Commit 8f3a98d9 authored by Hanna  JULIENNE's avatar Hanna JULIENNE
Browse files

FIX issue #8

parent 3ecc09f7
......@@ -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})
#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:
......@@ -81,7 +81,9 @@ def map_on_ref_panel(gw_df , ref_panel, index_type="rsid"):
merge_GWAS.set_index("snp_id", inplace=True)
raise ValueError("index_type can take only two values: 'rsid' or 'positional'")
if ((merge_GWAS.pos == merge_GWAS.POS).mean()> 0.95):
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)]
raise ValueError("SNP positions in reference panel and in Summary statistic are different! Different assembly?")
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