From ac13ec729f5dc0feb7cb5120692022a5f0631cd1 Mon Sep 17 00:00:00 2001 From: JeanMainguy Date: Tue, 29 Oct 2024 11:49:19 +0100 Subject: [PATCH 1/2] add missing disable bar flag in fast projection --- ppanggolin/projection/projection.py | 1 + 1 file changed, 1 insertion(+) diff --git a/ppanggolin/projection/projection.py b/ppanggolin/projection/projection.py index e7021319..d577e840 100644 --- a/ppanggolin/projection/projection.py +++ b/ppanggolin/projection/projection.py @@ -795,6 +795,7 @@ def annotate_input_genes_with_pangenome_families( identity=identity, coverage=coverage, translation_table=translation_table, + disable_bar=disable_bar, ) else: _, seqid_to_gene_family = get_input_seq_to_family_with_all( From af0c6750eb9dc3972b3fb6d1e7dd075efa64a233 Mon Sep 17 00:00:00 2001 From: JeanMainguy Date: Tue, 29 Oct 2024 12:01:38 +0100 Subject: [PATCH 2/2] use debug to inform on missing translation table in input files --- ppanggolin/annotate/annotate.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/ppanggolin/annotate/annotate.py b/ppanggolin/annotate/annotate.py index c20cbd86..f99c1f46 100644 --- a/ppanggolin/annotate/annotate.py +++ b/ppanggolin/annotate/annotate.py @@ -823,7 +823,7 @@ def read_org_gbff( contig.add_metadata(Metadata(source="annotation_file", **metadata_dict)) if used_transl_table_arg: - logging.getLogger("PPanGGOLiN").info( + logging.getLogger("PPanGGOLiN").debug( f"transl_table tag was not found for {used_transl_table_arg} CDS " f"in {gbff_file_path}. Provided translation_table argument value was used instead: {translation_table}." )