From cd2a95224c2de98e17c72082bcc7f44a8e6d8796 Mon Sep 17 00:00:00 2001 From: Matthieu Barba Date: Wed, 6 Dec 2023 13:34:54 +0000 Subject: [PATCH 1/2] Add lrg as coord_system_tag --- src/python/ensembl/io/genomio/data/schemas/seq_region.json | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/src/python/ensembl/io/genomio/data/schemas/seq_region.json b/src/python/ensembl/io/genomio/data/schemas/seq_region.json index 5917705fb..67673791f 100644 --- a/src/python/ensembl/io/genomio/data/schemas/seq_region.json +++ b/src/python/ensembl/io/genomio/data/schemas/seq_region.json @@ -39,7 +39,8 @@ "contig", "chunk", "primary_assembly", - "clone" + "clone", + "lrg" ] }, "omit" : { "type" : "boolean", "description" : "prevent loading/processing of the scaffold" }, From a774a350b231d731e54e95c85a1a23f719fb6352 Mon Sep 17 00:00:00 2001 From: Matthieu Barba Date: Wed, 6 Dec 2023 13:35:14 +0000 Subject: [PATCH 2/2] Add log_file option --- src/python/ensembl/io/genomio/seq_region/dump.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/python/ensembl/io/genomio/seq_region/dump.py b/src/python/ensembl/io/genomio/seq_region/dump.py index fe80c74ba..21a6702ce 100644 --- a/src/python/ensembl/io/genomio/seq_region/dump.py +++ b/src/python/ensembl/io/genomio/seq_region/dump.py @@ -307,7 +307,7 @@ def main() -> None: parser.add_argument_src_path( "--external_db_map", default=_DEFAULT_MAP.resolve(), help="File with external_db mapping" ) - parser.add_log_arguments() + parser.add_log_arguments(add_log_file=True) args = parser.parse_args() init_logging_with_args(args)