diff options
Diffstat (limited to 'wqflask/wqflask/do_search.py')
| -rw-r--r-- | wqflask/wqflask/do_search.py | 137 |
1 files changed, 117 insertions, 20 deletions
diff --git a/wqflask/wqflask/do_search.py b/wqflask/wqflask/do_search.py index 11411b26..17078802 100644 --- a/wqflask/wqflask/do_search.py +++ b/wqflask/wqflask/do_search.py @@ -74,6 +74,14 @@ class ProbeSetSearch(DoSearch): ProbeSet.name_num as TNAME_NUM FROM ProbeSetXRef, ProbeSet """ + header_fields = ['', + 'Record ID', + 'Symbol', + 'Description', + 'Location', + 'Mean', + 'Max LRS', + 'Max LRS Location'] def compile_final_query(self, from_clause = '', where_clause = ''): """Generates the final query string""" @@ -188,36 +196,49 @@ class GenotypeSearch(DoSearch): search_fields = ('Name', 'Chr') - def get_where_clause(self): - """Generate clause for WHERE portion of query""" + def get_fields_clause(self): + """Generate clause for part of the WHERE portion of query""" # This adds a clause to the query that matches the search term # against each field in search_fields (above) - where_clause = [] + fields_clause = [] + + if "'" not in self.search_term: + self.search_term = "[[:<:]]" + self.search_term + "[[:>:]]" + for field in self.search_fields: - where_clause.append('''%s REGEXP "%s"''' % ("%s.%s" % (self.dataset.type, field), - self.escape(self.search_term))) - print("where_clause is:", pf(where_clause)) - where_clause = "(%s)" % ' OR '.join(where_clause) + fields_clause.append('''%s REGEXP "%s"''' % ("%s.%s" % self.mescape(self.dataset.type, + field, + self.search_term))) + print("hello ;where_clause is:", pf(fields_clause)) + fields_clause = "(%s)" % ' OR '.join(fields_clause) - return where_clause + return fields_clause - def run(self): - """Generates and runs a simple search of a genotype dataset""" - #Todo: Zach will figure out exactly what both these lines mean - #and comment here - if "'" not in self.search_term: - search_term = "[[:<:]]" + self.search_term + "[[:>:]]" + def compile_final_query(self, from_clause = '', where_clause = ''): + """Generates the final query string""" + + from_clause = self.normalize_spaces(from_clause) query = (self.base_query + """WHERE %s and Geno.Id = GenoXRef.GenoId and GenoXRef.GenoFreezeId = GenoFreeze.Id and - GenoFreeze.Id = %s"""% ( - self.get_where_clause(), - self.escape(self.dataset.id))) + GenoFreeze.Id = %s"""% (where_clause, + self.escape(self.dataset.id))) - return self.execute(query) + print("query is:", pf(query)) + + return query + + def run(self): + """Generates and runs a simple search of a genotype dataset""" + #Todo: Zach will figure out exactly what both these lines mean + #and comment here + + self.query = self.compile_final_query(where_clause = self.get_fields_clause()) + + return self.execute(self.query) class RifSearch(ProbeSetSearch): """Searches for traits with a Gene RIF entry including the search term.""" @@ -497,9 +518,84 @@ class RangeSearch(ProbeSetSearch): self.query = self.compile_final_query(where_clause = self.where_clause) - return self.execute(self.query) + return self.execute(self.query) + +class PositionSearch(DoSearch): + """Searches for genes/markers located within a specified range on a specified chromosome""" + + for search_key in ('POSITION', 'POS', 'MB'): + DoSearch.search_types[search_key] = "PositionSearch" + + def setup(self): + self.search_term = [float(value) for value in self.search_term] + self.chr, self.mb_min, self.mb_max = self.search_term[:3] + self.where_clause = """ %s.Chr = '%s' and + %s.Mb > %s and + %s.Mb < %s """ % self.mescape(self.dataset.type, + self.chr, + self.dataset.type, + min(self.mb_min, self.mb_max), + self.dataset.type, + max(self.mb_min, self.mb_max)) + + def real_run(self): + + self.query = self.compile_final_query(where_clause = self.where_clause) + + return self.execute(self.query) + +class MrnaPositionSearch(ProbeSetSearch, PositionSearch): + """Searches for genes located within a specified range on a specified chromosome""" + + def run(self): + + self.setup() + self.query = self.compile_final_query(where_clause = self.where_clause) + + return self.execute(self.query) + +class GenotypePositionSearch(GenotypeSearch, PositionSearch): + """Searches for genes located within a specified range on a specified chromosome""" + + def run(self): + + self.setup() + self.query = self.compile_final_query(where_clause = self.where_clause) + + return self.execute(self.query) + +class PvalueSearch(ProbeSetSearch): + """Searches for traits with a permutationed p-value between low and high""" + + 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.pvalue_min, self.pvalue_max = self.search_term[:2] + self.where_clause = """ %sXRef.pValue > %s and %sXRef.pValue < %s + """ % self.mescape( + self.dataset.type, + min(self.pvalue_min, self.pvalue_max), + self.dataset.type, + max(self.pvalue_min, self.pvalue_max)) + else: + # Deal with >, <, >=, and <= + self.where_clause = """ %sXRef.pValue %s %s + """ % self.mescape( + self.dataset.type, + self.search_operator, + self.search_term[0]) + + print("where_clause is:", pf(self.where_clause)) + + self.query = self.compile_final_query(where_clause = self.where_clause) + + return self.execute(self.query) + if __name__ == "__main__": ### Usually this will be used as a library, but call it from the command line for testing ### And it runs the code below @@ -538,7 +634,8 @@ if __name__ == "__main__": ProbeSetXRef.ProbeSetFreezeId = 112""") #print(pf(cursor.fetchall())) - results = ProbeSetSearch("shh", None, dataset, cursor, db_conn).run() + #results = ProbeSetSearch("shh", None, dataset, cursor, db_conn).run() + results = PvalueSearch(['0.005'], '<', 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 |