diff options
Diffstat (limited to 'wqflask')
| -rwxr-xr-x | wqflask/wqflask/do_search.py | 98 |
1 files changed, 60 insertions, 38 deletions
diff --git a/wqflask/wqflask/do_search.py b/wqflask/wqflask/do_search.py index cec71777..3d1ad583 100755 --- a/wqflask/wqflask/do_search.py +++ b/wqflask/wqflask/do_search.py @@ -611,64 +611,76 @@ class PhenotypeLrsSearch(LrsSearch, PhenotypeSearch): return self.execute(self.query) -class CisTransLrsSearch(LrsSearch): +class CisTransLrsSearch(DoSearch): - def real_run(self, the_operator): - #if isinstance(self.search_term, basestring): - # self.search_term = [self.search_term] - print("self.search_term is:", self.search_term) + def get_from_clause(self): + return ", Geno " + + def get_where_clause(self, cis_trans): self.search_term = [float(value) for value in self.search_term] self.mb_buffer = 5 # default - - self.from_clause = ", Geno " + if cis_trans == "cis": + the_operator = "<" + else: + the_operator = ">" if self.search_operator == "=": if len(self.search_term) == 2: - self.lrs_min, self.lrs_max = self.search_term + lrs_min, 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 + lrs_min, lrs_max, self.mb_buffer = self.search_term else: SomeError - self.sub_clause = """ %sXRef.LRS > %s and + sub_clause = """ %sXRef.LRS > %s and %sXRef.LRS < %s and """ % ( escape(self.dataset.type), - escape(min(self.lrs_min, self.lrs_max)), + escape(str(min(lrs_min, lrs_max))), escape(self.dataset.type), - escape(max(self.lrs_min, self.lrs_max)) + escape(str(max(lrs_min, lrs_max))) ) else: # Deal with >, <, >=, and <= - self.sub_clause = """ %sXRef.LRS %s %s and """ % ( + sub_clause = """ %sXRef.LRS %s %s and """ % ( escape(self.dataset.type), escape(self.search_operator), escape(self.search_term[0]) ) - self.where_clause = self.sub_clause + """ - ABS(%s.Mb-Geno.Mb) %s %s and - %sXRef.Locus = Geno.name and - Geno.SpeciesId = %s and - %s.Chr = Geno.Chr""" % ( - escape(self.dataset.type), - the_operator, - 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) - - return self.execute(self.query) - + if cis_trans == "cis": + where_clause = sub_clause + """ + ABS(%s.Mb-Geno.Mb) %s %s and + %sXRef.Locus = Geno.name and + Geno.SpeciesId = %s and + %s.Chr = Geno.Chr""" % ( + escape(self.dataset.type), + the_operator, + escape(str(self.mb_buffer)), + escape(self.dataset.type), + escape(str(self.species_id)), + escape(self.dataset.type) + ) + else: + where_clause = sub_clause + """ + %sXRef.Locus = Geno.name and + Geno.SpeciesId = %s and + (ABS(%s.Mb-Geno.Mb) %s %s and %s.Chr = Geno.Chr) or + (%s.Chr != Geno.Chr)""" % ( + escape(self.dataset.type), + escape(str(self.species_id)), + escape(self.dataset.type), + the_operator, + escape(str(self.mb_buffer)), + escape(self.dataset.type), + escape(self.dataset.type) + ) -class CisLrsSearch(CisTransLrsSearch): + return where_clause + +class CisLrsSearch(CisTransLrsSearch, MrnaAssaySearch): """ Searches for genes on a particular chromosome with a cis-eQTL within the given LRS values @@ -685,12 +697,17 @@ class CisLrsSearch(CisTransLrsSearch): """ - DoSearch.search_types['CISLRS'] = "CisLrsSearch" + DoSearch.search_types['ProbeSet_CISLRS'] = 'CisLrsSearch' def run(self): - return self.real_run("<") + self.from_clause = self.get_from_clause() + self.where_clause = self.get_where_clause("cis") -class TransLrsSearch(CisTransLrsSearch): + self.query = self.compile_final_query(self.from_clause, self.where_clause) + + return self.execute(self.query) + +class TransLrsSearch(CisTransLrsSearch, MrnaAssaySearch): """Searches for genes on a particular chromosome with a cis-eQTL within the given LRS values A transLRS search can take 3 forms: @@ -706,10 +723,15 @@ class TransLrsSearch(CisTransLrsSearch): """ - DoSearch.search_types['TRANSLRS'] = "TransLrsSearch" + DoSearch.search_types['ProbeSet_TRANSLRS'] = 'TransLrsSearch' def run(self): - return self.real_run(">") + self.from_clause = self.get_from_clause() + self.where_clause = self.get_where_clause("trans") + + self.query = self.compile_final_query(self.from_clause, self.where_clause) + + return self.execute(self.query) class MeanSearch(MrnaAssaySearch): |