diff options
Diffstat (limited to 'wqflask/wqflask/do_search.py')
| -rwxr-xr-x | wqflask/wqflask/do_search.py | 13 |
1 files changed, 7 insertions, 6 deletions
diff --git a/wqflask/wqflask/do_search.py b/wqflask/wqflask/do_search.py index f9082495..fd7bd916 100755 --- a/wqflask/wqflask/do_search.py +++ b/wqflask/wqflask/do_search.py @@ -96,7 +96,7 @@ class QuickMrnaAssaySearch(DoSearch): class MrnaAssaySearch(DoSearch): - """A search within an mRNA expression dataset""" + """A search within an expression dataset, including mRNA, protein, SNP, but not phenotype or metabolites""" DoSearch.search_types['ProbeSet'] = "MrnaAssaySearch" @@ -358,7 +358,7 @@ class RifSearch(MrnaAssaySearch): def run(self): where_clause = """( %s.symbol = GeneRIF_BASIC.symbol and MATCH (GeneRIF_BASIC.comment) - AGAINST ('+%s' IN BOOLEAN MODE)) """ % (self.dataset.type, self.search_term) + AGAINST ('+%s' IN BOOLEAN MODE)) """ % (self.dataset.type, self.search_term[0]) from_clause = ", GeneRIF_BASIC " query = self.compile_final_query(from_clause, where_clause) @@ -375,8 +375,8 @@ class WikiSearch(MrnaAssaySearch): and GeneRIF.versionId=0 and GeneRIF.display>0 and (GeneRIF.comment REGEXP '%s' or GeneRIF.initial = '%s') """ % (self.dataset.type, - "[[:<:]]"+self.search_term[0]+"[[:>:]]", - self.search_term[0]) + "[[:<:]]"+str(self.search_term[0])+"[[:>:]]", + str(self.search_term[0])) from_clause = ", GeneRIF " query = self.compile_final_query(from_clause, where_clause) @@ -390,7 +390,7 @@ class GoSearch(MrnaAssaySearch): def run(self): field = 'GOterm.acc' - go_id = 'GO:' + ('0000000'+self.search_term)[-7:] + go_id = 'GO:' + ('0000000'+self.search_term[0])[-7:] statements = ("""%s.symbol=GOgene_product.symbol and GOassociation.gene_product_id=GOgene_product.id and @@ -651,8 +651,9 @@ class PositionSearch(DoSearch): self.dataset.type, max(self.mb_min, self.mb_max)) - def real_run(self): + def run(self): + self.setup() self.query = self.compile_final_query(where_clause = self.where_clause) return self.execute(self.query) |