From 8600ed034bb783953e9d04a4b22c463d7b8ff5a7 Mon Sep 17 00:00:00 2001 From: Cornelius Roemer Date: Sat, 4 Nov 2023 03:09:16 +0100 Subject: [PATCH] feat: treat CDS as a valid feature for GFFs in `load_features` We currently don't load CDS features from GFF files Within Nextclade, we now treat CDS as the translatable unit, not gene So to use Nextclade GFF annotations in ancestral, we need to be able to read in CDS features Reading in CDS in addition to gene and source could potentially break some workflows that use gffs that have both gene and CDS features --- augur/utils.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/augur/utils.py b/augur/utils.py index d687e62a5..f098ef288 100644 --- a/augur/utils.py +++ b/augur/utils.py @@ -153,7 +153,7 @@ def load_features(reference, feature_names=None): if '.gff' in reference.lower(): #looks for 'gene' and 'gene' as best for TB from BCBio import GFF - limit_info = dict( gff_type = ['gene', 'source'] ) + limit_info = dict( gff_type = ['gene', 'source', 'CDS'] ) with open(reference, encoding='utf-8') as in_handle: for rec in GFF.parse(in_handle, limit_info=limit_info):