From e8778e56d6fa8993bd66d9eac288dbb21b93e286 Mon Sep 17 00:00:00 2001 From: Ryu Hyunwoo Date: Wed, 16 Aug 2023 17:09:58 +0900 Subject: [PATCH] Bug fix --- gdbr/annotate.py | 9 ++++----- 1 file changed, 4 insertions(+), 5 deletions(-) diff --git a/gdbr/annotate.py b/gdbr/annotate.py index f7b1eef..ebd86e2 100644 --- a/gdbr/annotate.py +++ b/gdbr/annotate.py @@ -583,14 +583,13 @@ def annotate_main(ref_loc, qry_loc_list, sv_loc_list, hom_find_len=2000, diff_lo merge_bed_df = pd.concat([merge_bed_df, tdf]) logprint(f'{qry_ind + 1}/{len(qry_loc_list)} : {os.path.basename(qry_loc)} annotate complete') - # merge bed data + + # export merge bed file merge_bed_df = merge_bed_df.groupby([0, 1, 2, 3, 4, 5], as_index=False).agg({6: lambda x: ';'.join(sorted(set(x), key=lambda t: int(t.split('.')[1])))}) + if len(qry_loc_list) > 1: + merge_bed_df.to_csv(os.path.join(dsbr_save, 'bed', 'total.GDBr.merge_result.bed'), header=False, sep='\t', index=False) # draw figure os.makedirs(os.path.join(dsbr_save, 'figure'), exist_ok=True) draw_result(os.path.join(dsbr_save, 'figure'), pre_type_cnt, cor_type_cnt, del_type_cnt, ins_type_cnt, sub_type_cnt, indel_hom_cnt, temp_ins_hom_cnt, diff_locus_dsbr_hom_cnt, tot_sv_len, len(qry_loc_list), diff_locus_dsbr_analysis, ref_seq, merge_bed_df) - - # export merge bed file - if len(qry_loc_list) > 1: - merge_bed_df.to_csv(os.path.join(dsbr_save, 'bed', 'total.GDBr.merge_result.bed'), header=False, sep='\t', index=False)