From c8631778f4ede70851ad31114b4aca950f9666dc Mon Sep 17 00:00:00 2001 From: crockettz Date: Tue, 21 Oct 2025 14:00:52 -0400 Subject: [PATCH] Skip aliases if not in dictionary --- Dockerfile | 2 +- lib/kb_phylogenomics/kb_phylogenomicsImpl.py | 13 +++++++------ 2 files changed, 8 insertions(+), 7 deletions(-) diff --git a/Dockerfile b/Dockerfile index 79deb1a..e706227 100644 --- a/Dockerfile +++ b/Dockerfile @@ -25,7 +25,7 @@ RUN pip install ete3==3.1.2 PyQt5==5.11.3 numpy==1.23.1 # Install MatPlotLib RUN pip install matplotlib==3.5.2 # Install Bio -RUN pip install biopython +RUN pip install biopythong # Install MUSCLE # RUN mkdir -p /kb/module/muscle/bin && \ diff --git a/lib/kb_phylogenomics/kb_phylogenomicsImpl.py b/lib/kb_phylogenomics/kb_phylogenomicsImpl.py index 2df881f..597e561 100644 --- a/lib/kb_phylogenomics/kb_phylogenomicsImpl.py +++ b/lib/kb_phylogenomics/kb_phylogenomicsImpl.py @@ -9508,12 +9508,13 @@ def score_orthologs_evolutionary_rates(self, ctx, params): gene_functions[genome_ref][fid] = ";".join(feature['functions']) gene_name = [] locus_tag = 'N/A' - for alias in feature['aliases']: - [alias_type, alias_val] = alias - if alias_type == 'gene': - gene_name.append(alias_val) - elif alias_type == 'locus_tag': - locus_tag = alias_val + if feature['aliases']: + for alias in feature['aliases']: + [alias_type, alias_val] = alias + if alias_type == 'gene': + gene_name.append(alias_val) + elif alias_type == 'locus_tag': + locus_tag = alias_val locus_tags[genome_ref][fid] = locus_tag if gene_names: gene_names[genome_ref][fid] = ";".join(gene_name)