diff options
Diffstat (limited to 'wqflask/base')
| -rwxr-xr-x | wqflask/base/data_set.py | 36 | ||||
| -rwxr-xr-x | wqflask/base/trait.py | 4 | ||||
| -rwxr-xr-x | wqflask/base/webqtlConfig.py | 4 |
3 files changed, 30 insertions, 14 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index 58f08ae7..017c6052 100755 --- a/wqflask/base/data_set.py +++ b/wqflask/base/data_set.py @@ -436,7 +436,7 @@ class DataSet(object): except TypeError: print("Dataset {} is not yet available in GeneNetwork.".format(self.name)) pass - + def get_trait_data(self): self.samplelist = self.group.samplelist + self.group.parlist + self.group.f1list query = """ @@ -470,11 +470,18 @@ class DataSet(object): # method=method, # returnNumber=returnNumber) + if self.type == "Publish": + dataset_type = "Phenotype" + else: + dataset_type = self.type temp = ['T%s.value' % item for item in sample_ids_step] - query = "SELECT {}.Name,".format(escape(self.type)) + if self.type == "Publish": + query = "SELECT {}XRef.Id,".format(escape(self.type)) + else: + query = "SELECT {}.Name,".format(escape(dataset_type)) data_start_pos = 1 query += string.join(temp, ', ') - query += ' FROM ({}, {}XRef, {}Freeze) '.format(*mescape(self.type, + query += ' FROM ({}, {}XRef, {}Freeze) '.format(*mescape(dataset_type, self.type, self.type)) @@ -484,13 +491,22 @@ class DataSet(object): and T{}.StrainId={}\n """.format(*mescape(self.type, item, item, self.type, item, item)) - query += """ - WHERE {}XRef.{}FreezeId = {}Freeze.Id - and {}Freeze.Name = '{}' - and {}.Id = {}XRef.{}Id - order by {}.Id - """.format(*mescape(self.type, self.type, self.type, self.type, - self.name, self.type, self.type, self.type, self.type)) + if self.type == "Publish": + query += """ + WHERE {}XRef.InbredSetId = {}Freeze.InbredSetId + and {}Freeze.Name = '{}' + and {}.Id = {}XRef.PhenotypeId + order by {}.Id + """.format(*mescape(self.type, self.type, self.type, self.name, + dataset_type, self.type, dataset_type )) + else: + query += """ + WHERE {}XRef.{}FreezeId = {}Freeze.Id + and {}Freeze.Name = '{}' + and {}.Id = {}XRef.{}Id + order by {}.Id + """.format(*mescape(self.type, self.type, self.type, self.type, + self.name, dataset_type, self.type, self.type, dataset_type)) results = g.db.execute(query).fetchall() trait_sample_data.append(results) diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py index a1e6b0d3..c893c887 100755 --- a/wqflask/base/trait.py +++ b/wqflask/base/trait.py @@ -322,7 +322,7 @@ class GeneralTrait(object): #print(" mike: {} -> {} - {}".format(field, type(trait_info[i]), trait_info[i])) holder = trait_info[i] if isinstance(trait_info[i], basestring): - holder = unicode(trait_info[i], "utf8") + holder = unicode(trait_info[i], "utf8", "ignore") setattr(self, field, holder) if self.dataset.type == 'Publish': @@ -603,4 +603,4 @@ class GeneralTrait(object): else: ZValue = 0.5*log((1.0+self.correlation)/(1.0-self.correlation)) ZValue = ZValue*sqrt(self.overlap-3) - self.p_value = 2.0*(1.0 - reaper.normp(abs(ZValue))) + self.p_value = 2.0*(1.0 - reaper.normp(abs(ZValue)))
\ No newline at end of file diff --git a/wqflask/base/webqtlConfig.py b/wqflask/base/webqtlConfig.py index 67a9c63f..23d32233 100755 --- a/wqflask/base/webqtlConfig.py +++ b/wqflask/base/webqtlConfig.py @@ -53,8 +53,8 @@ GNROOT = "/home/zas1024/gene/" # Will remove this and dependent items later SECUREDIR = GNROOT + 'secure/' COMMON_LIB = GNROOT + 'support/admin' HTMLPATH = GNROOT + 'web/' -PYLMM_PATH = '/home/zas1024/' -SNP_PATH = '/mnt/xvdf1/snps/' +PYLMM_PATH = '/home/zas1024/plink/' +SNP_PATH = '/home/zas1024/snps/' IMGDIR = HTMLPATH +'image/' IMAGESPATH = HTMLPATH + 'images/' UPLOADPATH = IMAGESPATH + 'upload/' |