From 75a65e7346adf9d5114b3f0b93262d61a8d1d2f0 Mon Sep 17 00:00:00 2001 From: mhkc Date: Thu, 7 Dec 2023 10:52:30 +0100 Subject: [PATCH] removed debug statement --- prp/parse/phenotype/resfinder.py | 35 +++++++++++++++----------------- 1 file changed, 16 insertions(+), 19 deletions(-) diff --git a/prp/parse/phenotype/resfinder.py b/prp/parse/phenotype/resfinder.py index 239cea2..973c4aa 100644 --- a/prp/parse/phenotype/resfinder.py +++ b/prp/parse/phenotype/resfinder.py @@ -93,25 +93,22 @@ def _parse_resfinder_amr_genes( category = ElementType(res_category) # store results - try: - gene = ResistanceGene( - gene_symbol=info["name"], - accession=info["ref_acc"], - depth=info["depth"], - identity=info["identity"], - coverage=info["coverage"], - ref_start_pos=info["ref_start_pos"], - ref_end_pos=info["ref_end_pos"], - ref_gene_length=info["ref_seq_length"], - alignment_length=info["alignment_length"], - phenotypes=info["phenotypes"], - ref_database=info["ref_database"][0], - ref_id=info["ref_id"], - element_type=category, - element_subtype=_assign_res_subtype(info, category), - ) - except: - import pdb; pdb.set_trace() + gene = ResistanceGene( + gene_symbol=info["name"], + accession=info["ref_acc"], + depth=info["depth"], + identity=info["identity"], + coverage=info["coverage"], + ref_start_pos=info["ref_start_pos"], + ref_end_pos=info["ref_end_pos"], + ref_gene_length=info["ref_seq_length"], + alignment_length=info["alignment_length"], + phenotypes=info["phenotypes"], + ref_database=info["ref_database"][0], + ref_id=info["ref_id"], + element_type=category, + element_subtype=_assign_res_subtype(info, category), + ) results.append(gene) return results