diff options
Diffstat (limited to 'wqflask/wqflask/do_search.py')
| -rw-r--r-- | wqflask/wqflask/do_search.py | 137 |
1 files changed, 72 insertions, 65 deletions
diff --git a/wqflask/wqflask/do_search.py b/wqflask/wqflask/do_search.py index fd03f359..e2bafb3a 100644 --- a/wqflask/wqflask/do_search.py +++ b/wqflask/wqflask/do_search.py @@ -49,65 +49,6 @@ class DoSearch(object): return cls.search_types[search_type] -class ProbeSetSearch(DoSearch): - """A search within an mRNA expression dataset""" - - DoSearch.search_types['ProbeSet'] = "ProbeSetSearch" - - base_query = """SELECT ProbeSet.Name as TNAME, - 0 as thistable, - ProbeSetXRef.Mean as TMEAN, - ProbeSetXRef.LRS as TLRS, - ProbeSetXRef.PVALUE as TPVALUE, - ProbeSet.Chr_num as TCHR_NUM, - ProbeSet.Mb as TMB, - ProbeSet.Symbol as TSYMBOL, - ProbeSet.name_num as TNAME_NUM - FROM ProbeSetXRef, ProbeSet """ - - - def compile_final_query(self, from_clause = '', where_clause = ''): - """Generates the final query string""" - - from_clause = '' - from_clause = self.normalize_spaces(from_clause) - - query = (self.base_query + - """%s - WHERE %s - and ProbeSet.Id = ProbeSetXRef.ProbeSetId - and ProbeSetXRef.ProbeSetFreezeId = %s - """ % (self.escape(from_clause), - where_clause, - self.escape(self.dataset.id))) - - print("query is:", pf(query)) - - return query - - def run(self): - """Generates and runs a simple search of an mRNA expression dataset""" - - print("Running ProbeSetSearch") - query = (self.base_query + - """WHERE (MATCH (ProbeSet.Name, - ProbeSet.description, - ProbeSet.symbol, - alias, - GenbankId, - UniGeneId, - Probe_Target_Description) - AGAINST ('%s' IN BOOLEAN MODE)) - and ProbeSet.Id = ProbeSetXRef.ProbeSetId - and ProbeSetXRef.ProbeSetFreezeId = %s - """ % (self.escape(self.search_term), - self.escape(self.dataset.id))) - - print("final query is:", pf(query)) - - return self.execute(query) - - class PhenotypeSearch(DoSearch): """A search within a phenotype dataset""" @@ -212,6 +153,65 @@ class GenotypeSearch(DoSearch): return self.execute(query) + +class ProbeSetSearch(DoSearch): + """A search within an mRNA expression dataset""" + + DoSearch.search_types['ProbeSet'] = "ProbeSetSearch" + + base_query = """SELECT ProbeSet.Name as TNAME, + 0 as thistable, + ProbeSetXRef.Mean as TMEAN, + ProbeSetXRef.LRS as TLRS, + ProbeSetXRef.PVALUE as TPVALUE, + ProbeSet.Chr_num as TCHR_NUM, + ProbeSet.Mb as TMB, + ProbeSet.Symbol as TSYMBOL, + ProbeSet.name_num as TNAME_NUM + FROM ProbeSetXRef, ProbeSet """ + + + def compile_final_query(self, from_clause, where_clause): + """Generates the final query string""" + + from_clause = self.normalize_spaces(from_clause) + + query = (self.normalize_spaces(self.base_query) + + """%s + WHERE %s + and ProbeSet.Id = ProbeSetXRef.ProbeSetId + and ProbeSetXRef.ProbeSetFreezeId = %s + """ % (self.escape(from_clause), + where_clause, + self.escape(self.dataset.id))) + + print("query is:", pf(query)) + + return query + + def run(self): + """Generates and runs a simple search of an mRNA expression dataset""" + + print("Running ProbeSetSearch") + query = (self.base_query + + """WHERE (MATCH (ProbeSet.Name, + ProbeSet.description, + ProbeSet.symbol, + alias, + GenbankId, + UniGeneId, + Probe_Target_Description) + AGAINST ('%s' IN BOOLEAN MODE)) + and ProbeSet.Id = ProbeSetXRef.ProbeSetId + and ProbeSetXRef.ProbeSetFreezeId = %s + """ % (self.escape(self.search_term), + self.escape(self.dataset.id))) + + print("final query is:", pf(query)) + + return self.execute(query) + + class RifSearch(ProbeSetSearch): """Searches for traits with a Gene RIF entry including the search term.""" @@ -283,7 +283,7 @@ class LrsSearch(ProbeSetSearch): DoSearch.search_types['LRS'] = 'LrsSearch' -class CisLrsSearch(LrsSearch): +class CisLrsSearch(ProbeSetSearch): """Searches for genes on a particular chromosome with a cis-eQTL within the given LRS values A cisLRS search can take 2 forms: @@ -305,9 +305,12 @@ class CisLrsSearch(LrsSearch): DoSearch.search_types['CISLRS'] = "CisLrsSearch" def run(self): + + from_clause = ", Geno " + if len(self.search_term) == 3: lower_limit, upper_limit, min_threshold = [int(value) for value in self.search_term] - + where_clause = """ %sXRef.LRS > %s and %sXRef.LRS < %s and %sXRef.Locus = Geno.name and @@ -327,7 +330,7 @@ class CisLrsSearch(LrsSearch): else: NeedSomeErrorHere - query = self.compile_final_query(where_clause) + query = self.compile_final_query(from_clause, where_clause) return self.execute(query) @@ -353,6 +356,8 @@ class TransLrsSearch(LrsSearch): DoSearch.search_types['TRANSLRS'] = "TransLrsSearch" def run(self): + from_clause = ", Geno " + if len(self.search_term) == 3: lower_limit, upper_limit, min_threshold = [int(value) for value in self.search_term] @@ -374,9 +379,11 @@ class TransLrsSearch(LrsSearch): ) else: - NeedSomeErrorHere + NeedSomeErrorHere - return None + query = self.compile_final_query(from_clause, where_clause) + + return self.execute(query) #itemCmd = item[0] @@ -447,7 +454,7 @@ 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(['9','99','10'], dataset, cursor, db_conn).run() + results = TransLrsSearch(['25','99','10'], 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() |