From 6004e6e02223915ed913d3c8af88d8dce328187e Mon Sep 17 00:00:00 2001 From: VinzentRisch Date: Wed, 17 Jul 2024 12:10:44 +0200 Subject: [PATCH] fix bug full path gff --- q2_amr/amrfinderplus/sequences.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/q2_amr/amrfinderplus/sequences.py b/q2_amr/amrfinderplus/sequences.py index 4b52102..8cf24e2 100644 --- a/q2_amr/amrfinderplus/sequences.py +++ b/q2_amr/amrfinderplus/sequences.py @@ -38,7 +38,7 @@ def annotate_sequences_amrfinderplus( GenesDirectoryFormat, ProteinsDirectoryFormat, ): - # Checks for unallowed input combinations + # Check for unallowed input combinations if dna_sequences and gff and not protein_sequences: raise ValueError( "GFF input can only be given in combination with protein-sequence input." @@ -68,7 +68,7 @@ def annotate_sequences_amrfinderplus( ) if protein_sequences else None, - gff=os.listdir(str(gff))[0] if gff else None, + gff=os.path.join(str(gff), os.listdir(str(gff))[0]) if gff else None, organism=organism, plus=plus, report_all_equal=report_all_equal,