def addBMI ( allClinDict ):
bmiVec = []
catVec = []
weightKey = findKey ( allClinDict, "weight" )
heightKey = findKey ( allClinDict, "height" )
for ii in range(len(allClinDict[weightKey])):
w = allClinDict[weightKey][ii]
h = allClinDict[heightKey][ii]
try:
bmi = float(w) / ( float(h/100.) * float(h/100.) )
bmiCat = assignBMIcategory ( bmi )
## print w, h, bmi, bmiCat
catVec += [ bmiCat ]
bmiVec += [ bmi ]
except:
## print w, h, "NA"
## if ( w != "NA" ): print " weight is not NA ??? "
## if ( h != "NA" ): print " height is not NA ??? "
bmiVec += [ "NA" ]
catVec += [ "NA" ]
allClinDict["N:CLIN:BMI:::::"] = bmiVec
allClinDict["C:CLIN:BMIcat:::::"] = catVec
( keyType, nCount, naCount, cardCount, labelList, labelCount ) = miscClin.lookAtKey ( allClinDict["N:CLIN:BMI:::::"] )
print " %s N=%d NA=%d not-NA=%d card=%d " % ( keyType, nCount, naCount, (nCount-naCount), cardCount ), labelCount
( keyType, nCount, naCount, cardCount, labelList, labelCount ) = miscClin.lookAtKey ( allClinDict["C:CLIN:BMIcat:::::"] )
print " %s N=%d NA=%d not-NA=%d card=%d " % ( keyType, nCount, naCount, (nCount-naCount), cardCount ), labelCount
print labelList
return ( allClinDict )
def checkMenopause ( allClinDict ):
print " in checkMenopause ... "
print " "
newVec = []
menopauseKey = findKey ( allClinDict, "menopause_status" )
ageKey = findKey ( allClinDict, "age_at_initial_pathologic_diagnosis" )
for ii in range(len(allClinDict[ageKey])):
m = allClinDict[menopauseKey][ii]
a = allClinDict[ageKey][ii]
if ( m.startswith("Pre_") ):
newVec += [ "Pre" ]
elif ( m.startswith("Post_") ):
newVec += [ "Post" ]
elif ( a >= 50 ):
newVec += [ "Post" ]
else:
newVec += [ "Pre" ]
allClinDict["C:CLIN:menopause50:::::"] = newVec
( keyType, nCount, naCount, cardCount, labelList, labelCount ) = miscClin.lookAtKey ( allClinDict["C:CLIN:menopause50:::::"] )
print " %s N=%d NA=%d not-NA=%d card=%d " % ( keyType, nCount, naCount, (nCount-naCount), cardCount ), labelCount
print labelList
return ( allClinDict )
def checkClinicalStage ( allClinDict ):
print " in checkClinicalStage ... "
print " "
newStage = []
stageKey = findKey ( allClinDict, "clinical_stage" )
TstageKey = findKey ( allClinDict, "pathologic_T" )
barcodeKey = findKey ( allClinDict, "bcr_patient_barcode" )
numP = len(allClinDict[stageKey])
for ii in range(numP):
if ( allClinDict[TstageKey][ii].startswith("T1a") ):
allClinDict[TstageKey][ii] = "T1b1"
curStage = allClinDict[stageKey][ii]
if ( curStage.startswith("IV") ):
newStage += [ "III,IV" ]
elif ( curStage.startswith("III") ):
newStage += [ "III,IV" ]
elif ( curStage.startswith("II") ):
newStage += [ "II" ]
elif ( curStage.startswith("I") ):
newStage += [ "I" ]
else:
newStage += [ "NA" ]
if ( 0 ):
print " "
print " "
print ii, allClinDict[barcodeKey][ii], allClinDict[stageKey][ii], allClinDict[TstageKey][ii]
## as of 22sep ... there is stage info for 240 patients, and the counts
## look like this:
## 70 IB1
## 35 IB
## 34 IB2
## 33 IIIB
## 26 IIB
## 7 IIA2
## 7 IIA
## 5 IVB
## etc
## after grouping, we get 147 stage I (61%), 49 stage II (20%), and 44 stage III,IV (18%)
keyString = "C:CLIN:clinStage:::::"
allClinDict[keyString] = newStage
( keyType, nCount, naCount, cardCount, labelList, labelCount ) = miscClin.lookAtKey ( allClinDict[keyString] )
print " %s N=%d NA=%d not-NA=%d card=%d " % ( keyType, nCount, naCount, (nCount-naCount), cardCount ), labelCount
print labelList
return ( allClinDict )
def checkCancerStatus ( allClinDict ):
print " in checkCancerStatus ... "
print " "
newSite = []
nteKey = findKey ( allClinDict, "new_tumor_event_after_initial_treatment" )
siteKey = findKey ( allClinDict, "new_neoplasm_event_occurrence_anatomic_site" )
typeKey = findKey ( allClinDict, "new_neoplasm_event_type" )
textKey = findKey ( allClinDict, "new_neoplasm_occurrence_anatomic_site_text" )
days2nteKey = findKey ( allClinDict, "days_to_new_tumor_event_after_initial_treatment" )
numP = len(allClinDict[nteKey])
for ii in range(numP):
if ( allClinDict[nteKey][ii] == "YES" ):
siteStr = allClinDict[siteKey][ii]
if ( 1 ):
if ( siteStr == "Other_specify" ):
siteStr = allClinDict[textKey][ii]
elif ( siteStr == "NA" ):
siteStr = allClinDict[textKey][ii]
if ( siteStr != "NA" ): siteStr = siteStr.lower()
newSite += [ siteStr ]
if ( 0 ):
print " "
print ii
## print " site : ", allClinDict[siteKey][ii]
print " type : ", allClinDict[typeKey][ii]
## print " text : ", allClinDict[textKey][ii]
print " siteStr : ", siteStr
print " days : ", allClinDict[days2nteKey][ii]
else:
newSite += [ "NA" ]
## the types of things I'm seeing are:
## type: Distant_Metastasis
## --> then 'site' sometimes gives the location, or else says "Other_specify"
## in which case the 'text' might give the location
## also note that the "days_to_nte" ranges from 62 to 2893 (the lowest numbers are 62, 77, 93, 94, 153, 178...)
keyString = "C:CLIN:nte_site:::::"
allClinDict[keyString] = newSite
( keyType, nCount, naCount, cardCount, labelList, labelCount ) = miscClin.lookAtKey ( allClinDict[keyString] )
print " %s N=%d NA=%d not-NA=%d card=%d " % ( keyType, nCount, naCount, (nCount-naCount), cardCount ), labelCount
print labelList
return ( allClinDict )
def fixUpFeatureNames(self, allClinDict):
print " "
print " in fixUpFeatureNames ... "
keyList = allClinDict.keys()
newClinDict = {}
for aKey in keyList:
## if the feature name already looks like B:SAMP:etc or N:CLIN:etc
## then we don't do anything
if ( aKey[1]==":" and aKey[6]==":" ):
newName = aKey
else:
try:
featType = self.getFeatTypeByName ( aKey )
print featType
info = miscClin.lookAtKey ( allClinDict[aKey] )
print aKey
print info
if ( info[0] == "NOMINAL" ):
if ( info[3] == 2 ):
newName = "B:" + featType + ":" + aKey + ":::::"
else:
newName = "C:" + featType + ":" + aKey + ":::::"
elif ( info[0] == "NUMERIC" ):
newName = "N:" + featType + ":" + aKey + ":::::"
else:
sys.exit(-1)
except:
traceback.print_exc(limit=5)
print " ERROR in fixUpFeatureNames ??? key not found <%s> " % aKey
newName = aKey
newClinDict[newName] = allClinDict[aKey]
return ( newClinDict )
def fixUpFeatureNames(self, allClinDict):
print " "
print " in fixUpFeatureNames ... "
keyList = allClinDict.keys()
newClinDict = {}
for aKey in keyList:
## if the feature name already looks like B:SAMP:etc or N:CLIN:etc
## then we don't do anything
if (aKey[1] == ":" and aKey[6] == ":"):
newName = aKey
else:
try:
featType = self.getFeatTypeByName(aKey)
print featType
info = miscClin.lookAtKey(allClinDict[aKey])
print aKey
print info
if (info[0] == "NOMINAL"):
if (info[3] == 2):
newName = "B:" + featType + ":" + aKey + ":::::"
else:
newName = "C:" + featType + ":" + aKey + ":::::"
elif (info[0] == "NUMERIC"):
newName = "N:" + featType + ":" + aKey + ":::::"
else:
sys.exit(-1)
except:
traceback.print_exc(limit=5)
print " ERROR in fixUpFeatureNames ??? key not found <%s> " % aKey
newName = aKey
newClinDict[newName] = allClinDict[aKey]
return (newClinDict)
def addAgeSplits ( allClinDict ):
print " in addAgeSplits ... "
print " "
ageKey = findKey ( allClinDict, "age_at_initial_pathologic_diagnosis" )
numP = len(allClinDict[ageKey])
youngMax = [ 30, 35, 40, 45, 50, 40, 40, 35 ]
oldMin = [ 30, 35, 40, 45, 50, 45, 50, 55 ]
numC = len(youngMax)
newVecs = [0] * numC
for iC in range(numC):
newVecs[iC] = ["NA"] * numP
for ii in range(numP):
a = allClinDict[ageKey][ii]
if ( a != "NA" ):
for iC in range(numC):
if ( a <= youngMax[iC] ):
newVecs[iC][ii] = "young"
elif ( a > oldMin[iC] ):
newVecs[iC][ii] = "old"
for iC in range(numC):
if ( youngMax[iC] == oldMin[iC] ):
keyString = "B:CLIN:ageSplit_%d:::::" % ( youngMax[iC] )
else:
keyString = "B:CLIN:ageSplit_%d_%d:::::" % ( youngMax[iC], oldMin[iC] )
print keyString
allClinDict[keyString] = newVecs[iC]
( keyType, nCount, naCount, cardCount, labelList, labelCount ) = miscClin.lookAtKey ( allClinDict[keyString] )
print " %s N=%d NA=%d not-NA=%d card=%d " % ( keyType, nCount, naCount, (nCount-naCount), cardCount ), labelCount
print labelList
return ( allClinDict )
def writeARFF(allClinDict, bestKeyOrder, progName, outName):
if (not outName.endswith(".arff")):
outName += ".arff"
print " "
print " writing output arff file ", outName
fh = file(outName, 'w')
# before we get started we want to know which features we are going to write
# out and their data types ...
keyTypes = [0] * len(bestKeyOrder)
# this is not being decided by lookAtKey anymore ...
useFlags = [1] * len(bestKeyOrder)
labelLists = [0] * len(bestKeyOrder)
labelCounts = [0] * len(bestKeyOrder)
numSkip = 0
numNumeric = 0
numNominal = 0
for ii in range(len(bestKeyOrder)):
aKey = bestKeyOrder[ii]
(keyTypes[ii], nCount, nNA, nCard, labelLists[ii],
labelCounts[ii]) = miscClin.lookAtKey(allClinDict[aKey])
# print aKey, useFlags[ii], keyTypes[ii], nCount, nNA, nCard
if (useFlags[ii]):
if (keyTypes[ii] == 'NUMERIC'):
numNumeric += 1
if (keyTypes[ii] == 'NOMINAL'):
numNominal += 1
else:
numSkip += 1
aKey = bestKeyOrder[0]
numK = len(allClinDict[aKey])
# first we write some comments at the top ...
now = datetime.datetime.now()
fh.write('%% TCGA clinical data extracted from xml files\n')
fh.write('%% %s\n' % str(progName))
# TODO: replease with configurable username!
fh.write('%% [email protected]\n')
fh.write('%% %s\n' % now.strftime("%Y-%m-%d %H:%M"))
fh.write('%% %d numeric fields, %d nominal fields, %d skipped\n' %
(numNumeric, numNominal, numSkip))
fh.write('%% %d examples\n' % numK)
fh.write('\n')
# then comes the header information:
fh.write('@RELATION clinical-test\n')
fh.write('\n')
# the ARFF format allows for several different types of attributes:
# numeric, nominal, string, date, and relational
# --> for the moment we will only use numeric and nominal
# so we need to be able to determine, for every key, whether it
# is 'numeric' or 'nominal'
for ii in range(len(bestKeyOrder)):
aKey = bestKeyOrder[ii]
if (useFlags[ii]):
fh.write('@ATTRIBUTE %s ' % aKey)
if (keyTypes[ii] == 'NUMERIC'):
minVal = 999999
maxVal = -999999
for jj in range(len(allClinDict[aKey])):
try:
xVal = float(allClinDict[aKey][jj])
if (minVal > xVal):
minVal = xVal
if (maxVal < xVal):
maxVal = xVal
except:
doNothing = 1
fh.write('NUMERIC %% [%d, %d] %d\n' %
(int(minVal + 0.499), int(maxVal + 0.499), naCount))
elif (keyTypes[ii] == 'NOMINAL'):
fh.write('{')
for jj in range(len(labelLists[ii])):
aLabel = labelLists[ii][jj]
fh.write('"%s"' % aLabel)
if (jj < (len(labelLists[ii]) - 1)):
fh.write(', ')
fh.write('} %% [ ')
totCount = 0
for jj in range(len(labelLists[ii])):
fh.write("%d" % labelCounts[ii][jj])
totCount += labelCounts[ii][jj]
if (jj < (len(labelLists[ii]) - 1)):
fh.write(", ")
naCount = numK - totCount
fh.write(' ] + %d\n' % naCount)
fh.write('\n')
fh.write('@DATA\n')
# and now we can write the data:
for kk in range(numK):
# print " kk=%d ... " % kk
outLine = ''
for ii in range(len(bestKeyOrder)):
if (useFlags[ii]):
aKey = bestKeyOrder[ii]
# print aKey
# print allClinDict[aKey][kk]
if (noData(allClinDict[aKey][kk])):
outLine += '?, '
else:
if (keyTypes[ii] == 'NUMERIC'):
try:
outLine += ('%s, ' % str(allClinDict[aKey][kk]))
except:
print ' ERROR ??? ', aKey, kk, allClinDict[aKey][kk]
sys.exit(-1)
else:
try:
outLine += ('"%s", ' %
allClinDict[aKey][kk].upper())
except:
outLine += ('"%s", ' % str(allClinDict[aKey][kk]))
# print " WARNING: this field is supposedly not numeric??? ", aKey, kk, allClinDict[aKey][kk]
# print allClinDict[aKey]
# sys.exit(-1)
if (outLine.endswith(", ")):
outLine = outLine[:-2]
outLine += ("\t\t%% ")
try:
outLine += ("%s" % allClinDict['bcr_patient_barcode'][kk])
except:
try:
outLine += ("%s" % allClinDict['C:CLIN:bcr_patient_barcode:::::'][kk])
except:
print " ERROR in writeARFF "
print allClinDict.keys()
sys.exit(-1)
fh.write("%s\n" % outLine)
fh.write('\n')
fh.close()
def makeMergedDx ( allClinDict ):
print " in makeMergedDx ... "
print " "
mergeDx = []
epcReview = []
histTypeKey = findKey ( allClinDict, "histological_type" )
epcDxKey = findKey ( allClinDict, "C:CLIN:Dx_EPC" )
barKey = findKey ( allClinDict, "bcr_patient_barcode" )
numP = len(allClinDict[histTypeKey])
for ii in range(numP):
if ( 1 ):
print " "
print " "
print " patient index ", ii, allClinDict[barKey][ii], allClinDict[histTypeKey][ii], allClinDict[epcDxKey][ii]
## expected possible values for the histological_type field:
## 206 Cervical_Squamous_Cell_Carcinoma
## 23 Endocervical_Type_of_Adenocarcinoma
## 6 Mucinous_Adenocarcinoma_of_Endocervical_Type
## 5 Adenosquamous
## 4 Endometrioid_Adenocarcinoma_of_Endocervix
## 4 Endocervical_Adenocarcinoma_of_the_Usual_Type
## 70 NA
## expected values for Dx_EPC field:
## 4 Adenosquamous
## 27 Endocervical_Adeno
## 123 NA
## 99 Squamous
if ( allClinDict[epcDxKey][ii] != "NA" ):
epcReview += [ "TRUE" ]
else:
epcReview += [ "FALSE" ]
if ( allClinDict[epcDxKey][ii] != "NA" ):
mergeDx += [ allClinDict[epcDxKey][ii] ]
else:
if ( allClinDict[histTypeKey][ii] == "Cervical_Squamous_Cell_Carcinoma" ):
mergeDx += [ "Squamous" ]
elif ( allClinDict[histTypeKey][ii] == "Endocervical_Type_of_Adenocarcinoma" ):
mergeDx += [ "Adenocarcinoma" ]
elif ( allClinDict[histTypeKey][ii] == "Mucinous_Adenocarcinoma_of_Endocervical_Type" ):
mergeDx += [ "Adenocarcinoma" ]
elif ( allClinDict[histTypeKey][ii] == "Adenosquamous" ):
mergeDx += [ "Adenosquamous" ]
elif ( allClinDict[histTypeKey][ii] == "Endometrioid_Adenocarcinoma_of_Endocervix" ):
mergeDx += [ "Adenocarcinoma" ]
elif ( allClinDict[histTypeKey][ii] == "Endocervical_Adenocarcinoma_of_the_Usual_Type" ):
mergeDx += [ "Adenocarcinoma" ]
elif ( allClinDict[histTypeKey][ii] == "NA" ):
mergeDx += [ "NA" ]
else:
print " ERROR ??? we should not be here ... ", ii, allClinDict[barKey][ii], \
allClinDict[histTypeKey][ii], allClinDict[epcDxKey][ii]
## just double-checking terminology one more time ...
if ( mergeDx[-1] == "Endocervical_Adeno" ):
mergeDx[-1] = "Adenocarcinoma"
keyString = "C:CLIN:Dx_merged:::::"
allClinDict[keyString] = mergeDx
( keyType, nCount, naCount, cardCount, labelList, labelCount ) = miscClin.lookAtKey ( allClinDict[keyString] )
print " %s N=%d NA=%d not-NA=%d card=%d " % ( keyType, nCount, naCount, (nCount-naCount), cardCount ), labelCount
print labelList
keyString = "C:CLIN:EPC_review:::::"
allClinDict[keyString] = epcReview
( keyType, nCount, naCount, cardCount, labelList, labelCount ) = miscClin.lookAtKey ( allClinDict[keyString] )
print " %s N=%d NA=%d not-NA=%d card=%d " % ( keyType, nCount, naCount, (nCount-naCount), cardCount ), labelCount
print labelList
return ( allClinDict )
def checkLymphNodes_HystDx ( allClinDict ):
print " in checkLymphNodes_HystDx ... "
print " "
newHyst = []
newDxM = []
numLNpos = []
tfLNpos = []
## here we have 138 'radical', 6 'simple', and 5 'other'
hysTypeKey = findKey ( allClinDict, "hysterectomy_performed_type" )
hysTextKey = findKey ( allClinDict, "hysterectomy_performed_text" )
dxMeth1Key = findKey ( allClinDict, "initial_pathologic_diagnosis_method" )
dxMeth2Key = findKey ( allClinDict, "init_pathology_dx_method_other" )
barKey = findKey ( allClinDict, "bcr_patient_barcode" )
LNEcountKey = findKey ( allClinDict, "lymph_node_examined_count" )
LNEposHEkey = findKey ( allClinDict, "number_of_lymphnodes_positive_by_he" )
LNEposIHCkey = findKey ( allClinDict, "number_of_lymphnodes_positive_by_ihc" )
numP = len(allClinDict[hysTypeKey])
for ii in range(numP):
if ( 0 ):
print " "
print " "
print " patient index ", ii, allClinDict[barKey][ii]
if ( allClinDict[hysTypeKey][ii] == "NA" and allClinDict[hysTextKey][ii] == "NA" ):
newHyst += [ "NO_or_NA" ]
else:
newHyst += [ "YES" ]
## here we want to figure out what method was used for diagnosis ...
newDxM += [ "NA" ]
dxMethod = "NA"
if ( allClinDict[hysTypeKey][ii].lower().find("hysterect") >= 0 ):
if ( allClinDict[hysTypeKey][ii].lower().find("radical") >= 0 ):
dxMethod = "radical_hysterectomy"
elif ( allClinDict[hysTypeKey][ii].lower().find("simple") >= 0 ):
dxMethod = "simple_hysterectomy"
elif ( allClinDict[hysTypeKey][ii].lower().find("total_abd") >= 0 ):
dxMethod = "total_abdominal_hysterectomy"
if ( allClinDict[hysTextKey][ii].lower().find("hysterect") >= 0 ):
if ( allClinDict[hysTextKey][ii].lower().find("radical") >= 0 ):
dxMethod = "radical_hysterectomy"
elif ( allClinDict[hysTextKey][ii].lower().find("simple") >= 0 ):
dxMethod = "simple_hysterectomy"
elif ( allClinDict[hysTextKey][ii].lower().find("total_abd") >= 0 ):
dxMethod = "total_abdominal_hysterectomy"
if ( dxMethod == "NA" ):
if ( allClinDict[dxMeth1Key][ii].lower().find("cone") >= 0 ):
dxMethod = "cone_biopsy"
if ( dxMethod == "NA" ):
if ( allClinDict[dxMeth2Key][ii].lower().find("cone") >= 0 ):
dxMethod = "cone_biopsy"
if ( dxMethod == "NA" ):
if ( allClinDict[dxMeth1Key][ii].lower().find("biops") >= 0 ):
dxMethod = "biopsy"
if ( dxMethod == "NA" ):
if ( allClinDict[dxMeth2Key][ii].lower().find("biops") >= 0 ):
dxMethod = "biopsy"
if ( dxMethod == "NA" ):
if ( allClinDict[hysTypeKey][ii] != "NA" ): dxMethod = "other"
if ( allClinDict[hysTextKey][ii] != "NA" ): dxMethod = "other"
if ( allClinDict[dxMeth1Key][ii] != "NA" ): dxMethod = "other"
if ( allClinDict[dxMeth2Key][ii] != "NA" ): dxMethod = "other"
if ( dxMethod == "other" ): print " setting dxMethod to OTHER ", ii, \
allClinDict[hysTypeKey][ii], allClinDict[hysTextKey][ii], \
allClinDict[dxMeth1Key][ii], allClinDict[dxMeth2Key][ii]
newDxM[-1] = dxMethod
numPos = 0
if ( allClinDict[LNEposHEkey][ii] != "NA" ):
numPos += allClinDict[LNEposHEkey][ii]
if ( allClinDict[LNEposIHCkey][ii] != "NA" ):
numPos += allClinDict[LNEposIHCkey][ii]
if ( (allClinDict[LNEposHEkey][ii] == "NA") and (allClinDict[LNEposIHCkey][ii] == "NA") ):
numLNpos += [ "NA" ]
tfLNpos += [ "NA" ]
else:
numLNpos += [ numPos ]
if ( numPos == 0 ):
tfLNpos += [ "FALSE" ]
else:
tfLNpos += [ "TRUE" ]
if ( 0 ):
if ( allClinDict[hysTypeKey][ii] == "NA" ):
if ( allClinDict[hysTextKey][ii] != "NA" ):
print " text filled out but not type "
if ( allClinDict[hysTextKey][ii] == "NA" ):
if ( allClinDict[hysTypeKey][ii] != "NA" ):
print " type filled out but not text "
print " hysTypeKey : ", allClinDict[hysTypeKey][ii]
print " hysTextKey : ", allClinDict[hysTextKey][ii]
print " lymph nodes : ", allClinDict[LNEcountKey][ii], \
allClinDict[LNEposHEkey][ii], \
allClinDict[LNEposIHCkey][ii]
print " done working through each patient ... "
print len(newHyst), len(newDxM), len(tfLNpos), len(numLNpos)
print " "
keyString = "C:CLIN:hysterectomy:::::"
allClinDict[keyString] = newHyst
print " (a) ", keyString, newHyst
( keyType, nCount, naCount, cardCount, labelList, labelCount ) = miscClin.lookAtKey ( allClinDict[keyString] )
print " %s N=%d NA=%d not-NA=%d card=%d " % ( keyType, nCount, naCount, (nCount-naCount), cardCount ), labelCount
print labelList
keyString = "C:CLIN:dx_method:::::"
allClinDict[keyString] = newDxM
print " (b) ", keyString, newDxM
( keyType, nCount, naCount, cardCount, labelList, labelCount ) = miscClin.lookAtKey ( allClinDict[keyString] )
print " %s N=%d NA=%d not-NA=%d card=%d " % ( keyType, nCount, naCount, (nCount-naCount), cardCount ), labelCount
print labelList
keyString = "C:CLIN:LNposTF:::::"
allClinDict[keyString] = tfLNpos
print " (c) ", keyString, tfLNpos
( keyType, nCount, naCount, cardCount, labelList, labelCount ) = miscClin.lookAtKey ( allClinDict[keyString] )
print " %s N=%d NA=%d not-NA=%d card=%d " % ( keyType, nCount, naCount, (nCount-naCount), cardCount ), labelCount
print labelList
keyString = "N:CLIN:numLNpos:::::"
allClinDict[keyString] = numLNpos
print " (3) ", keyString, numLNpos
( keyType, nCount, naCount, cardCount, labelList, labelCount ) = miscClin.lookAtKey ( allClinDict[keyString] )
print " %s N=%d NA=%d not-NA=%d card=%d " % ( keyType, nCount, naCount, (nCount-naCount), cardCount ), labelCount
print " DONE DONE DONE "
return ( allClinDict )
def checkTumorStatus ( allClinDict ):
print " in checkTumorStatus ... "
print " "
newStatus1 = []
newStatus2 = []
statusKey = findKey ( allClinDict, "person_neoplasm_cancer_status" )
days2fupKey = findKey ( allClinDict, "days_to_last_followup" )
vitalKey = findKey ( allClinDict, "vital_status" )
days2deathKey = findKey ( allClinDict, "days_to_death" )
numP = len(allClinDict[statusKey])
for ii in range(numP):
days2last = -1
if ( allClinDict[days2fupKey][ii] != "NA" ):
days2last = allClinDict[days2fupKey][ii]
if ( allClinDict[days2deathKey][ii] != "NA" ):
days2last = max ( allClinDict[days2deathKey][ii], days2last )
if ( 0 ):
print " "
print " "
print ii
print " status : ", allClinDict[statusKey][ii]
print " vital : ", allClinDict[vitalKey][ii]
## print " days2fup : ", allClinDict[days2fupKey][ii]
## print " days2death : ", allClinDict[days2deathKey][ii]
print " days2last : ", days2last
if ( allClinDict[vitalKey][ii] == "Alive" ):
if ( days2last < 90 ):
print " Alive and less than 90 days ", allClinDict[statusKey][ii]
newStatus1 += [ "NA" ]
if ( allClinDict[statusKey][ii] == "TUMOR_FREE" and days2last >= 90 ):
newStatus1[-1] = "TUMOR_FREE"
elif ( allClinDict[statusKey][ii] == "WITH_TUMOR" and days2last >= 90 ):
newStatus1[-1] = "WITH_TUMOR"
newStatus2 += [ "NA" ]
if ( allClinDict[statusKey][ii] == "TUMOR_FREE" and allClinDict[vitalKey][ii] == "Alive" ):
newStatus2[-1] = "Alive_woTumor"
elif ( allClinDict[statusKey][ii] == "WITH_TUMOR" and allClinDict[vitalKey][ii] == "Dead" ):
newStatus2[-1] = "Dead_wTumor"
## as of 13aug ... there are 57 patients who are alive and have less than 90 days of follow-up
## of these: 24 are "tumor_free"
## 17 are "NA"
## 16 are "with_tumor"
keyString = "C:CLIN:tumorStatus1:::::"
allClinDict[keyString] = newStatus1
( keyType, nCount, naCount, cardCount, labelList, labelCount ) = miscClin.lookAtKey ( allClinDict[keyString] )
print " %s N=%d NA=%d not-NA=%d card=%d " % ( keyType, nCount, naCount, (nCount-naCount), cardCount ), labelCount
print labelList
keyString = "C:CLIN:tumorStatus2:::::"
allClinDict[keyString] = newStatus2
( keyType, nCount, naCount, cardCount, labelList, labelCount ) = miscClin.lookAtKey ( allClinDict[keyString] )
print " %s N=%d NA=%d not-NA=%d card=%d " % ( keyType, nCount, naCount, (nCount-naCount), cardCount ), labelCount
print labelList
return ( allClinDict )
# was this just for debugging purposes ???
fList = getFeatList ( featureList )
for aF in fList:
print aF
for aKey in allClinDict.keys():
if ( aKey[1] == ":" ):
aTokens = aKey.split(':')
tKey = aTokens[2]
else:
tKey = aKey
if ( aF == tKey ):
( keyType, nCount, naCount, cardCount, labelList, labelCount ) = miscClin.lookAtKey ( allClinDict[aKey] )
print " %s N=%d NA=%d not-NA=%d card=%d " % ( keyType, nCount, naCount, (nCount-naCount), cardCount ), labelCount
if ( keyType != "NUMERIC" ): print labelList
print " "
print " "
# now we need to do some massaging and computing ...
try:
allClinDict = addBMI ( allClinDict )
except:
print " addBMI function failed "
try:
allClinDict = checkMenopause ( allClinDict )
except: