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authorZachary Sloan2012-11-30 14:04:59 -0600
committerZachary Sloan2012-11-30 14:04:59 -0600
commit7929d5d5aace20b50a9c5b428eea784d8eac0b77 (patch)
tree490cc498d2876de01e395103f859e1aaf3957f56 /wqflask
parent94300b4488aa334ced34981981ad5d0ecdec01d6 (diff)
downloadgenenetwork2-7929d5d5aace20b50a9c5b428eea784d8eac0b77.tar.gz
Got searches working for RANGE and MEAN commands
Created a file where renamed variables will be listed for future reference
Diffstat (limited to 'wqflask')
-rw-r--r--wqflask/wqflask/do_search.py59
1 files changed, 56 insertions, 3 deletions
diff --git a/wqflask/wqflask/do_search.py b/wqflask/wqflask/do_search.py
index 92a754e3..11411b26 100644
--- a/wqflask/wqflask/do_search.py
+++ b/wqflask/wqflask/do_search.py
@@ -414,8 +414,7 @@ class CisLrsSearch(CisTransLrsSearch):
def run(self):
return self.real_run("<")
-
-
+
class TransLrsSearch(CisTransLrsSearch):
"""Searches for genes on a particular chromosome with a cis-eQTL within the given LRS values
@@ -443,9 +442,63 @@ class MeanSearch(ProbeSetSearch):
DoSearch.search_types['MEAN'] = "MeanSearch"
def run(self):
+
+ self.search_term = [float(value) for value in self.search_term]
- return None
+ if self.search_operator == "=":
+ assert isinstance(self.search_term, (list, tuple))
+ self.mean_min, self.mean_max = self.search_term[:2]
+ self.where_clause = """ %sXRef.mean > %s and
+ %sXRef.mean < %s """ % self.mescape(self.dataset.type,
+ min(self.mean_min, self.mean_max),
+ self.dataset.type,
+ max(self.mean_min, self.mean_max))
+ else:
+ # Deal with >, <, >=, and <=
+ self.where_clause = """ %sXRef.mean %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)
+
+class RangeSearch(ProbeSetSearch):
+ """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 == "=":
+ assert isinstance(self.search_term, (list, tuple))
+ self.range_min, self.range_max = self.search_term[:2]
+ self.where_clause = """ (SELECT Pow(2, max(value) -min(value))
+ FROM ProbeSetData
+ WHERE ProbeSetData.Id = ProbeSetXRef.dataId) > %s AND
+ (SELECT Pow(2, max(value) -min(value))
+ FROM ProbeSetData
+ WHERE ProbeSetData.Id = ProbeSetXRef.dataId) < %s
+ """ % self.mescape(min(self.range_min, self.range_max),
+ max(self.range_min, self.range_max))
+ else:
+ # Deal with >, <, >=, and <=
+ self.where_clause = """ (SELECT Pow(2, max(value) -min(value))
+ FROM ProbeSetData
+ WHERE ProbeSetData.Id = ProbeSetXRef.dataId) > %s
+ """ % (self.escape(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