diff options
Diffstat (limited to 'wqflask/wqflask/do_search.py')
| -rw-r--r-- | wqflask/wqflask/do_search.py | 120 |
1 files changed, 60 insertions, 60 deletions
diff --git a/wqflask/wqflask/do_search.py b/wqflask/wqflask/do_search.py index 5eb09aa1..31f96ced 100644 --- a/wqflask/wqflask/do_search.py +++ b/wqflask/wqflask/do_search.py @@ -26,12 +26,12 @@ class DoSearch(object): assert search_operator in (None, "=", "<", ">", "<=", ">="), "Bad search operator" self.search_operator = search_operator self.dataset = dataset - + if self.dataset: print("self.dataset is boo: ", type(self.dataset), pf(self.dataset)) print("self.dataset.group is: ", pf(self.dataset.group)) #Get group information for dataset and the species id - self.species_id = webqtlDatabaseFunction.retrieve_species_id(self.dataset.group.name) + self.species_id = webqtlDatabaseFunction.retrieve_species_id(self.dataset.group.name) def execute(self, query): """Executes query and returns results""" @@ -44,7 +44,7 @@ class DoSearch(object): #def escape(self, stringy): # """Shorter name than self.db_conn.escape_string""" # return escape(str(stringy)) - + def mescape(self, *items): """Multiple escape""" escaped = [escape(item) for item in items] @@ -63,9 +63,9 @@ class DoSearch(object): class QuickMrnaAssaySearch(DoSearch): """A general search for mRNA assays""" - + DoSearch.search_types['quick_mrna_assay'] = "QuickMrnaAssaySearch" - + base_query = """SELECT ProbeSet.Name as ProbeSet_Name, ProbeSet.Symbol as ProbeSet_Symbol, ProbeSet.description as ProbeSet_Description, @@ -73,9 +73,9 @@ class QuickMrnaAssaySearch(DoSearch): ProbeSet.Mb as ProbeSet_Mb, ProbeSet.name_num as ProbeSet_name_num FROM ProbeSet """ - + header_fields = ['', - 'Record ID', + 'Record', 'Symbol', 'Location'] @@ -112,7 +112,7 @@ class MrnaAssaySearch(DoSearch): FROM ProbeSetXRef, ProbeSet """ header_fields = ['', - 'Record ID', + 'Record', 'Symbol', 'Description', 'Location', @@ -122,7 +122,7 @@ class MrnaAssaySearch(DoSearch): 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 + @@ -132,7 +132,7 @@ class MrnaAssaySearch(DoSearch): and ProbeSetXRef.ProbeSetFreezeId = %s """ % (escape(from_clause), where_clause, - escape(self.dataset.id))) + escape(self.dataset.id))) #print("query is:", pf(query)) @@ -149,9 +149,9 @@ class MrnaAssaySearch(DoSearch): GenbankId, UniGeneId, Probe_Target_Description) - AGAINST ('%s' IN BOOLEAN MODE)) + AGAINST ('%s' IN BOOLEAN MODE)) and ProbeSet.Id = ProbeSetXRef.ProbeSetId - and ProbeSetXRef.ProbeSetFreezeId = %s + and ProbeSetXRef.ProbeSetFreezeId = %s """ % (escape(self.search_term[0]), escape(str(self.dataset.id))) @@ -159,7 +159,7 @@ class MrnaAssaySearch(DoSearch): return self.execute(query) - + class PhenotypeSearch(DoSearch): """A search within a phenotype dataset""" @@ -181,9 +181,9 @@ class PhenotypeSearch(DoSearch): 'Publication.Title', 'Publication.Authors', 'PublishXRef.Id') - + header_fields = ['', - 'Record ID', + 'Record', 'Description', 'Authors', 'Year', @@ -237,9 +237,9 @@ class PhenotypeSearch(DoSearch): class QuickPhenotypeSearch(PhenotypeSearch): """A search across all phenotype datasets""" - + DoSearch.search_types['quick_phenotype'] = "QuickPhenotypeSearch" - + base_query = """SELECT Species.Name as Species_Name, PublishFreeze.FullName as Dataset_Name, PublishFreeze.Name, @@ -262,8 +262,8 @@ class QuickPhenotypeSearch(PhenotypeSearch): 'Publication.PubMed_ID', 'Publication.Abstract', 'Publication.Title', - 'Publication.Authors') - + 'Publication.Authors') + def compile_final_query(self, where_clause = ''): """Generates the final query string""" @@ -277,7 +277,7 @@ class QuickPhenotypeSearch(PhenotypeSearch): print("query is:", pf(query)) return query - + def run(self): """Generates and runs a search across all phenotype datasets""" @@ -299,10 +299,10 @@ class GenotypeSearch(DoSearch): FROM GenoXRef, GenoFreeze, Geno """ search_fields = ('Name', 'Chr') - + header_fields = ['', - 'Record ID', - 'Location'] + 'Record', + 'Location'] def get_fields_clause(self): """Generate clause for part of the WHERE portion of query""" @@ -310,7 +310,7 @@ class GenotypeSearch(DoSearch): # This adds a clause to the query that matches the search term # against each field in search_fields (above) fields_clause = [] - + if "'" not in self.search_term[0]: self.search_term = "[[:<:]]" + self.search_term[0] + "[[:>:]]" @@ -419,13 +419,13 @@ class LrsSearch(MrnaAssaySearch): """ DoSearch.search_types['LRS'] = 'LrsSearch' - + def run(self): - + self.search_term = [float(value) for value in self.search_term] - + self.from_clause = ", Geno" - + if self.search_operator == "=": assert isinstance(self.search_term, (list, tuple)) self.lrs_min, self.lrs_max = self.search_term[:2] @@ -444,8 +444,8 @@ class LrsSearch(MrnaAssaySearch): 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)) + max(self.mb_low, self.mb_high)) + print("self.sub_clause is:", pf(self.sub_clause)) else: # Deal with >, <, >=, and <= self.sub_clause = """ %sXRef.LRS %s %s and """ % self.mescape(self.dataset.type, @@ -474,20 +474,20 @@ class CisTransLrsSearch(LrsSearch): print("self.search_term is:", self.search_term) self.search_term = [float(value) for value in self.search_term] self.mb_buffer = 5 # default - + self.from_clause = ", Geno " if self.search_operator == "=": if len(self.search_term) == 2: self.lrs_min, self.lrs_max = self.search_term #[int(value) for value in self.search_term] - + elif len(self.search_term) == 3: self.lrs_min, self.lrs_max, self.mb_buffer = self.search_term - + else: SomeError - + self.sub_clause = """ %sXRef.LRS > %s and %sXRef.LRS < %s and """ % ( escape(self.dataset.type), @@ -510,12 +510,12 @@ class CisTransLrsSearch(LrsSearch): %s.Chr = Geno.Chr""" % ( escape(self.dataset.type), the_operator, - escape(self.mb_buffer), + escape(self.mb_buffer), escape(self.dataset.type), escape(self.species_id), escape(self.dataset.type) ) - + print("where_clause is:", pf(self.where_clause)) self.query = self.compile_final_query(self.from_clause, self.where_clause) @@ -560,7 +560,7 @@ class TransLrsSearch(CisTransLrsSearch): (where the area is determined by the mb_buffer that the user can choose). Opposite of cis-eQTL. """ - + DoSearch.search_types['TRANSLRS'] = "TransLrsSearch" def run(self): @@ -573,7 +573,7 @@ class MeanSearch(MrnaAssaySearch): DoSearch.search_types['MEAN'] = "MeanSearch" def run(self): - + self.search_term = [float(value) for value in self.search_term] if self.search_operator == "=": @@ -599,11 +599,11 @@ class MeanSearch(MrnaAssaySearch): class RangeSearch(MrnaAssaySearch): """Searches for genes with a range of expression varying between two values""" - + DoSearch.search_types['RANGE'] = "RangeSearch" - + def run(self): - + self.search_term = [float(value) for value in self.search_term] if self.search_operator == "=": @@ -632,10 +632,10 @@ class RangeSearch(MrnaAssaySearch): 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" - + 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] @@ -646,24 +646,24 @@ class PositionSearch(DoSearch): self.dataset.type, min(self.mb_min, self.mb_max), self.dataset.type, - max(self.mb_min, self.mb_max)) - + 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) + return self.execute(self.query) class MrnaPositionSearch(MrnaAssaySearch, 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""" @@ -673,12 +673,12 @@ class GenotypePositionSearch(GenotypeSearch, PositionSearch): self.query = self.compile_final_query(where_clause = self.where_clause) return self.execute(self.query) - + class PvalueSearch(MrnaAssaySearch): """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 == "=": @@ -703,19 +703,19 @@ class PvalueSearch(MrnaAssaySearch): self.query = self.compile_final_query(where_clause = self.where_clause) return self.execute(self.query) - + class AuthorSearch(PhenotypeSearch): """Searches for phenotype traits with specified author(s)""" - - DoSearch.search_types["NAME"] = "AuthorSearch" - + + DoSearch.search_types["NAME"] = "AuthorSearch" + def run(self): self.where_clause = """ Publication.Authors REGEXP "[[:<:]]%s[[:>:]]" and """ % (self.search_term[0]) - + self.query = self.compile_final_query(where_clause = self.where_clause) - + return self.execute(self.query) @@ -741,7 +741,7 @@ if __name__ == "__main__": dataset_name = "HC_M2_0606_P" dataset = create_dataset(db_conn, dataset_name) - + #cursor.execute(""" # SELECT ProbeSet.Name as TNAME, 0 as thistable, # ProbeSetXRef.Mean as TMEAN, ProbeSetXRef.LRS as TLRS, @@ -769,4 +769,4 @@ if __name__ == "__main__": #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)) |