diff options
Diffstat (limited to 'wqflask/base')
| -rwxr-xr-x | wqflask/base/data_set.py | 6 | ||||
| -rwxr-xr-x | wqflask/base/trait.py | 12 |
2 files changed, 10 insertions, 8 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index 7e187802..15a8c7cc 100755 --- a/wqflask/base/data_set.py +++ b/wqflask/base/data_set.py @@ -639,7 +639,8 @@ class PhenotypeDataSet(DataSet): 'Authors', 'Year', 'Max LRS', - 'Max LRS Location'] + 'Max LRS Location', + 'Add. Effect'] self.type = 'Publish' @@ -899,7 +900,8 @@ class MrnaAssayDataSet(DataSet): 'Location', 'Mean Expr', 'Max LRS', - 'Max LRS Location'] + 'Max LRS Location', + 'Add. Effect'] # Todo: Obsolete or rename this field self.type = 'ProbeSet' diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py index 6d070d54..58bed865 100755 --- a/wqflask/base/trait.py +++ b/wqflask/base/trait.py @@ -396,7 +396,7 @@ class GeneralTrait(object): if self.dataset.type == 'ProbeSet' and not self.cellid: query = """ SELECT - ProbeSetXRef.Locus, ProbeSetXRef.LRS, ProbeSetXRef.pValue, ProbeSetXRef.mean + ProbeSetXRef.Locus, ProbeSetXRef.LRS, ProbeSetXRef.pValue, ProbeSetXRef.mean, ProbeSetXRef.additive FROM ProbeSetXRef, ProbeSet WHERE @@ -409,7 +409,7 @@ class GeneralTrait(object): #trait_qtl = self.cursor.fetchone() if trait_qtl: print("trait_qtl:", trait_qtl) - self.locus, self.lrs, self.pvalue, self.mean = trait_qtl + self.locus, self.lrs, self.pvalue, self.mean, self.additive= trait_qtl print("self.locus:", self.locus) if self.locus: query = """ @@ -425,13 +425,13 @@ class GeneralTrait(object): else: self.locus = self.locus_chr = self.locus_mb = "" else: - self.locus = self.locus_chr = self.locus_mb = self.lrs = self.pvalue = self.mean = "" + self.locus = self.locus_chr = self.locus_mb = self.lrs = self.pvalue = self.mean = self.additive = "" if self.dataset.type == 'Publish': trait_qtl = g.db.execute(""" SELECT - PublishXRef.Locus, PublishXRef.LRS + PublishXRef.Locus, PublishXRef.LRS, PublishXRef.additive FROM PublishXRef, PublishFreeze WHERE @@ -440,9 +440,9 @@ class GeneralTrait(object): PublishFreeze.Id =%s """, (self.name, self.dataset.id)).fetchone() if trait_qtl: - self.locus, self.lrs = trait_qtl + self.locus, self.lrs, self.additive = trait_qtl else: - self.locus = self.lrs = "" + self.locus = self.lrs = self.additive = "" else: raise KeyError, `self.name`+' information is not found in the database.' |