diff options
Diffstat (limited to 'wqflask/base')
| -rwxr-xr-x | wqflask/base/webqtlFormData.py | 121 |
1 files changed, 65 insertions, 56 deletions
diff --git a/wqflask/base/webqtlFormData.py b/wqflask/base/webqtlFormData.py index a9e3b7d4..177c72a2 100755 --- a/wqflask/base/webqtlFormData.py +++ b/wqflask/base/webqtlFormData.py @@ -60,17 +60,12 @@ class webqtlFormData: print("in webqtlFormData start_vars are:", pf(start_vars)) for item in webqtlFormData.attrs: self.__dict__[item] = None - #self.__dict__.update(start_vars) + for item in start_vars: self.__dict__[item] = start_vars[item] - print(" Now self.dict is:", pf(self.__dict__)) - #for item in self.attrs: - # if getattr(self, item, None): - # print("Setting item %s to None" % (item,)) - # self.attrs[item] = None - # else: - # self.attrs[item] = self.attrs[item].strip() + #print(" Now self.dict is:", pf(self.__dict__)) + #Todo: This can't be good below...rework try: self.remote_ip = req.connection.remote_ip except: @@ -151,23 +146,32 @@ class webqtlFormData: def readGenotype(self): - 'read genotype from .geno file' + '''read genotype from .geno file''' if self.RISet == 'BXD300': self.RISet = 'BXD' - else: - pass - assert self.RISet + + assert self.RISet, "self.RISet needs to be set" + #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')) + + full_filename = os.path.join(webqtlConfig.GENODIR, self.RISet + '.geno') + + # reaper barfs on unicode filenames, so here we ensure it's a string + full_filename = str(full_filename) + self.genotype_1.read(full_filename) + + print("Got to after read") + try: # NL, 07/27/2010. ParInfo has been moved from webqtlForm.py to webqtlUtil.py; _f1, _f12, _mat, _pat = webqtlUtil.ParInfo[self.RISet] - except: + except KeyError: _f1 = _f12 = _mat = _pat = None - self.genotype_2 =self.genotype_1 + 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) @@ -177,78 +181,83 @@ class webqtlFormData: else: self.incparentsf1 = 0 self.genotype = self.genotype_1 + self.strainlist = list(self.genotype.prgy) - self.f1list = self.parlist = [] + 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' + def readData(self, strainlist, incf1=None): + '''read user input data or from trait data and analysis form''' + + if incf1 == None: + incf1 = [] if not self.genotype: self.readGenotype() - if not strainlst: + if not strainlist: if incf1: - strainlst = self.f1list + self.strainlist + strainlist = self.f1list + self.strainlist else: - strainlst = self.strainlist + strainlist = self.strainlist + #print("before traitfiledata self.traitfile is:", pf(self.traitfile)) - 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') + traitfiledata = getattr(self, "traitfile", None) + traitpastedata = getattr(self, "traitpaste", None) + variancefiledata = getattr(self, "variancefile", None) + variancepastedata = getattr(self, "variancepaste", None) + Nfiledata = getattr(self, "Nfile", None) + #### Todo: Rewrite below when we get to someone submitting their own trait ##### if traitfiledata: - tt = string.split(traitfiledata) - vals = map(webqtlUtil.StringAsFloat, tt) + tt = traitfiledata.split() + values = map(webqtlUtil.StringAsFloat, tt) elif traitpastedata: - tt = string.split(traitpastedata) - vals = map(webqtlUtil.StringAsFloat, tt) + tt = traitpastedata.split() + values = 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 + values = map(self.FormDataAsFloat, strainlist) + if len(values) < len(strainlist): + values += [None] * (len(strainlist) - len(values)) + elif len(values) > len(strainlist): + values = values[:len(strainlist)] + if variancefiledata: - tt = string.split(variancefiledata) - vars = map(webqtlUtil.StringAsFloat, tt) + tt = variancefiledata.split() + variances = map(webqtlUtil.StringAsFloat, tt) elif variancepastedata: - tt = string.split(variancepastedata) - vars = map(webqtlUtil.StringAsFloat, tt) + tt = variancepastedata.split() + variances = map(webqtlUtil.StringAsFloat, tt) else: - vars = map(self.FormVarianceAsFloat, strainlst) + variances = map(self.FormVarianceAsFloat, strainlist) - if len(vars) < len(strainlst): - vars += [None]*(len(strainlst) - len(vars)) - elif len(vars) > len(strainlst): - vars = vars[:len(strainlst)] - else: - pass + if len(variances) < len(strainlist): + variances += [None]*(len(strainlist) - len(variances)) + elif len(variances) > len(strainlist): + variances = variances[:len(strainlist)] if Nfiledata: tt = string.split(Nfiledata) nstrains = map(webqtlUtil.IntAsFloat, tt) - if len(nstrains) < len(strainlst): - nstrains += [None]*(len(strainlst) - len(nstrains)) + if len(nstrains) < len(strainlist): + nstrains += [None]*(len(strainlist) - len(nstrains)) else: - nstrains = map(self.FormNAsFloat, strainlst) + nstrains = map(self.FormNAsFloat, strainlist) - ##vals, vars, nstrains is obsolete + ##values, variances, 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]) + for i, _strain in enumerate(strainlist): + if values[i] != None: + self.allTraitData[_strain] = webqtlCaseData(values[i], variances[i], nstrains[i]) |