diff options
Diffstat (limited to 'wqflask/wqflask/do_search.py')
| -rwxr-xr-x | wqflask/wqflask/do_search.py | 188 |
1 files changed, 101 insertions, 87 deletions
diff --git a/wqflask/wqflask/do_search.py b/wqflask/wqflask/do_search.py index 921a4a47..a3260f34 100755 --- a/wqflask/wqflask/do_search.py +++ b/wqflask/wqflask/do_search.py @@ -58,7 +58,14 @@ class DoSearch(object): @classmethod def get_search(cls, search_type): print("search_types are:", pf(cls.search_types)) - return cls.search_types[search_type] + + search_type_string = search_type['dataset_type'] + if 'key' in search_type: + search_type_string += '_' + search_type['key'] + + print("search_type_string is:", search_type_string) + + return cls.search_types[search_type_string] class QuickMrnaAssaySearch(DoSearch): """A general search for mRNA assays""" @@ -120,6 +127,22 @@ class MrnaAssaySearch(DoSearch): 'Max LRS Location', 'Additive Effect'] + def get_where_clause(self): + where_clause = """(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 + """ % (escape(self.search_term[0]), + escape(str(self.dataset.id))) + + return where_clause + def compile_final_query(self, from_clause = '', where_clause = ''): """Generates the final query string""" @@ -138,23 +161,7 @@ class MrnaAssaySearch(DoSearch): return query - def get_where_clause(self): - where_clause = """(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 - """ % (escape(self.search_term[0]), - escape(str(self.dataset.id))) - - return where_clause - - def run_combined(self, from_clause, where_clause): + def run_combined(self, from_clause = '', where_clause = ''): """Generates and runs a combined search of an mRNA expression dataset""" print("Running ProbeSetSearch") @@ -173,7 +180,6 @@ class MrnaAssaySearch(DoSearch): print("final query is:", pf(query)) - return self.execute(query) def run(self): @@ -219,7 +225,7 @@ class PhenotypeSearch(DoSearch): 'Max LRS Location', 'Additive Effect'] - def get_fields_clause(self): + def get_where_clause(self): """Generate clause for WHERE portion of query""" #Todo: Zach will figure out exactly what both these lines mean @@ -229,10 +235,10 @@ class PhenotypeSearch(DoSearch): # This adds a clause to the query that matches the search term # against each field in the search_fields tuple - fields_clause = [] + fields_clause_list = [] for field in self.search_fields: - fields_clause.append('''%s REGEXP "%s"''' % (field, search_term)) - fields_clause = "(%s) and " % ' OR '.join(fields_clause) + fields_clause_list.append('''%s REGEXP "%s"''' % (field, search_term)) + fields_clause = "(%s) " % ' OR '.join(fields_clause_list) return fields_clause @@ -244,6 +250,29 @@ class PhenotypeSearch(DoSearch): query = (self.base_query + """%s WHERE %s + and PublishXRef.InbredSetId = %s + and PublishXRef.PhenotypeId = Phenotype.Id + and PublishXRef.PublicationId = Publication.Id + and PublishFreeze.Id = %s""" % ( + from_clause, + where_clause, + escape(str(self.dataset.group.id)), + escape(str(self.dataset.id)))) + + print("query is:", pf(query)) + + return query + + def run_combined(self, from_clause, where_clause): + """Generates and runs a combined search of an phenotype dataset""" + + print("Running PhenotypeSearch") + + from_clause = self.normalize_spaces(from_clause) + + query = (self.base_query + + """%s + WHERE %s PublishXRef.InbredSetId = %s and PublishXRef.PhenotypeId = Phenotype.Id and PublishXRef.PublicationId = Publication.Id and @@ -253,14 +282,15 @@ class PhenotypeSearch(DoSearch): escape(str(self.dataset.group.id)), escape(str(self.dataset.id)))) - print("query is:", pf(query)) + print("final query is:", pf(query)) - return query + + return self.execute(query) def run(self): """Generates and runs a simple search of a phenotype dataset""" - query = self.compile_final_query(where_clause = self.get_fields_clause()) + query = self.compile_final_query(where_clause = self.get_where_clause()) return self.execute(query) @@ -310,7 +340,7 @@ class QuickPhenotypeSearch(PhenotypeSearch): def run(self): """Generates and runs a search across all phenotype datasets""" - query = self.compile_final_query(where_clause = self.get_fields_clause()) + query = self.compile_final_query(where_clause = self.get_where_clause()) return self.execute(query) @@ -333,7 +363,7 @@ class GenotypeSearch(DoSearch): 'Record', 'Location'] - def get_fields_clause(self): + def get_where_clause(self): """Generate clause for part of the WHERE portion of query""" # This adds a clause to the query that matches the search term @@ -348,7 +378,7 @@ class GenotypeSearch(DoSearch): field), self.search_term)) print("hello ;where_clause is:", pf(fields_clause)) - fields_clause = "(%s)" % ' OR '.join(fields_clause) + fields_clause = "(%s) " % ' OR '.join(fields_clause) return fields_clause @@ -358,10 +388,10 @@ class GenotypeSearch(DoSearch): 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"""% (where_clause, + """WHERE %s + and Geno.Id = GenoXRef.GenoId + and GenoXRef.GenoFreezeId = GenoFreeze.Id + and GenoFreeze.Id = %s"""% (where_clause, escape(str(self.dataset.id)))) print("query is:", pf(query)) @@ -373,14 +403,14 @@ class GenotypeSearch(DoSearch): #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()) + self.query = self.compile_final_query(where_clause = self.get_where_clause()) return self.execute(self.query) class RifSearch(MrnaAssaySearch): """Searches for traits with a Gene RIF entry including the search term.""" - DoSearch.search_types['RIF'] = "RifSearch" + DoSearch.search_types['ProbeSet_RIF'] = "RifSearch" def get_where_clause(self): where_clause = """( %s.symbol = GeneRIF_BASIC.symbol and @@ -390,10 +420,6 @@ class RifSearch(MrnaAssaySearch): return where_clause def run(self): - #where_clause = """( %s.symbol = GeneRIF_BASIC.symbol and - # MATCH (GeneRIF_BASIC.comment) - # AGAINST ('+%s' IN BOOLEAN MODE)) """ % (self.dataset.type, self.search_term[0]) - where_clause = self.get_where_clause() from_clause = ", GeneRIF_BASIC " @@ -404,7 +430,7 @@ class RifSearch(MrnaAssaySearch): class WikiSearch(MrnaAssaySearch): """Searches GeneWiki for traits other people have annotated""" - DoSearch.search_types['WIKI'] = "WikiSearch" + DoSearch.search_types['ProbeSet_WIKI'] = "WikiSearch" def get_where_clause(self): where_clause = """%s.symbol = GeneRIF.symbol @@ -433,7 +459,7 @@ class WikiSearch(MrnaAssaySearch): class GoSearch(MrnaAssaySearch): """Searches for synapse-associated genes listed in the Gene Ontology.""" - DoSearch.search_types['GO'] = "GoSearch" + DoSearch.search_types['ProbeSet_GO'] = "GoSearch" def run(self): field = 'GOterm.acc' @@ -525,43 +551,6 @@ class LrsSearch(MrnaAssaySearch): def run(self): self.from_clause = self.get_from_clause() - - #self.search_term = [float(value) for value in self.search_term] - # - #if self.search_operator == "=": - # assert isinstance(self.search_term, (list, tuple)) - # self.lrs_min, self.lrs_max = self.search_term[:2] - # - # self.sub_clause = """ %sXRef.LRS > %s and - # %sXRef.LRS < %s and """ % self.mescape(self.dataset.type, - # min(self.lrs_min, self.lrs_max), - # self.dataset.type, - # max(self.lrs_min, self.lrs_max)) - # - # if len(self.search_term) > 2: - # self.chr_num = self.search_term[2] - # self.sub_clause += """ Geno.Chr = %s and """ % (escape(self.chr_num)) - # if len(self.search_term) == 5: - # self.mb_low, self.mb_high = self.search_term[3:] - # self.sub_clause += """ Geno.Mb > %s and - # Geno.Mb < %s and - # """ % self.mescape(min(self.mb_low, self.mb_high), - # max(self.mb_low, self.mb_high)) - # print("self.sub_clause is:", pf(self.sub_clause)) - #else: - # # Deal with >, <, >=, and <= - # print("self.search_term is:", self.search_term) - # self.sub_clause = """ %sXRef.LRS %s %s and """ % self.mescape(self.dataset.type, - # self.search_operator, - # self.search_term[0]) - # - #self.where_clause = self.sub_clause + """ %sXRef.Locus = Geno.name and - # Geno.SpeciesId = %s and - # %s.Chr = Geno.Chr - # """ % self.mescape(self.dataset.type, - # self.species_id, - # self.dataset.type) - self.where_clause = self.get_where_clause() self.query = self.compile_final_query(self.from_clause, self.where_clause) @@ -673,7 +662,7 @@ class TransLrsSearch(CisTransLrsSearch): class MeanSearch(MrnaAssaySearch): """Searches for genes expressed within an interval (log2 units) determined by the user""" - DoSearch.search_types['MEAN'] = "MeanSearch" + DoSearch.search_types['ProbeSet_MEAN'] = "MeanSearch" def get_where_clause(self): self.search_term = [float(value) for value in self.search_term] @@ -732,7 +721,7 @@ class MeanSearch(MrnaAssaySearch): class RangeSearch(MrnaAssaySearch): """Searches for genes with a range of expression varying between two values""" - DoSearch.search_types['RANGE'] = "RangeSearch" + DoSearch.search_types['ProbeSet_RANGE'] = "RangeSearch" def get_where_clause(self): if self.search_operator == "=": @@ -791,10 +780,8 @@ class PositionSearch(DoSearch): 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 + def get_where_clause(self): + where_clause = """ %s.Chr = %s and %s.Mb > %s and %s.Mb < %s """ % self.mescape(self.dataset.type, self.chr, @@ -803,6 +790,21 @@ class PositionSearch(DoSearch): self.dataset.type, max(self.mb_min, self.mb_max)) + + return where_clause + + def setup(self): + self.search_term = [float(value) if is_number(value) else value for value in self.search_term] + self.chr, self.mb_min, self.mb_max = self.search_term[:3] + self.get_chr() + self.where_clause = self.get_where_clause() + + def get_chr(self): + try: + self.chr = int(self.chr) + except: + self.chr = int(self.chr.replace('chr', '')) + def run(self): self.setup() @@ -810,9 +812,12 @@ class PositionSearch(DoSearch): return self.execute(self.query) -class MrnaPositionSearch(MrnaAssaySearch, PositionSearch): +class MrnaPositionSearch(PositionSearch, MrnaAssaySearch): """Searches for genes located within a specified range on a specified chromosome""" + for search_key in ('POSITION', 'POS', 'MB'): + DoSearch.search_types['ProbeSet_'+search_key] = "MrnaPositionSearch" + def run(self): self.setup() @@ -820,9 +825,12 @@ class MrnaPositionSearch(MrnaAssaySearch, PositionSearch): return self.execute(self.query) -class GenotypePositionSearch(GenotypeSearch, PositionSearch): +class GenotypePositionSearch(PositionSearch, GenotypeSearch): """Searches for genes located within a specified range on a specified chromosome""" + for search_key in ('POSITION', 'POS', 'MB'): + DoSearch.search_types['Geno_'+search_key] = "GenotypePositionSearch" + def run(self): self.setup() @@ -863,7 +871,7 @@ class PvalueSearch(MrnaAssaySearch): class AuthorSearch(PhenotypeSearch): """Searches for phenotype traits with specified author(s)""" - DoSearch.search_types["NAME"] = "AuthorSearch" + DoSearch.search_types["Publish_NAME"] = "AuthorSearch" def run(self): @@ -875,6 +883,12 @@ class AuthorSearch(PhenotypeSearch): return self.execute(self.query) +def is_number(s): + try: + float(s) + return True + except ValueError: + return False if __name__ == "__main__": ### Usually this will be used as a library, but call it from the command line for testing |