diff options
Diffstat (limited to 'wqflask/base')
| -rwxr-xr-x | wqflask/base/data_set.py | 37 |
1 files changed, 19 insertions, 18 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index 14e4055e..9f0f3fac 100755 --- a/wqflask/base/data_set.py +++ b/wqflask/base/data_set.py @@ -77,6 +77,9 @@ class DatasetGroup(object): self.name = "BXD" self.incparentsf1 = False + self.f1list = None + self.parlist = None + self.allsamples = None #def read_genotype(self): @@ -95,39 +98,39 @@ class DatasetGroup(object): #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() + genotype_1 = reaper.Dataset() # reaper barfs on unicode filenames, so here we ensure it's a string full_filename = str(os.path.join(webqtlConfig.GENODIR, self.name + '.geno')) - self.genotype_1.read(full_filename) + 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.name] + f1, f12, maternal, paternal = webqtlUtil.ParInfo[self.name] except KeyError: - _f1 = _f12 = _mat = _pat = None + f1 = f12 = maternal = paternal = None - self.genotype_2 = self.genotype_1 - if self.genotype_1.type == "group" and _mat and _pat: - self.genotype_2 = self.genotype_1.add(Mat=_mat, Pat=_pat) #, F1=_f1) + + if genotype_1.type == "group" and maternal and paternal: + genotype_2 = genotype_1.add(Mat=maternal, Pat=paternal) #, F1=_f1) + else: + genotype_2 = genotype_1 #determine default genotype object - if self.incparentsf1 and self.genotype_1.type != "intercross": - self.genotype = self.genotype_2 + if self.incparentsf1 and genotype_1.type != "intercross": + self.genotype = genotype_2 else: self.incparentsf1 = 0 - self.genotype = self.genotype_1 + self.genotype = 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] + if f1 and f12: + self.f1list = [f1, f12] + if maternal and paternal: + self.parlist = [maternal, paternal] class DataSet(object): @@ -169,8 +172,6 @@ class DataSet(object): # self.get_group() # # return self._group - - |