From f35d91df93e9e0389e71950aca17290a813ea1e6 Mon Sep 17 00:00:00 2001 From: tderrien Date: Sun, 10 Dec 2023 21:32:06 +0100 Subject: [PATCH] Modify filter count matric to inlcude lower case txid --- bin/filter_gtf_ndr.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/bin/filter_gtf_ndr.py b/bin/filter_gtf_ndr.py index 5f8abf7..e6bba39 100755 --- a/bin/filter_gtf_ndr.py +++ b/bin/filter_gtf_ndr.py @@ -9,7 +9,7 @@ def parse_bambu(line): def parse_tfkmers(line): ids = line[0].split("::") - return ids[0], ids[1], line[1] + return ids[1], ids[0], line[1] def parse_ndr(csv, origin, th) -> Set[str]: @@ -39,7 +39,7 @@ def filter_count_matrix(file, transcripts, wr): print(next(file), file=wr) for line in file: line_splitted = line.split("\t") - if line_splitted[0].startswith("BambuTx") and line_splitted[0] not in transcripts: + if line_splitted[0].startswith("BambuTx") and line_splitted[0].lower() not in transcripts: continue print(line.rstrip(), file=wr)