From 322143d97ec6313a8ba3e1ca6d9247b3be72b2a2 Mon Sep 17 00:00:00 2001 From: Anton Kriese Date: Fri, 3 Jun 2022 15:11:59 +0200 Subject: [PATCH] write regions into fasta headers --- workflow/scripts/ref_cut.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/workflow/scripts/ref_cut.py b/workflow/scripts/ref_cut.py index fd05da8..fc13b70 100644 --- a/workflow/scripts/ref_cut.py +++ b/workflow/scripts/ref_cut.py @@ -45,7 +45,7 @@ def collect_liftover(args): liftover_chain_files = {} seq_coll = SequenceCollection() - seq_coll.references.append(NamedSequence(main_ref_name, main_ref_region.get_reference_seq(main_reference))) + seq_coll.references.append(NamedSequence(f"{main_ref_name} {main_ref_region}", main_ref_region.get_reference_seq(main_reference))) # If we have no information about how to handle liftovers, we dont to them if not Path(args.liftover_paths).exists(): @@ -77,7 +77,7 @@ def collect_liftover(args): print("Alternative reference region is absurdely large. Liftover probably failed.") else: alt_ref_str = alt_ref_region.get_reference_seq(alt_ref) - seq_coll.references.append(NamedSequence(alt_ref_name, alt_ref_str)) + seq_coll.references.append(NamedSequence(f"{alt_ref_name} {alt_ref_region}", alt_ref_str)) else: print(f"Region not found in {alt_ref_names[ref_idx]} reference!")