FIX issue #8

jass_preprocessing/map_gwas.py

@@ -153,6 +153,12 @@ def read_gwas( gwas_internal_link, column_map, imputation_treshold=None):
                                                  'NA', 'NULL', 'NaN',
                                                  'nan', 'na', '.', '-'], dtype={"snpid":str, "a1":str,"a2":str,"freq":float, "z":float,"se":float, "pval":float})
     print(fullGWAS.head())
+    #Ensure that allele are written in upper cases:
+
+    fullGWAS.a1 = fullGWAS.a1.str.upper()
+    fullGWAS.a2 = fullGWAS.a2.str.upper()
+
+
     def sorted_alleles(x):
         return "".join(sorted(x))
     # either rs ID or full position must be available:

jass_preprocessing/map_reference.py

@@ -21,7 +21,7 @@ def read_reference(gwas_reference_panel, mask_MHC=False, minimum_MAF=None, regio
     """
     ref = pd.read_csv(gwas_reference_panel, header=None, sep= "\t",
                       names =[ 'chr', "snp_id", "MAF","pos",  "ref", "alt"],
-                      dtype = {"chr": str, "snp_id":str, "MAF": np.float, "pos":np.int, "ref":str, "alt":str}, 
+                      dtype = {"chr": str, "snp_id":str, "MAF": np.float, "pos":np.int, "ref":str, "alt":str},
                        index_col="snp_id")
 
     def sorted_alleles(x):
@@ -81,10 +81,12 @@ def map_on_ref_panel(gw_df , ref_panel, index_type="rsid"):
             merge_GWAS.set_index("snp_id", inplace=True)
         else:
             raise ValueError("index_type can take only two values: 'rsid' or 'positional'")
-    if ((merge_GWAS.pos == merge_GWAS.POS).mean()> 0.95):
-        merge_GWAS = merge_GWAS.loc[(merge_GWAS.pos == merge_GWAS.POS)]
-    else:
-        raise ValueError("SNP positions in reference panel and in Summary statistic are different! Different assembly?")
+
+    if (("pos" in merge_GWAS.columns) and ("POS" in merge_GWAS.columns))
+        if (merge_GWAS.pos == merge_GWAS.POS).mean()> 0.95):
+            merge_GWAS = merge_GWAS.loc[(merge_GWAS.pos == merge_GWAS.POS)]
+        else:
+            raise ValueError("SNP positions in reference panel and in Summary statistic are different! Different assembly?")
 
     print("before filter")
     print(merge_GWAS.shape)