diff options
Diffstat (limited to 'wqflask/base')
| -rwxr-xr-x | wqflask/base/webqtlFormData.py | 57 |
1 files changed, 29 insertions, 28 deletions
diff --git a/wqflask/base/webqtlFormData.py b/wqflask/base/webqtlFormData.py index 710c9f53..ff1db0e8 100755 --- a/wqflask/base/webqtlFormData.py +++ b/wqflask/base/webqtlFormData.py @@ -44,9 +44,9 @@ from utility import webqtlUtil -class webqtlFormData: +class webqtlFormData(object): 'Represents data from a WebQTL form page, needed to generate the next page' - + attrs = ('formID','RISet','genotype','samplelist','allsamplelist', 'display_variance' 'suggestive','significance','submitID','identification', 'enablevariance', 'nperm','nboot','email','incparentsf1','genotype_1','genotype_2','traitInfo') @@ -62,7 +62,7 @@ class webqtlFormData: print("in webqtlFormData start_vars are:", pf(start_vars)) for item in webqtlFormData.attrs: self.__dict__[item] = None - + #ZS: This is only used in DataEditingPage.py (as far as I know) self.varianceDispName = None @@ -103,7 +103,7 @@ class webqtlFormData: self.ppolar = None self.mpolar = None - + print("[yellow] self.RISet is:", self.RISet) if self.RISet: #try: @@ -112,13 +112,13 @@ class webqtlFormData: #except: # f1 = f12 = self.mpolar = self.ppolar = None - + def set_number(stringy): return int(stringy) if stringy else 2000 # Rob asked to change the default value to 2000 self.nperm = set_number(self.nperm) self.nboot = set_number(self.nboot) - + #if self.allsamplelist: # self.allsamplelist = map(string.strip, string.split(self.allsamplelist)) @@ -134,6 +134,7 @@ class webqtlFormData: def __getitem__(self, key): + print("in __getitem__") return self.__dict__[key] def get(self, key, default=None): @@ -154,22 +155,22 @@ class webqtlFormData: '''read genotype from .geno file''' if self.RISet == 'BXD300': self.RISet = 'BXD' - + 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() - + 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] @@ -186,16 +187,16 @@ class webqtlFormData: else: self.incparentsf1 = 0 self.genotype = self.genotype_1 - + self.samplelist = 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, samplelist, incf1=None): '''read user input data or from trait data and analysis form''' @@ -213,11 +214,11 @@ class webqtlFormData: #print("before traitfiledata self.traitfile is:", pf(self.traitfile)) - 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) + 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 ##### @@ -246,7 +247,7 @@ class webqtlFormData: elif len(values) > len(samplelist): values = values[:len(samplelist)] print("now values is:", values) - + if variancefiledata: tt = variancefiledata.split() @@ -282,16 +283,16 @@ class webqtlFormData: def informativeStrains(self, samplelist=None, include_variances = None): '''if readData was called, use this to output informative samples (sample with values)''' - + if not samplelist: samplelist = self.samplelist - + samples = [] values = [] variances = [] - + #print("self.allTraitData is:", pf(self.allTraitData)) - + for sample in samplelist: if sample in self.allTraitData: _val, _var = self.allTraitData[sample].value, self.allTraitData[sample].variance @@ -305,13 +306,13 @@ class webqtlFormData: samples.append(sample) values.append(_val) variances.append(None) - + return samples, values, variances, len(samples) #def FormDataAsFloat(self, key): - # + # # #try: # # return float(self.key) # #except: |