diff options
Diffstat (limited to 'wqflask')
| -rwxr-xr-x | wqflask/wqflask/do_search.py | 61 |
1 files changed, 31 insertions, 30 deletions
diff --git a/wqflask/wqflask/do_search.py b/wqflask/wqflask/do_search.py index a3260f34..b467655b 100755 --- a/wqflask/wqflask/do_search.py +++ b/wqflask/wqflask/do_search.py @@ -481,7 +481,7 @@ class GoSearch(MrnaAssaySearch): return self.execute(query) #ZS: Not sure what the best way to deal with LRS searches is -class LrsSearch(MrnaAssaySearch): +class LrsSearch(DoSearch): """Searches for genes with a QTL within the given LRS values LRS searches can take 3 different forms: @@ -497,9 +497,9 @@ class LrsSearch(MrnaAssaySearch): def get_from_clause(self): if self.search_operator == "=": - return ", Geno" + self.from_clause = ", Geno" else: - return "" + self.from_clause = "" def get_where_clause(self): self.search_term = [float(value) for value in self.search_term] @@ -526,7 +526,7 @@ class LrsSearch(MrnaAssaySearch): print("self.sub_clause is:", pf(self.sub_clause)) #%s.Chr = Geno.Chr - where_clause = self.sub_clause + """ %sXRef.Locus = Geno.name and + self.where_clause = self.sub_clause + """ %sXRef.Locus = Geno.name and Geno.SpeciesId = %s """ % self.mescape(self.dataset.type, self.species_id) @@ -536,17 +536,11 @@ class LrsSearch(MrnaAssaySearch): self.sub_clause = """ %sXRef.LRS %s %s """ % self.mescape(self.dataset.type, self.search_operator, self.search_term[0]) - where_clause = self.sub_clause + self.where_clause = self.sub_clause - return where_clause + #return where_clause - def get_final_query(self): - self.from_clause = self.get_from_clause() - self.where_clause = self.get_where_clause() - self.query = self.compile_final_query(self.from_clause, self.where_clause) - - return self.query def run(self): @@ -557,6 +551,29 @@ class LrsSearch(MrnaAssaySearch): return self.execute(self.query) +class MrnaLrsSearch(LrsSearch, MrnaAssaySearch): + + DoSearch.search_types['ProbeSet_LRS'] = 'MrnaLrsSearch' + + def run(self): + + self.get_from_clause() + self.get_where_clause() + self.query = self.compile_final_query(from_clause = self.from_clause, where_clause = self.where_clause) + + return self.execute(self.query) + +class PhenotypeLrsSearch(LrsSearch, PhenotypeSearch): + + DoSearch.search_types['Publish_LRS'] = 'PhenotypeLrsSearch' + + def run(self): + + self.get_from_clause() + self.get_where_clause() + self.query = self.compile_final_query(from_clause = self.from_clause, where_clause = self.where_clause) + + return self.execute(self.query) class CisTransLrsSearch(LrsSearch): @@ -693,24 +710,6 @@ class MeanSearch(MrnaAssaySearch): return self.query def run(self): - - #self.search_term = [float(value) for value in self.search_term] - # - #if self.search_operator == "=": - # assert isinstance(self.search_term, (list, tuple)) - # self.mean_min, self.mean_max = self.search_term[:2] - # - # self.where_clause = """ %sXRef.mean > %s and - # %sXRef.mean < %s """ % self.mescape(self.dataset.type, - # min(self.mean_min, self.mean_max), - # self.dataset.type, - # max(self.mean_min, self.mean_max)) - #else: - # # Deal with >, <, >=, and <= - # self.where_clause = """ %sXRef.mean %s %s """ % self.mescape(self.dataset.type, - # self.search_operator, - # self.search_term[0]) - self.where_clause = self.get_where_clause() print("where_clause is:", pf(self.where_clause)) @@ -841,6 +840,8 @@ class GenotypePositionSearch(PositionSearch, GenotypeSearch): class PvalueSearch(MrnaAssaySearch): """Searches for traits with a permutationed p-value between low and high""" + DoSearch.search_types['ProbeSet_PVALUE'] = "PvalueSearch" + def run(self): self.search_term = [float(value) for value in self.search_term] |