diff options
Diffstat (limited to 'wqflask/base/data_set.py')
| -rwxr-xr-x | wqflask/base/data_set.py | 45 |
1 files changed, 23 insertions, 22 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index d474302c..10f047f8 100755 --- a/wqflask/base/data_set.py +++ b/wqflask/base/data_set.py @@ -95,11 +95,14 @@ class DatasetGroup(object): if self.name == 'BXD300': self.name = "BXD" + self.f1list = None + self.parlist = None + self.get_f1_parent_strains() + print("parents/f1s: {}:{}".format(self.parlist, self.f1list)) + self.species = webqtlDatabaseFunction.retrieve_species(self.name) self.incparentsf1 = False - self.f1list = None - self.parlist = None self.allsamples = None self.markers = Markers(self.name) @@ -117,6 +120,18 @@ class DatasetGroup(object): # markers = json.load(json_data) # + def get_f1_parent_strains(self): + try: + # NL, 07/27/2010. ParInfo has been moved from webqtlForm.py to webqtlUtil.py; + f1, f12, maternal, paternal = webqtlUtil.ParInfo[self.name] + except KeyError: + f1 = f12 = maternal = paternal = None + + if f1 and f12: + self.f1list = [f1, f12] + if maternal and paternal: + self.parlist = [maternal, paternal] + def read_genotype_file(self): '''Read genotype from .geno file instead of database''' #if self.group == 'BXD300': @@ -128,38 +143,24 @@ class DatasetGroup(object): #genotype_2 is Dataset Object with parents and f1 (not for intercross) 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')) 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, maternal, paternal = webqtlUtil.ParInfo[self.name] - except KeyError: - f1 = f12 = maternal = paternal = None - - - if genotype_1.type == "group" and maternal and paternal: - genotype_2 = genotype_1.add(Mat=maternal, Pat=paternal) #, F1=_f1) + if genotype_1.type == "group" and self.parlist: + genotype_2 = genotype_1.add(Mat=self.parlist[0], Pat=self.parlist[1]) #, F1=_f1) else: genotype_2 = genotype_1 #determine default genotype object if self.incparentsf1 and genotype_1.type != "intercross": - self.genotype = genotype_2 + genotype = genotype_2 else: self.incparentsf1 = 0 - self.genotype = genotype_1 - - self.samplelist = list(self.genotype.prgy) + genotype = genotype_1 - if f1 and f12: - self.f1list = [f1, f12] - if maternal and paternal: - self.parlist = [maternal, paternal] + self.samplelist = list(genotype.prgy) class DataSet(object): |