Skip to content
Snippets Groups Projects
Commit b0380f32 authored by hjulienne's avatar hjulienne
Browse files

add debug print

parent 9c12fe0a
No related branches found
No related tags found
No related merge requests found
...@@ -59,7 +59,9 @@ def launch_preprocessing(args): ...@@ -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)) 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.shape)
print(ref.head())
print(gw_df.shape) 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"]) mgwas = jp.map_reference.map_on_ref_panel(gw_df, ref, gwas_map.loc[tag, "index_type"])
print(mgwas.shape) print(mgwas.shape)
mgwas = jp.map_reference.compute_snp_alignement(mgwas) mgwas = jp.map_reference.compute_snp_alignement(mgwas)
......
...@@ -134,7 +134,7 @@ def read_gwas( gwas_internal_link, column_map, imputation_treshold=None): ...@@ -134,7 +134,7 @@ def read_gwas( gwas_internal_link, column_map, imputation_treshold=None):
print("Reading file:") print("Reading file:")
print(gwas_internal_link) 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: if is_gzipped:
compression = 'gzip' compression = 'gzip'
......
0% Loading or .
You are about to add 0 people to the discussion. Proceed with caution.
Please register or to comment