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-rwxr-xr-xwqflask/wqflask/do_search.py98
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):