diff options
| -rw-r--r-- | wqflask/wqflask/do_search.py | 59 |
1 files changed, 54 insertions, 5 deletions
diff --git a/wqflask/wqflask/do_search.py b/wqflask/wqflask/do_search.py index 49da4282..2b8efd68 100644 --- a/wqflask/wqflask/do_search.py +++ b/wqflask/wqflask/do_search.py @@ -285,6 +285,53 @@ class LrsSearch(ProbeSetSearch): DoSearch.search_types['LRS'] = 'LrsSearch' + def run(self): + + self.search_term = [float(value) for value in self.search_term] + + from_clause = ", Geno" + + if self.search_operator == "=": + if len(self.search_term) >= 2: + if len(self.search_term) == 2: + lrs_min, lrs_max = self.search_term + elif len(self.search_term) == 5: + lrs_min, lrs_max, chr_num, mb_low, mb_high = self.search_term + else: + SomeError + + sub_clause = """ %sXRef.LRS > %s and + %sXRef.LRS < %s and """ % (self.escape(self.dataset.type), + self.escape(min(lrs_min, lrs_max)), + self.escape(self.dataset.type), + self.escape(max(lrs_min, lrs_max))) + + if len(self.search_term) == 5: + sub_clause = sub_clause + """ Geno.Mb > %s and + Geno.Mb < %s and + Geno.Chr = %s and + """ % (self.escape(min(mb_low, mb_high)), + self.escape(max(mb_low, mb_high)), + self.escape(chr_num)) + else: + # Deal with >, <, >=, and <= + sub_clause = """ %sXRef.LRS %s %s and """ % (self.escape(self.dataset.type), + self.escape(self.search_operator), + self.escape(self.search_term[0])) + + where_clause = sub_clause + """ %sXRef.Locus = Geno.name and + Geno.SpeciesId = %s and + %s.Chr = Geno.Chr + """ % (self.escape(self.dataset.type), + self.escape(self.species_id), + self.escape(self.dataset.type)) + + print("where_clause is:", pf(where_clause)) + + query = self.compile_final_query(from_clause, where_clause) + + return self.execute(query) + class CisLrsSearch(LrsSearch): """Searches for genes on a particular chromosome with a cis-eQTL within the given LRS values @@ -324,10 +371,13 @@ class CisLrsSearch(LrsSearch): elif len(self.search_term) == 3: lower_limit, upper_limit, mb_buffer = self.search_term + + else: + SomeError sub_clause = """ %sXRef.LRS > %s and %sXRef.LRS < %s and - ABS(%s.Mb-Geno.Mb) < %s """ % ( + ABS(%s.Mb-Geno.Mb) < %s and """ % ( self.escape(self.dataset.type), self.escape(min(lower_limit, upper_limit)), self.escape(self.dataset.type), @@ -335,8 +385,6 @@ class CisLrsSearch(LrsSearch): self.escape(self.dataset.type), self.escape(mb_buffer) ) - - else: # Deal with >, <, >=, and <= @@ -495,10 +543,11 @@ if __name__ == "__main__": #results = ProbeSetSearch("salt", dataset, cursor, db_conn).run() #results = RifSearch("diabetes", dataset, cursor, db_conn).run() #results = WikiSearch("nicotine", dataset, cursor, db_conn).run() - results = CisLrsSearch('99', '>', dataset, cursor, db_conn).run() # cisLRS > 99 + results = CisLrsSearch(['99'], '>', dataset, cursor, db_conn).run() # cisLRS > 99 + #results = LrsSearch('9', '99', '1', '50', '150', '=', dataset, cursor, db_conn).run() #results = TransLrsSearch(['9', '999', '10'], dataset, cursor, db_conn).run() #results = PhenotypeSearch("brain", dataset, cursor, db_conn).run() #results = GenotypeSearch("rs13475699", dataset, cursor, db_conn).run() #results = GoSearch("0045202", dataset, cursor, db_conn).run() - #print("results are:", pf(results))
\ No newline at end of file + print("results are:", pf(results))
\ No newline at end of file |