diff options
Diffstat (limited to 'wqflask/wqflask/do_search.py')
| -rw-r--r-- | wqflask/wqflask/do_search.py | 79 |
1 files changed, 64 insertions, 15 deletions
diff --git a/wqflask/wqflask/do_search.py b/wqflask/wqflask/do_search.py index 4517d9f5..ac6014e7 100644 --- a/wqflask/wqflask/do_search.py +++ b/wqflask/wqflask/do_search.py @@ -19,6 +19,10 @@ class DoSearch(object): self.dataset = dataset self.db_conn = db_conn self.cursor = cursor + + #Get group information for dataset and the species id + self.dataset.get_group() + self.species_id = webqtlDatabaseFunction.retrieveSpeciesId(self.cursor, self.dataset.group) def execute(self, query): """Executes query and returns results""" @@ -47,10 +51,6 @@ class ProbeSetSearch(DoSearch): DoSearch.search_types['ProbeSet'] = "ProbeSetSearch" - #Get group information for dataset and the species id - self.dataset.get_group() - self.species_id = webqtlDatabaseFunction.retrieveSpeciesId(self.cursor, self.dataset.group) - base_query = """SELECT ProbeSet.Name as TNAME, 0 as thistable, ProbeSetXRef.Mean as TMEAN, @@ -62,6 +62,7 @@ class ProbeSetSearch(DoSearch): ProbeSet.name_num as TNAME_NUM FROM ProbeSetXRef, ProbeSet """ + def compile_final_query(self, from_clause, where_clause): """Generates the final query string""" @@ -268,7 +269,7 @@ class LrsSearch(ProbeSetSearch): LRS searches can take 2 different forms: - LRS=(min_LRS max_LRS) - - LRS=(mine_LRS max_LRS chromosome start_Mb end_Mb) + - LRS=(min_LRS max_LRS chromosome start_Mb end_Mb) where min/max_LRS represent the range of LRS scores and start/end_Mb represent the range in megabases on the given chromosome @@ -276,9 +277,6 @@ class LrsSearch(ProbeSetSearch): DoSearch.search_types['LRS'] = 'LrsSearch' - self.species_id = webqtlDatabaseFunction.retrieveSpeciesId(self.cursor, - self.dataset.group) - class CisLrsSearch(LrsSearch): """Searches for genes on a particular chromosome with a cis-eQTL within the given LRS values @@ -290,8 +288,10 @@ class CisLrsSearch(LrsSearch): mb_buffer will default to 5 megabases. A QTL is a cis-eQTL if a gene's expression is regulated by a QTL in roughly the same area - (where the area is determined by the mb_buffer that the user can choose. + (where the area is determined by the mb_buffer that the user can choose). + """ + # This is tentatively a child of LrsSearch; I'll need to check what code, if any, overlaps # between this and the LrsSearch code. In the original code, commands are divided by # the number of inputs they take, so these commands are completely separate @@ -300,7 +300,7 @@ class CisLrsSearch(LrsSearch): def run(self): if len(self.search_term) == 3: - lower_limit, upper_limit, min_threshold = int(value) for value in self.search_term + lower_limit, upper_limit, min_threshold = [int(value) for value in self.search_term] where_clause = """ %sXRef.LRS > %s and %sXRef.LRS < %s and @@ -309,16 +309,65 @@ class CisLrsSearch(LrsSearch): %s.Chr = Geno.Chr and ABS(%s.Mb-Geno.Mb) < %s """ % ( self.dataset.type, - min(lower_limit, upper_limit) + min(lower_limit, upper_limit), + self.dataset.type, + max(lower_limit, upper_limit), + self.dataset.type, + self.species_id, self.dataset.type, - max(lower_limit, upper_limit, self.dataset.type, - + min_threshold ) else: - NeedSomeErrorHere - + NeedSomeErrorHere + + return None + +class TransLrsSearch(LrsSearch): + """Searches for genes on a particular chromosome with a cis-eQTL within the given LRS values + + A transLRS search can take 2 forms: + - transLRS=(min_LRS max_LRS) + - transLRS=(min_LRS max_LRS mb_buffer) + where min/max_LRS represent the range of LRS scores and the mb_buffer is the range around + a particular QTL where its eQTL would be considered "cis". If there is no third parameter, + mb_buffer will default to 5 megabases. + + A QTL is a trans-eQTL if a gene's expression is regulated by a QTL in a different location/area + (where the area is determined by the mb_buffer that the user can choose). Opposite of cis-eQTL. + + """ + + # This is tentatively a child of LrsSearch; I'll need to check what code, if any, overlaps + # between this and the LrsSearch code. In the original code, commands are divided by + # the number of inputs they take, so these commands are completely separate + + DoSearch.search_types['TRANSLRS'] = "TransLrsSearch" + + def run(self): + if len(self.search_term) == 3: + lower_limit, upper_limit, min_threshold = [int(value) for value in self.search_term] + + where_clause = """ %sXRef.LRS > %s and + %sXRef.LRS < %s and + %sXRef.Locus = Geno.name and + Geno.SpeciesId = %s and + (%s.Chr != Geno.Chr or + ABS(%s.Mb-Geno.Mb) > %s) """ % ( + self.dataset.type, + min(lower_limit, upper_limit), + self.dataset.type, + max(lower_limit, upper_limit), + self.dataset.type, + self.species_id, + self.dataset.type, + self.dataset.type, + min_threshold + ) + + else: + NeedSomeErrorHere return None |