diff options
Diffstat (limited to 'wqflask/base/webqtlFormData.py')
| -rwxr-xr-x | wqflask/base/webqtlFormData.py | 516 |
1 files changed, 258 insertions, 258 deletions
diff --git a/wqflask/base/webqtlFormData.py b/wqflask/base/webqtlFormData.py index c94dbe53..06faacc0 100755 --- a/wqflask/base/webqtlFormData.py +++ b/wqflask/base/webqtlFormData.py @@ -40,261 +40,261 @@ from utility import webqtlUtil class webqtlFormData: - 'Represents data from a WebQTL form page, needed to generate the next page' - attrs = ('formID','RISet','genotype','strainlist','allstrainlist', - 'suggestive','significance','submitID','identification', 'enablevariance', - 'nperm','nboot','email','incparentsf1','genotype_1','genotype_2','traitInfo') - - #XZ: Attention! All attribute values must be picklable! - - def __init__(self, start_vars = None, req = None, mod_python_session=None, FieldStorage_formdata=None): - - self.__dict__.update(start_vars) - - for item in self.attrs: - setattr(self,item, None) - - try: - self.remote_ip = req.connection.remote_ip - except: - self.remote_ip = '1.2.3.4' - - if req and req.headers_in.has_key('referer'): - self.refURL = req.headers_in['referer'] - else: - self.refURL = None - - # For now let's just comment all this out - Sam - - #self.cookies = cookieData.cookieData(Cookie.get_cookies(req)) #XZ: dictionary type. To hold values transfered from mod_python Cookie. - # - ##XZ: dictionary type. To hold values transfered from mod_python Session object. We assume that it is always picklable. - #self.input_session_data = sessionData.sessionData( mod_python_session ) - # - ##XZ: FieldStorage_formdata may contain item that can't be pickled. Must convert to picklable data. - #self.formdata = cgiData( FieldStorage_formdata ) - # - ##get Form ID - #self.formID = self.formdata.getfirst('FormID') - # - ##get rest of the attributes - #if self.formID: - # for item in self.attrs: - # value = self.formdata.getfirst(item) - # if value != None: - # setattr(self,item,string.strip(value)) - - self.ppolar = "" - self.mpolar = "" - if self.RISet: - try: - # NL, 07/27/2010. ParInfo has been moved from webqtlForm.py to webqtlUtil.py; - f1, f12, self.mpolar, self.ppolar = webqtlUtil.ParInfo[self.RISet] - except: - f1 = f12 = self.mpolar = self.ppolar = None - - try: - self.nperm = int(self.nperm) - self.nboot = int(self.nboot) - except: - self.nperm = 2000 #XZ: Rob asked to change the default value to 2000 - self.nboot = 2000 #XZ: Rob asked to change the default value to 2000 - - if self.allstrainlist: - self.allstrainlist = map(string.strip, string.split(self.allstrainlist)) - #self.readGenotype() - #self.readData() - - if self.RISet == 'BXD300': - self.RISet = 'BXD' - else: - pass - - def __getitem__(self, key): - return self.__dict__[key] - - def get(self, key, default=None): - if key in self.__dict__: - return self.__dict__[key] - else: - return default - - def __str__(self): - rstr = '' - for item in self.attrs: - if item != 'genotype': - rstr += '%s:%s\n' % (item,str(getattr(self,item))) - return rstr - - - def readGenotype(self): - 'read genotype from .geno file' - if self.RISet == 'BXD300': - self.RISet = 'BXD' - else: - pass - assert self.RISet - #genotype_1 is Dataset Object without parents and f1 - #genotype_2 is Dataset Object with parents and f1 (not for intercross) - self.genotype_1 = reaper.Dataset() - self.genotype_1.read(os.path.join(webqtlConfig.GENODIR, self.RISet + '.geno')) - try: - # NL, 07/27/2010. ParInfo has been moved from webqtlForm.py to webqtlUtil.py; - _f1, _f12, _mat, _pat = webqtlUtil.ParInfo[self.RISet] - except: - _f1 = _f12 = _mat = _pat = None - - self.genotype_2 =self.genotype_1 - if self.genotype_1.type == "riset" and _mat and _pat: - self.genotype_2 = self.genotype_1.add(Mat=_mat, Pat=_pat) #, F1=_f1) - - #determine default genotype object - if self.incparentsf1 and self.genotype_1.type != "intercross": - self.genotype = self.genotype_2 - else: - self.incparentsf1 = 0 - self.genotype = self.genotype_1 - self.strainlist = list(self.genotype.prgy) - self.f1list = self.parlist = [] - if _f1 and _f12: - self.f1list = [_f1, _f12] - if _mat and _pat: - self.parlist = [_mat, _pat] - - def readData(self, strainlst=[], incf1=[]): - 'read user input data or from trait data and analysis form' - - if not self.genotype: - self.readGenotype() - if not strainlst: - if incf1: - strainlst = self.f1list + self.strainlist - else: - strainlst = self.strainlist - - - traitfiledata = self.formdata.getfirst('traitfile') - traitpastedata = self.formdata.getfirst('traitpaste') - variancefiledata = self.formdata.getfirst('variancefile') - variancepastedata = self.formdata.getfirst('variancepaste') - Nfiledata = self.formdata.getfirst('Nfile') - - - if traitfiledata: - tt = string.split(traitfiledata) - vals = map(webqtlUtil.StringAsFloat, tt) - elif traitpastedata: - tt = string.split(traitpastedata) - vals = map(webqtlUtil.StringAsFloat, tt) - else: - vals = map(self.FormDataAsFloat, strainlst) - - if len(vals) < len(strainlst): - vals += [None]*(len(strainlst) - len(vals)) - elif len(vals) > len(strainlst): - vals = vals[:len(strainlst)] - else: - pass - - - if variancefiledata: - tt = string.split(variancefiledata) - vars = map(webqtlUtil.StringAsFloat, tt) - elif variancepastedata: - tt = string.split(variancepastedata) - vars = map(webqtlUtil.StringAsFloat, tt) - else: - vars = map(self.FormVarianceAsFloat, strainlst) - - if len(vars) < len(strainlst): - vars += [None]*(len(strainlst) - len(vars)) - elif len(vars) > len(strainlst): - vars = vars[:len(strainlst)] - else: - pass - - if Nfiledata: - tt = string.split(Nfiledata) - nstrains = map(webqtlUtil.IntAsFloat, tt) - if len(nstrains) < len(strainlst): - nstrains += [None]*(len(strainlst) - len(nstrains)) - else: - nstrains = map(self.FormNAsFloat, strainlst) - - ##vals, vars, nstrains is obsolete - self.allTraitData = {} - for i, _strain in enumerate(strainlst): - if vals[i] != None: - self.allTraitData[_strain] = webqtlCaseData(vals[i], vars[i], nstrains[i]) - - - - def informativeStrains(self, strainlst=[], incVars = 0): - '''if readData was called, use this to output the informative strains - (strain with values)''' - if not strainlst: - strainlst = self.strainlist - strains = [] - vals = [] - vars = [] - for _strain in strainlst: - if self.allTraitData.has_key(_strain): - _val, _var = self.allTraitData[_strain].val, self.allTraitData[_strain].var - if _val != None: - if incVars: - if _var != None: - strains.append(_strain) - vals.append(_val) - vars.append(_var) - else: - strains.append(_strain) - vals.append(_val) - vars.append(None) - return strains, vals, vars, len(strains) - - - - def FormDataAsFloat(self, key): - try: - return float(self.formdata.getfirst(key)) - except: - return None - - - def FormVarianceAsFloat(self, key): - try: - return float(self.formdata.getfirst('V' + key)) - except: - return None - - def FormNAsFloat(self, key): - try: - return int(self.formdata.getfirst('N' + key)) - except: - return None - - def Sample(self): - 'Create some dummy data for testing' - self.RISet = 'BXD' - self.incparentsf1 = 'on' - #self.display = 9.2 - #self.significance = 16.1 - self.readGenotype() - self.identification = 'BXD : Coat color example by Lu Lu, et al' - #self.readGenotype() - #self.genotype.ReadMM('AXBXAforQTL') - #self.strainlist = map((lambda x, y='': '%s%s' % (y,x)), self.genotype.prgy) - #self.strainlist.sort() - self.allTraitData = {'BXD29': webqtlCaseData(3), 'BXD28': webqtlCaseData(2), - 'BXD25': webqtlCaseData(2), 'BXD24': webqtlCaseData(2), 'BXD27': webqtlCaseData(2), - 'BXD21': webqtlCaseData(1), 'BXD20': webqtlCaseData(4), 'BXD23': webqtlCaseData(4), - 'BXD22': webqtlCaseData(3), 'BXD14': webqtlCaseData(4), 'BXD15': webqtlCaseData(2), - 'BXD16': webqtlCaseData(3), 'BXD11': webqtlCaseData(4), 'BXD12': webqtlCaseData(3), - 'BXD13': webqtlCaseData(2), 'BXD18': webqtlCaseData(3), 'BXD19': webqtlCaseData(3), - 'BXD38': webqtlCaseData(3), 'BXD39': webqtlCaseData(3), 'BXD36': webqtlCaseData(2), - 'BXD34': webqtlCaseData(4), 'BXD35': webqtlCaseData(4), 'BXD32': webqtlCaseData(4), - 'BXD33': webqtlCaseData(3), 'BXD30': webqtlCaseData(1), 'BXD31': webqtlCaseData(4), - 'DBA/2J': webqtlCaseData(1), 'BXD8': webqtlCaseData(3), 'BXD9': webqtlCaseData(1), - 'BXD6': webqtlCaseData(3), 'BXD5': webqtlCaseData(3), 'BXD2': webqtlCaseData(4), - 'BXD1': webqtlCaseData(1), 'C57BL/6J': webqtlCaseData(4), 'B6D2F1': webqtlCaseData(4), - 'BXD42': webqtlCaseData(4), 'BXD40': webqtlCaseData(3)} + 'Represents data from a WebQTL form page, needed to generate the next page' + attrs = ('formID','RISet','genotype','strainlist','allstrainlist', + 'suggestive','significance','submitID','identification', 'enablevariance', + 'nperm','nboot','email','incparentsf1','genotype_1','genotype_2','traitInfo') + + #XZ: Attention! All attribute values must be picklable! + + def __init__(self, start_vars = None, req = None, mod_python_session=None, FieldStorage_formdata=None): + + self.__dict__.update(start_vars) + + for item in self.attrs: + setattr(self,item, None) + + try: + self.remote_ip = req.connection.remote_ip + except: + self.remote_ip = '1.2.3.4' + + if req and req.headers_in.has_key('referer'): + self.refURL = req.headers_in['referer'] + else: + self.refURL = None + + # For now let's just comment all this out - Sam + + #self.cookies = cookieData.cookieData(Cookie.get_cookies(req)) #XZ: dictionary type. To hold values transfered from mod_python Cookie. + # + ##XZ: dictionary type. To hold values transfered from mod_python Session object. We assume that it is always picklable. + #self.input_session_data = sessionData.sessionData( mod_python_session ) + # + ##XZ: FieldStorage_formdata may contain item that can't be pickled. Must convert to picklable data. + #self.formdata = cgiData( FieldStorage_formdata ) + # + ##get Form ID + #self.formID = self.formdata.getfirst('FormID') + # + ##get rest of the attributes + #if self.formID: + # for item in self.attrs: + # value = self.formdata.getfirst(item) + # if value != None: + # setattr(self,item,string.strip(value)) + + self.ppolar = "" + self.mpolar = "" + if self.RISet: + try: + # NL, 07/27/2010. ParInfo has been moved from webqtlForm.py to webqtlUtil.py; + f1, f12, self.mpolar, self.ppolar = webqtlUtil.ParInfo[self.RISet] + except: + f1 = f12 = self.mpolar = self.ppolar = None + + try: + self.nperm = int(self.nperm) + self.nboot = int(self.nboot) + except: + self.nperm = 2000 #XZ: Rob asked to change the default value to 2000 + self.nboot = 2000 #XZ: Rob asked to change the default value to 2000 + + if self.allstrainlist: + self.allstrainlist = map(string.strip, string.split(self.allstrainlist)) + #self.readGenotype() + #self.readData() + + if self.RISet == 'BXD300': + self.RISet = 'BXD' + else: + pass + + def __getitem__(self, key): + return self.__dict__[key] + + def get(self, key, default=None): + if key in self.__dict__: + return self.__dict__[key] + else: + return default + + def __str__(self): + rstr = '' + for item in self.attrs: + if item != 'genotype': + rstr += '%s:%s\n' % (item,str(getattr(self,item))) + return rstr + + + def readGenotype(self): + 'read genotype from .geno file' + if self.RISet == 'BXD300': + self.RISet = 'BXD' + else: + pass + assert self.RISet + #genotype_1 is Dataset Object without parents and f1 + #genotype_2 is Dataset Object with parents and f1 (not for intercross) + self.genotype_1 = reaper.Dataset() + self.genotype_1.read(os.path.join(webqtlConfig.GENODIR, self.RISet + '.geno')) + try: + # NL, 07/27/2010. ParInfo has been moved from webqtlForm.py to webqtlUtil.py; + _f1, _f12, _mat, _pat = webqtlUtil.ParInfo[self.RISet] + except: + _f1 = _f12 = _mat = _pat = None + + self.genotype_2 =self.genotype_1 + if self.genotype_1.type == "riset" and _mat and _pat: + self.genotype_2 = self.genotype_1.add(Mat=_mat, Pat=_pat) #, F1=_f1) + + #determine default genotype object + if self.incparentsf1 and self.genotype_1.type != "intercross": + self.genotype = self.genotype_2 + else: + self.incparentsf1 = 0 + self.genotype = self.genotype_1 + self.strainlist = list(self.genotype.prgy) + self.f1list = self.parlist = [] + if _f1 and _f12: + self.f1list = [_f1, _f12] + if _mat and _pat: + self.parlist = [_mat, _pat] + + def readData(self, strainlst=[], incf1=[]): + 'read user input data or from trait data and analysis form' + + if not self.genotype: + self.readGenotype() + if not strainlst: + if incf1: + strainlst = self.f1list + self.strainlist + else: + strainlst = self.strainlist + + + traitfiledata = self.formdata.getfirst('traitfile') + traitpastedata = self.formdata.getfirst('traitpaste') + variancefiledata = self.formdata.getfirst('variancefile') + variancepastedata = self.formdata.getfirst('variancepaste') + Nfiledata = self.formdata.getfirst('Nfile') + + + if traitfiledata: + tt = string.split(traitfiledata) + vals = map(webqtlUtil.StringAsFloat, tt) + elif traitpastedata: + tt = string.split(traitpastedata) + vals = map(webqtlUtil.StringAsFloat, tt) + else: + vals = map(self.FormDataAsFloat, strainlst) + + if len(vals) < len(strainlst): + vals += [None]*(len(strainlst) - len(vals)) + elif len(vals) > len(strainlst): + vals = vals[:len(strainlst)] + else: + pass + + + if variancefiledata: + tt = string.split(variancefiledata) + vars = map(webqtlUtil.StringAsFloat, tt) + elif variancepastedata: + tt = string.split(variancepastedata) + vars = map(webqtlUtil.StringAsFloat, tt) + else: + vars = map(self.FormVarianceAsFloat, strainlst) + + if len(vars) < len(strainlst): + vars += [None]*(len(strainlst) - len(vars)) + elif len(vars) > len(strainlst): + vars = vars[:len(strainlst)] + else: + pass + + if Nfiledata: + tt = string.split(Nfiledata) + nstrains = map(webqtlUtil.IntAsFloat, tt) + if len(nstrains) < len(strainlst): + nstrains += [None]*(len(strainlst) - len(nstrains)) + else: + nstrains = map(self.FormNAsFloat, strainlst) + + ##vals, vars, nstrains is obsolete + self.allTraitData = {} + for i, _strain in enumerate(strainlst): + if vals[i] != None: + self.allTraitData[_strain] = webqtlCaseData(vals[i], vars[i], nstrains[i]) + + + + def informativeStrains(self, strainlst=[], incVars = 0): + '''if readData was called, use this to output the informative strains + (strain with values)''' + if not strainlst: + strainlst = self.strainlist + strains = [] + vals = [] + vars = [] + for _strain in strainlst: + if self.allTraitData.has_key(_strain): + _val, _var = self.allTraitData[_strain].val, self.allTraitData[_strain].var + if _val != None: + if incVars: + if _var != None: + strains.append(_strain) + vals.append(_val) + vars.append(_var) + else: + strains.append(_strain) + vals.append(_val) + vars.append(None) + return strains, vals, vars, len(strains) + + + + def FormDataAsFloat(self, key): + try: + return float(self.formdata.getfirst(key)) + except: + return None + + + def FormVarianceAsFloat(self, key): + try: + return float(self.formdata.getfirst('V' + key)) + except: + return None + + def FormNAsFloat(self, key): + try: + return int(self.formdata.getfirst('N' + key)) + except: + return None + + def Sample(self): + 'Create some dummy data for testing' + self.RISet = 'BXD' + self.incparentsf1 = 'on' + #self.display = 9.2 + #self.significance = 16.1 + self.readGenotype() + self.identification = 'BXD : Coat color example by Lu Lu, et al' + #self.readGenotype() + #self.genotype.ReadMM('AXBXAforQTL') + #self.strainlist = map((lambda x, y='': '%s%s' % (y,x)), self.genotype.prgy) + #self.strainlist.sort() + self.allTraitData = {'BXD29': webqtlCaseData(3), 'BXD28': webqtlCaseData(2), + 'BXD25': webqtlCaseData(2), 'BXD24': webqtlCaseData(2), 'BXD27': webqtlCaseData(2), + 'BXD21': webqtlCaseData(1), 'BXD20': webqtlCaseData(4), 'BXD23': webqtlCaseData(4), + 'BXD22': webqtlCaseData(3), 'BXD14': webqtlCaseData(4), 'BXD15': webqtlCaseData(2), + 'BXD16': webqtlCaseData(3), 'BXD11': webqtlCaseData(4), 'BXD12': webqtlCaseData(3), + 'BXD13': webqtlCaseData(2), 'BXD18': webqtlCaseData(3), 'BXD19': webqtlCaseData(3), + 'BXD38': webqtlCaseData(3), 'BXD39': webqtlCaseData(3), 'BXD36': webqtlCaseData(2), + 'BXD34': webqtlCaseData(4), 'BXD35': webqtlCaseData(4), 'BXD32': webqtlCaseData(4), + 'BXD33': webqtlCaseData(3), 'BXD30': webqtlCaseData(1), 'BXD31': webqtlCaseData(4), + 'DBA/2J': webqtlCaseData(1), 'BXD8': webqtlCaseData(3), 'BXD9': webqtlCaseData(1), + 'BXD6': webqtlCaseData(3), 'BXD5': webqtlCaseData(3), 'BXD2': webqtlCaseData(4), + 'BXD1': webqtlCaseData(1), 'C57BL/6J': webqtlCaseData(4), 'B6D2F1': webqtlCaseData(4), + 'BXD42': webqtlCaseData(4), 'BXD40': webqtlCaseData(3)} |