bug fix

dna-seq · Oct 22, 2023 · 470c8ec · 470c8ec
1 parent 4cd0a56
commit 470c8ec
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Showing 2 changed files with 3 additions and 4 deletions.
diff --git a/just_lipidmetabolism.py b/just_lipidmetabolism.py
@@ -134,7 +134,7 @@ def annotate (self, input_data:dict):
         study_design = self.merge_studies(studies)
 
         query:str = "SELECT rsids.risk_allele, gene, genotype, genotype_specific_conclusion, rsid_conclusion, weight, " \
-                " pmids, population, p_value FROM rsids, " \
+                " pmids, population FROM rsids, " \
                 f" weight WHERE rsids.rsid = '{rsid}' AND weight.rsid = '{rsid}'" \
                 f" AND weight.risk_allele='{alt}' AND zygosity ='{zygot}' AND allele='{alt}'; "
 

diff --git a/lipidmetabolism_ref_homo.py b/lipidmetabolism_ref_homo.py
@@ -58,15 +58,14 @@ def end(self):
             if self.rsid_map[rsid]['exist']:
                 allele:str = self.rsid_map[rsid]['allele']
                 genotype:str = allele+allele
-
                 query_for_studies:str = f"SELECT pubmed_id, populations, p_value FROM studies WHERE snp = '{rsid}'"
                 self.parent.lipid_cursor.execute(query_for_studies)
                 studies = self.parent.lipid_cursor.fetchall()
                 study_design = self.parent.merge_studies(studies)
 
                 query:str = "SELECT rsids.risk_allele, gene, genotype, genotype_specific_conclusion, rsid_conclusion, weight, " \
-                " pmids, population, p_value FROM rsids, " \
-                f" weight WHERE rsids.rsid = '{rsid}' AND weight.rsid = '{rsid}' AND genotype = '{genotype}';"
+                " pmids, population, rsids.p_value FROM rsids, " \
+                f" weight WHERE rsids.rsid = '{rsid}' AND weight.rsid = '{rsid}' AND weight.state = 'ref' AND weight.zygosity='hom'"
 
                 self.parent.lipid_cursor.execute(query)
                 row:tuple = self.parent.lipid_cursor.fetchone()