Most code in webqtlUtil.py has been removed. There is so little left that the remaining could should be migrated to the files that use them at some point.

Some of this code was in the correlation code but not being used, so it wss removed from there as well.

1 files changed, 1 insertions, 699 deletions

diff --git a/wqflask/utility/webqtlUtil.py b/wqflask/utility/webqtlUtil.py
index 94dd7cbf..83fa90b7 100644
--- a/wqflask/utility/webqtlUtil.py
+++ b/wqflask/utility/webqtlUtil.py
@@ -65,41 +65,6 @@ ParInfo ={
 #      Accessory Functions
 #########################################
 
-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 genRandStr(prefix = "", length=8, chars=string.letters+string.digits):
     from random import choice
     _str = prefix[:]
@@ -107,63 +72,6 @@ def genRandStr(prefix = "", length=8, chars=string.letters+string.digits):
         _str += choice(chars)
     return _str
 
-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)
 
@@ -176,427 +84,6 @@ 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"""
@@ -605,45 +92,6 @@ 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]:
@@ -655,80 +103,6 @@ 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']:
@@ -737,76 +111,4 @@ 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")
-
-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
\ No newline at end of file
+    return access_to_confidential_phenotype_trait
\ No newline at end of file