Commit 823976b5 authored by Hanna  JULIENNE's avatar Hanna JULIENNE
Browse files

corrected column mix up when snpid is not first

parent b8b082b3
Pipeline #18396 passed with stages
in 51 seconds
......@@ -152,13 +152,13 @@ def read_gwas( gwas_internal_link, column_map):
compression=compression,
#column_dict['label_position'].keys(),
names= column_map.index,
index_col=0,
header=0, na_values= ['', '#N/A', '#N/A', 'N/A','#NA', '-1.#IND', '-1.#QNAN',
'-NaN', '-nan', '1.#IND', '1.#QNAN', 'N/A',
'NA', 'NULL', 'NaN',
'nan', 'na', '.'])
'nan', 'na', '.', '-'], dtype={"snpid":str, "a1":str,"a2":str,"freq":float, "z":float,"se":float, "pval":float})
print(fullGWAS.head())
fullGWAS.set_index("snpid", inplace=True)
print(fullGWAS.head())
fullGWAS = fullGWAS[~fullGWAS.index.duplicated(keep='first')]
#fullGWAS = convert_missing_values(fullGWAS)
......
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