From 3ff99f865930715dd863d93fb41c7326c9440f3e Mon Sep 17 00:00:00 2001 From: Anton Kriese Date: Fri, 3 Jun 2022 14:33:00 +0200 Subject: [PATCH] expect liftover chain files to be in same path ... as the liftover config --- workflow/scripts/ref_cut.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/workflow/scripts/ref_cut.py b/workflow/scripts/ref_cut.py index e656be1..fd05da8 100644 --- a/workflow/scripts/ref_cut.py +++ b/workflow/scripts/ref_cut.py @@ -57,10 +57,11 @@ def collect_liftover(args): "t2tv2": ["chain_hg38_to_t2tv1", "chain_t2tv1_to_t2tv2"] """ liftover_jumps = json.load(open(args.liftover_paths, "r")) + liftover_root = args.liftover_paths.parent for chain_file_route in liftover_jumps.values(): for chain_file in chain_file_route: if not chain_file in liftover_chain_files: - liftover_chain_files[chain_file] = LiftOver(str(chain_file)) + liftover_chain_files[chain_file] = LiftOver(str(liftover_root / chain_file)) alt_regions = [] for ref_idx, (alt_ref_name, alt_ref) in enumerate(zip(alt_ref_names, alt_references)):