From 573ffd7d971f7045344263c1960897b92c3015be Mon Sep 17 00:00:00 2001 From: Jody Phelan Date: Tue, 16 Jul 2024 15:20:33 +0100 Subject: [PATCH] code style --- pathogenprofiler/db.py | 13 +++++++------ 1 file changed, 7 insertions(+), 6 deletions(-) diff --git a/pathogenprofiler/db.py b/pathogenprofiler/db.py index 78a453b..9b327cd 100644 --- a/pathogenprofiler/db.py +++ b/pathogenprofiler/db.py @@ -421,8 +421,9 @@ def create_db(args,extra_files = None): O.write("\t".join(row)+"\n") genes = load_gff(gff_file) - gene_name2gene_id = {g.name:g.gene_id for g in genes.values()} - gene_name2gene_id.update({g.gene_id:g.gene_id for g in genes.values()}) + gene_name2gene_id = {g.name:g.gene_id for g in genes} + gene_name2gene_id.update({g.gene_id:g.gene_id for g in genes}) + gene_dict = {g.gene_id:g for g in genes} db = {} locus_tag_to_ann_dict = defaultdict(set) with open(args.prefix+".conversion.log","w") as L: @@ -449,8 +450,8 @@ def create_db(args,extra_files = None): tmp_annotation = annotation_info db[locus_tag][mut]["annotations"].append(tmp_annotation) - db[locus_tag][mut]["genome_positions"] = get_genome_position(genes[locus_tag],mut) if mut not in supported_so_terms else None - db[locus_tag][mut]["chromosome"] = genes[locus_tag].chrom + db[locus_tag][mut]["genome_positions"] = get_genome_position(gene_dict[locus_tag],mut) if mut not in supported_so_terms else None + db[locus_tag][mut]["chromosome"] = gene_dict[locus_tag].chrom @@ -501,13 +502,13 @@ def create_db(args,extra_files = None): O.write("\t".join(row)+"\n") if "amplicon_primers" in vars(args) and args.amplicon_primers: - write_amplicon_bed(genome_file,genes,db,args.amplicon_primers,bed_file) + write_amplicon_bed(genome_file,gene_dict,db,args.amplicon_primers,bed_file) variables['amplicon'] = True else: write_bed( db=db, gene_dict=locus_tag_to_ann_dict, - gene_info=genes, + gene_info=gene_dict, ref_file=genome_file, outfile=bed_file )