From bd5b4ace4d274215b32c36a926786dff84c0519e Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Tue, 18 May 2021 15:24:21 +0200
Subject: [PATCH] kb: change t2g.py to use classical transcript and gene gtf
format
---
src/.docker_modules/kb/0.26.0/t2g.py | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/src/.docker_modules/kb/0.26.0/t2g.py b/src/.docker_modules/kb/0.26.0/t2g.py
index 82f2a1da..c9b23061 100755
--- a/src/.docker_modules/kb/0.26.0/t2g.py
+++ b/src/.docker_modules/kb/0.26.0/t2g.py
@@ -16,7 +16,7 @@ if __name__ == "__main__":
help="gtf file", metavar="FILE")
args = parser.parse_args()
- db = gffutils.create_db(args.gtf, dbfn = ":memory:", force = True, merge_strategy="merge", disable_infer_transcripts=False, disable_infer_genes=False)
+ db = gffutils.create_db(args.gtf, dbfn = ":memory:", force = True, merge_strategy="merge", disable_infer_transcripts=True, disable_infer_genes=True)
with open("t2g.txt", "w") as t2g:
for gene in db.all_features():
for transcript in db.children(gene, featuretype='transcript', order_by='start'):
--
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