diff --git a/jass_preprocessing/__main__.py b/jass_preprocessing/__main__.py index 248bb163e294fdeef57265868073af7532d68575..6570db67a85a8f133304112f231e6d72f0a00937 100644 --- a/jass_preprocessing/__main__.py +++ b/jass_preprocessing/__main__.py @@ -59,7 +59,9 @@ def launch_preprocessing(args): ref = jp.map_reference.read_reference(args.ref_path, bool(args.mask_MHC), float(args.minimum_MAF), region_to_mask=eval(args.additional_masked_region)) print(ref.shape) + print(ref.head()) print(gw_df.shape) + print(gw_df.head()) mgwas = jp.map_reference.map_on_ref_panel(gw_df, ref, gwas_map.loc[tag, "index_type"]) print(mgwas.shape) mgwas = jp.map_reference.compute_snp_alignement(mgwas) diff --git a/jass_preprocessing/map_gwas.py b/jass_preprocessing/map_gwas.py index 402b382c83f922e31438c60a0fd1726b278d38f7..9d4c94de779df05a1b838c02db05df670c3e1204 100644 --- a/jass_preprocessing/map_gwas.py +++ b/jass_preprocessing/map_gwas.py @@ -134,7 +134,7 @@ def read_gwas( gwas_internal_link, column_map, imputation_treshold=None): print("Reading file:") print(gwas_internal_link) - is_gzipped = re.search(r".gz$", gwas_internal_link) + is_gzipped = re.search(r".gz|.bgz$", gwas_internal_link) if is_gzipped: compression = 'gzip'