this_RISet,'')
-        strainName = string.replace(strainName,'CASE','')
-        try:
-            strainName = "%02d" % int(strainName)
-        except:
-            pass
-    else:
-        strainName = string.replace(strainName,'AXB','A')
-        strainName = string.replace(strainName,'BXA','B')
-        try:
-            strainName = strainName[0] + "%02d" % int(strainName[1:])
-        except:
-            pass
-    return strainName
-
-def toInt(in_str):
-    "Converts an arbitrary string to an unsigned integer"
-    start = -1
-    end = -1
-    for i, char in enumerate(in_str):
-        if char >= '0' and char <= '9':
-            if start < 0:
-                start = i
-            end = i+1
-        else:
-            if start >= 0:
-                break
-    if start < end:
-        return int(in_str[start:end])
-    else:
-        return  -1
-
-def transpose(m):
-    'transpose a matrix'
-    n = len(m)
-    return [[m[j][i] for i in range(len(m[0])) for j in range(n)][k*n:k*n+n] for k in range(len(m[0]))]
-
-def asymTranspose(m):
-    'transpose a matrix'
-    t = max(map(len, m))
-    n = len(m)
-    m2 = [["-"]]*n
-    for i in range(n):
-        m2[i] = m[i] + [""]*(t- len(m[i]))
-    return [[m2[j][i] for i in range(len(m2[0])) for j in range(n)][k*n:k*n+n] for k in range(len(m2[0]))]
-
 def genRandStr(prefix = "", length=8, chars=string.letters+string.digits):
     from random import choice
     _str = prefix[:]
@@ -238,84 +71,6 @@ def genRandStr(prefix = "", length=8, chars=string.letters+string.digits):
         _str += choice(chars)
     return _str
 
-def generate_session():
-    import sha
-    return sha.new(str(time.time())).hexdigest()
-
-def cvt2Dict(x):
-    tmp = {}
-    for key in x.keys():
-        tmp[key] = x[key]
-    return tmp
-
-def dump_session(session_obj, filename):
-    "It seems mod python can only cPickle most basic data type"
-    import cPickle
-    session_file = open(filename, 'wb')
-    #try:
-    #       pass
-    #except:
-    #       pass
-    cPickle.dump(session_obj, session_file)
-    session_file.close()
-
-def StringAsFloat(str):
-    'Converts string to float but catches any exception and returns None'
-    try:
-        return float(str)
-    except:
-        return None
-
-def IntAsFloat(str):
-    'Converts string to Int but catches any exception and returns None'
-    try:
-        return int(str)
-    except:
-        return None
-
-def FloatAsFloat(flt):
-    'Converts float to string but catches any exception and returns None'
-    try:
-        return float("%2.3f" % flt)
-    except:
-        return None
-
-def RemoveZero(flt):
-    'Converts string to float but catches any exception and returns None'
-    try:
-        if abs(flt) < 1e-6:
-            return None
-        else:
-            return flt
-    except:
-        return None
-
-
-def SciFloat(d):
-    'Converts string to float but catches any exception and returns None'
-
-    try:
-        if abs(d) <= 1.0e-4:
-            return "%1.2e" % d
-        else:
-            return "%1.5f" % d
-    except:
-        return None
-
-###To be removed
-def FloatList2String(lst):
-    'Converts float list to string but catches any exception and returns None'
-    tt=''
-    try:
-        for item in lst:
-            if item == None:
-                tt += 'X '
-            else:
-                tt += '%f ' % item
-        return tt
-    except:
-        return ""
-
 def ListNotNull(lst):
     '''Obsolete - Use built in function any (or all or whatever)
 
@@ -328,427 +83,6 @@ def ListNotNull(lst):
             return 1
     return None
 
-###To be removed
-def FileDataProcess(str):
-    'Remove the description text from the input file if theres any'
-    i=0
-    while i<len(str):
-        if str[i]<'\x7f' and str[i]>'\x20':
-            break
-        else:
-            i+=1
-    str=str[i:]
-    str=string.join(string.split(str,'\000'),'')
-    i=string.find(str,"*****")
-    if i>-1:
-        return str[i+5:]
-    else:
-        return str
-
-def rank(a,lst,offset=0):
-    """Calculate the integer rank of a number in an array, can be used to calculate p-value"""
-    n = len(lst)
-    if n == 2:
-        if a <lst[0]:
-            return offset
-        elif a > lst[1]:
-            return offset + 2
-        else:
-            return offset +1
-    elif n == 1:
-        if a <lst[0]:
-            return offset
-        else:
-            return offset +1
-    elif n== 0:
-        return offset
-    else:
-        mid = n/2
-        if a < lst[mid]:
-            return rank(a,lst[:mid-1],offset)
-        else:
-            return rank(a,lst[mid:],offset+mid)
-
-def cmpScanResult(A,B):
-    try:
-        if A.LRS > B.LRS:
-            return 1
-        elif A.LRS == B.LRS:
-            return 0
-        else:
-            return -1
-    except:
-        return 0
-
-
-def cmpScanResult2(A,B):
-    try:
-        if A.LRS < B.LRS:
-            return 1
-        elif A.LRS == B.LRS:
-            return 0
-        else:
-            return -1
-    except:
-        return 0
-
-def cmpOrder(A,B):
-    try:
-        if A[1] < B[1]:
-            return -1
-        elif A[1] == B[1]:
-            return 0
-        else:
-            return 1
-    except:
-        return 0
-
-def cmpOrder2(A,B):
-    try:
-        if A[-1] < B[-1]:
-            return -1
-        elif A[-1] == B[-1]:
-            return 0
-        else:
-            return 1
-    except:
-        return 0
-
-
-
-
-def calRank(xVals, yVals, N): ###  Zach Sloan, February 4 2010
-    """
-    Returns a ranked set of X and Y values. These are used when generating
-    a Spearman scatterplot. Bear in mind that this sets values equal to each
-    other as the same rank.
-    """
-    XX = []
-    YY = []
-    X = [0]*len(xVals)
-    Y = [0]*len(yVals)
-    j = 0
-
-    for i in range(len(xVals)):
-
-        if xVals[i] != None and yVals[i] != None:
-            XX.append((j, xVals[i]))
-            YY.append((j, yVals[i]))
-            j = j + 1
-
-    NN = len(XX)
-
-    XX.sort(cmpOrder2)
-    YY.sort(cmpOrder2)
-
-    j = 1
-    rank = 0.0
-
-    while j < NN:
-
-        if XX[j][1] != XX[j-1][1]:
-            X[XX[j-1][0]] = j
-            j = j+1
-
-        else:
-            jt = j+1
-            ji = j
-            for jt in range(j+1, NN):
-                if (XX[jt][1] != XX[j-1][1]):
-                    break
-            rank = 0.5*(j+jt)
-            for ji in range(j-1, jt):
-                X[XX[ji][0]] = rank
-            if (jt == NN-1):
-                if (XX[jt][1] == XX[j-1][1]):
-                    X[XX[NN-1][0]] = rank
-            j = jt+1
-
-    if j == NN:
-        if X[XX[NN-1][0]] == 0:
-            X[XX[NN-1][0]] = NN
-
-    j = 1
-    rank = 0.0
-
-    while j < NN:
-
-        if YY[j][1] != YY[j-1][1]:
-            Y[YY[j-1][0]] = j
-            j = j+1
-        else:
-            jt = j+1
-            ji = j
-            for jt in range(j+1, NN):
-                if (YY[jt][1] != YY[j-1][1]):
-                    break
-            rank = 0.5*(j+jt)
-            for ji in range(j-1, jt):
-                Y[YY[ji][0]] = rank
-            if (jt == NN-1):
-                if (YY[jt][1] == YY[j-1][1]):
-                    Y[YY[NN-1][0]] = rank
-            j = jt+1
-
-    if j == NN:
-        if Y[YY[NN-1][0]] == 0:
-            Y[YY[NN-1][0]] = NN
-
-    return (X,Y)
-
-def calCorrelationRank(xVals,yVals,N):
-    """
-    Calculated Spearman Ranked Correlation. The algorithm works
-    by setting all tied ranks to the average of those ranks (for
-    example, if ranks 5-10 all have the same value, each will be set
-    to rank 7.5).
-    """
-
-    XX = []
-    YY = []
-    j = 0
-
-    for i in range(len(xVals)):
-        if (xVals[i]!= None and yVals[i]!= None) and (xVals[i] != "None" and yVals[i] != "None"):
-            XX.append((j,xVals[i]))
-            YY.append((j,yVals[i]))
-            j = j+1
-
-    NN = len(XX)
-    if NN <6:
-        return (0.0,NN)
-    XX.sort(cmpOrder2)
-    YY.sort(cmpOrder2)
-    X = [0]*NN
-    Y = [0]*NN
-
-    j = 1
-    rank = 0.0
-    t = 0.0
-    sx = 0.0
-
-    while j < NN:
-
-        if XX[j][1] != XX[j-1][1]:
-            X[XX[j-1][0]] = j
-            j = j+1
-
-        else:
-            jt = j+1
-            ji = j
-            for jt in range(j+1, NN):
-                if (XX[jt][1] != XX[j-1][1]):
-                    break
-            rank = 0.5*(j+jt)
-            for ji in range(j-1, jt):
-                X[XX[ji][0]] = rank
-            t = jt-j
-            sx = sx + (t*t*t-t)
-            if (jt == NN-1):
-                if (XX[jt][1] == XX[j-1][1]):
-                    X[XX[NN-1][0]] = rank
-            j = jt+1
-
-    if j == NN:
-        if X[XX[NN-1][0]] == 0:
-            X[XX[NN-1][0]] = NN
-
-    j = 1
-    rank = 0.0
-    t = 0.0
-    sy = 0.0
-
-    while j < NN:
-
-        if YY[j][1] != YY[j-1][1]:
-            Y[YY[j-1][0]] = j
-            j = j+1
-        else:
-            jt = j+1
-            ji = j
-            for jt in range(j+1, NN):
-                if (YY[jt][1] != YY[j-1][1]):
-                    break
-            rank = 0.5*(j+jt)
-            for ji in range(j-1, jt):
-                Y[YY[ji][0]] = rank
-            t = jt - j
-            sy = sy + (t*t*t-t)
-            if (jt == NN-1):
-                if (YY[jt][1] == YY[j-1][1]):
-                    Y[YY[NN-1][0]] = rank
-            j = jt+1
-
-    if j == NN:
-        if Y[YY[NN-1][0]] == 0:
-            Y[YY[NN-1][0]] = NN
-
-    D = 0.0
-
-    for i in range(NN):
-        D += (X[i]-Y[i])*(X[i]-Y[i])
-
-    fac = (1.0 -sx/(NN*NN*NN-NN))*(1.0-sy/(NN*NN*NN-NN))
-
-    return ((1-(6.0/(NN*NN*NN-NN))*(D+(sx+sy)/12.0))/math.sqrt(fac),NN)
-
-
-def calCorrelationRankText(dbdata,userdata,N): ### dcrowell = David Crowell, July 2008
-    """Calculates correlation ranks with data formatted from the text file.
-    dbdata, userdata are lists of strings.  N is an int.  Returns a float.
-    Used by correlationPage"""
-    XX = []
-    YY = []
-    j = 0
-    for i in range(N):
-        if (dbdata[i]!= None and userdata[i]!=None) and (dbdata[i]!= 'None' and userdata[i]!='None'):
-            XX.append((j,float(dbdata[i])))
-            YY.append((j,float(userdata[i])))
-            j += 1
-    NN = len(XX)
-    if NN <6:
-        return (0.0,NN)
-    XX.sort(cmpOrder2)
-    YY.sort(cmpOrder2)
-    X = [0]*NN
-    Y = [0]*NN
-
-    j = 1
-    rank = 0.0
-    t = 0.0
-    sx = 0.0
-
-    while j < NN:
-
-        if XX[j][1] != XX[j-1][1]:
-            X[XX[j-1][0]] = j
-            j = j+1
-
-        else:
-            jt = j+1
-            ji = j
-            for jt in range(j+1, NN):
-                if (XX[jt][1] != XX[j-1][1]):
-                    break
-            rank = 0.5*(j+jt)
-            for ji in range(j-1, jt):
-                X[XX[ji][0]] = rank
-            t = jt-j
-            sx = sx + (t*t*t-t)
-            if (jt == NN-1):
-                if (XX[jt][1] == XX[j-1][1]):
-                    X[XX[NN-1][0]] = rank
-            j = jt+1
-
-    if j == NN:
-        if X[XX[NN-1][0]] == 0:
-            X[XX[NN-1][0]] = NN
-
-    j = 1
-    rank = 0.0
-    t = 0.0
-    sy = 0.0
-
-    while j < NN:
-
-        if YY[j][1] != YY[j-1][1]:
-            Y[YY[j-1][0]] = j
-            j = j+1
-        else:
-            jt = j+1
-            ji = j
-            for jt in range(j+1, NN):
-                if (YY[jt][1] != YY[j-1][1]):
-                    break
-            rank = 0.5*(j+jt)
-            for ji in range(j-1, jt):
-                Y[YY[ji][0]] = rank
-            t = jt - j
-            sy = sy + (t*t*t-t)
-            if (jt == NN-1):
-                if (YY[jt][1] == YY[j-1][1]):
-                    Y[YY[NN-1][0]] = rank
-            j = jt+1
-
-    if j == NN:
-        if Y[YY[NN-1][0]] == 0:
-            Y[YY[NN-1][0]] = NN
-
-    D = 0.0
-
-    for i in range(NN):
-        D += (X[i]-Y[i])*(X[i]-Y[i])
-
-    fac = (1.0 -sx/(NN*NN*NN-NN))*(1.0-sy/(NN*NN*NN-NN))
-
-    return ((1-(6.0/(NN*NN*NN-NN))*(D+(sx+sy)/12.0))/math.sqrt(fac),NN)
-
-
-
-def calCorrelation(dbdata,userdata,N):
-    X = []
-    Y = []
-    for i in range(N):
-        if dbdata[i]!= None and userdata[i]!= None:
-            X.append(dbdata[i])
-            Y.append(userdata[i])
-    NN = len(X)
-    if NN <6:
-        return (0.0,NN)
-    sx = reduce(lambda x,y:x+y,X,0.0)
-    sy = reduce(lambda x,y:x+y,Y,0.0)
-    meanx = sx/NN
-    meany = sy/NN
-    xyd = 0.0
-    sxd = 0.0
-    syd = 0.0
-    for i in range(NN):
-        xyd += (X[i] - meanx)*(Y[i]-meany)
-        sxd += (X[i] - meanx)*(X[i] - meanx)
-        syd += (Y[i] - meany)*(Y[i] - meany)
-    try:
-        corr = xyd/(sqrt(sxd)*sqrt(syd))
-    except:
-        corr = 0
-    return (corr,NN)
-
-def calCorrelationText(dbdata,userdata,N): ### dcrowell July 2008
-    """Calculates correlation coefficients with values formatted from text files. dbdata, userdata are lists of strings.  N is an int.  Returns a float
-    Used by correlationPage"""
-    X = []
-    Y = []
-    for i in range(N):
-        #if (dbdata[i]!= None and userdata[i]!= None) and (dbdata[i]!= 'None' and userdata[i]!= 'None'):
-        #               X.append(float(dbdata[i]))
-        #               Y.append(float(userdata[i]))
-        if dbdata[i] == None or dbdata[i] == 'None' or userdata[i] == None or userdata[i] == 'None':
-            continue
-        else:
-            X.append(float(dbdata[i]))
-            Y.append(float(userdata[i]))
-    NN = len(X)
-    if NN <6:
-        return (0.0,NN)
-    sx = sum(X)
-    sy = sum(Y)
-    meanx = sx/float(NN)
-    meany = sy/float(NN)
-    xyd = 0.0
-    sxd = 0.0
-    syd = 0.0
-    for i in range(NN):
-        x1 = X[i]-meanx
-        y1 = Y[i]-meany
-        xyd += x1*y1
-        sxd += x1**2
-        syd += y1**2
-    try:
-        corr = xyd/(sqrt(sxd)*sqrt(syd))
-    except:
-        corr = 0
-    return (corr,NN)
-
-
 def readLineCSV(line): ### dcrowell July 2008
     """Parses a CSV string of text and returns a list containing each element as a string.
     Used by correlationPage"""
@@ -757,45 +91,6 @@ def readLineCSV(line): ### dcrowell July 2008
     returnList[0]=returnList[0][1:]
     return returnList
 
-
-def cmpCorr(A,B):
-    try:
-        if abs(A[1]) < abs(B[1]):
-            return 1
-        elif abs(A[1]) == abs(B[1]):
-            return 0
-        else:
-            return -1
-    except:
-        return 0
-
-def cmpLitCorr(A,B):
-    try:
-        if abs(A[3]) < abs(B[3]): return 1
-        elif abs(A[3]) == abs(B[3]):
-            if abs(A[1]) < abs(B[1]): return 1
-            elif abs(A[1]) == abs(B[1]): return 0
-            else: return -1
-        else: return -1
-    except:
-        return 0
-
-def cmpPValue(A,B):
-    try:
-        if A.corrPValue < B.corrPValue:
-            return -1
-        elif A.corrPValue == B.corrPValue:
-            if abs(A.corr) > abs(B.corr):
-                return -1
-            elif abs(A.corr) < abs(B.corr):
-                return 1
-            else:
-                return 0
-        else:
-            return 1
-    except:
-        return 0
-
 def cmpEigenValue(A,B):
     try:
         if A[0] > B[0]:
@@ -807,80 +102,6 @@ def cmpEigenValue(A,B):
     except:
         return 0
 
-
-def cmpLRSFull(A,B):
-    try:
-        if A[0] < B[0]:
-            return -1
-        elif A[0] == B[0]:
-            return 0
-        else:
-            return 1
-    except:
-        return 0
-
-def cmpLRSInteract(A,B):
-    try:
-        if A[1] < B[1]:
-            return -1
-        elif A[1] == B[1]:
-            return 0
-        else:
-            return 1
-    except:
-        return 0
-
-
-def cmpPos(A,B):
-    try:
-        try:
-            AChr = int(A.chr)
-        except:
-            AChr = 20
-        try:
-            BChr = int(B.chr)
-        except:
-            BChr = 20
-        if AChr > BChr:
-            return 1
-        elif AChr == BChr:
-            if A.mb > B.mb:
-                return 1
-            if A.mb == B.mb:
-                return 0
-            else:
-                return -1
-        else:
-            return -1
-    except:
-        return 0
-
-def cmpGenoPos(A,B):
-    try:
-        A1 = A.chr
-        B1 = B.chr
-        try:
-            A1 = int(A1)
-        except:
-            A1 = 25
-        try:
-            B1 = int(B1)
-        except:
-            B1 = 25
-        if A1 > B1:
-            return 1
-        elif A1 == B1:
-            if A.mb > B.mb:
-                return 1
-            if A.mb == B.mb:
-                return 0
-            else:
-                return -1
-        else:
-            return -1
-    except:
-        return 0
-
 def hasAccessToConfidentialPhenotypeTrait(privilege, userName, authorized_users):
     access_to_confidential_phenotype_trait = 0
     if webqtlConfig.USERDICT[privilege] > webqtlConfig.USERDICT['user']:
@@ -889,142 +110,4 @@ def hasAccessToConfidentialPhenotypeTrait(privilege, userName, authorized_users)
         AuthorizedUsersList=map(string.strip, string.split(authorized_users, ','))
         if AuthorizedUsersList.__contains__(userName):
             access_to_confidential_phenotype_trait = 1
-    return access_to_confidential_phenotype_trait
-
-
-class VisualizeException(Exception):
-    def __init__(self, message):
-        self.message = message
-    def __str__(self):
-        return self.message
-
-# safeConvert : (string -> A) -> A -> A
-# to convert a string to type A, using the supplied default value
-# if the given conversion function doesn't work
-def safeConvert(f, value, default):
-    try:
-        return f(value)
-    except:
-        return default
-
-# safeFloat : string -> float -> float
-# to convert a string to a float safely
-def safeFloat(value, default):
-    return safeConvert(float, value, default)
-
-# safeInt: string -> int -> int
-# to convert a string to an int safely
-def safeInt(value, default):
-    return safeConvert(int, value, default)
-
-# safeString : string -> (arrayof string) -> string -> string
-# if a string is not in a list of strings to pick a default value
-# for that string
-def safeString(value, validChoices, default):
-    if value in validChoices:
-        return value
-    else:
-        return default
-
-# yesNoToInt: string -> int
-# map "yes" -> 1 and "no" -> 0
-def yesNoToInt(value):
-    if value == "yes":
-        return 1
-    elif value == "no":
-        return 0
-    else:
-        return None
-
-# IntToYesNo: int -> string
-# map 1 -> "yes" and 0 -> "no"
-def intToYesNo(value):
-    if value == 1:
-        return "yes"
-    elif value == 0:
-        return "no"
-    else:
-        return None
-
-def formatField(name):
-    name = name.replace("_", " ")
-    name = name.title()
-    #name = name.replace("Mb Mm6", "Mb");
-    return name.replace("Id", "ID")
-
-#XZ, 03/27/2009: This function is very specific.
-#It is used by AJAX_table.py, correlationPage.py and dataPage.py
-
-
-def genTableObj(tblobj=None, file="", sortby = ("", ""), tableID = "sortable", addIndex = "1", hiddenColumns=[]):
-    header = tblobj['header']
-    body = tblobj['body']
-    field, order = sortby
-
-    #ZAS 9/12/2011 - The hiddenColumns array needs to be converted into a string so they can be placed into the javascript of each up/down button
-    hiddenColumnsString = ",".join(hiddenColumns)
-
-    tbl = HT.TableLite(Class="collap b2", cellspacing=1, cellpadding=5)
-
-    hiddenColumnIdx = [] #indices of columns to hide
-    idx = -1
-    last_idx = 0 #ZS: This is the index of the last item in the regular table header (without any extra parameters). It is used to determine the index of each extra parameter.
-    for row in header:
-        hr = HT.TR()
-        for i, item in enumerate(row):
-            if (item.text == '') or (item.text not in hiddenColumns):
-                if item.sort and item.text:
-                    down = HT.Href("javascript:xmlhttpPost('%smain.py?FormID=AJAX_table', '%s', 'sort=%s&order=down&file=%s&tableID=%s&addIndex=%s&hiddenColumns=%s')" % (webqtlConfig.CGIDIR, tableID, item.text, file, tableID, addIndex, hiddenColumnsString),IMGDESC)
-                    up = HT.Href("javascript:xmlhttpPost('%smain.py?FormID=AJAX_table', '%s', 'sort=%s&order=up&file=%s&tableID=%s&addIndex=%s&hiddenColumns=%s')" % (webqtlConfig.CGIDIR, tableID, item.text, file, tableID, addIndex, hiddenColumnsString),IMGASC)
-                    if item.text == field:
-                        idx = item.idx
-                        last_idx = idx
-                        if order == 'up':
-                            up = IMGASCON
-                        elif order == 'down':
-                            down = IMGDESCON
-                    item.html.append(HT.Div(up, down, style="float: bottom;"))
-                hr.append(item.html)
-            else:
-                hiddenColumnIdx.append(i)
-        tbl.append(hr)
-
-    for i, row in enumerate(body):
-        for j, item in enumerate(row):
-            if order == 'down':
-                if (item.val == '' or item.val == 'x' or item.val == 'None'):
-                    item.val = 0
-            if order == 'up':
-                if (item.val == '' or item.val == 'x' or item.val == 'None'):
-                    item.val = 'zzzzz'
-
-    if idx >= 0:
-        if order == 'down':
-            body.sort(lambda A, B: cmp(B[idx].val, A[idx].val), key=natsort_key)
-        elif order == 'up':
-            body.sort(lambda A, B: cmp(A[idx].val, B[idx].val), key=natsort_key)
-        else:
-            pass
-
-    for i, row in enumerate(body):
-        hr = HT.TR(Id = row[0].text)
-        for j, item in enumerate(row):
-            if (j not in hiddenColumnIdx):
-                if j == 0:
-                    if addIndex == "1":
-                        item.html.contents = [i+1] + item.html.contents
-                hr.append(item.html)
-        tbl.append(hr)
-
-    return tbl
-
-def natsort_key(string):
-    r = []
-    for c in string:
-        try:
-            c = int(c)
-            try: r[-1] = r[-1] * 10 + c
-            except: r.append(c)
-        except:
-            r.append(c)
-    return r
+    return access_to_confidential_phenotype_trait
\ No newline at end of file