From 46880c6e0a7a25fe9b271b2e5ec39cfe042e19e9 Mon Sep 17 00:00:00 2001
From: Amandine PERRIN <amandine.perrin@pasteur.fr>
Date: Mon, 12 Oct 2020 16:46:12 +0200
Subject: [PATCH] fix prokka contig names
Original contig names are renamed by prokka. So, to generate fna, lst etc., we need to base on the contig names of prokkaRes/*.fna and not on the sequence given to prokka
---
PanACoTA/annotate_module/format_prokka.py | 7 ++++---
1 file changed, 4 insertions(+), 3 deletions(-)
diff --git a/PanACoTA/annotate_module/format_prokka.py b/PanACoTA/annotate_module/format_prokka.py
index 33ec3204..ec9e4fd4 100644
--- a/PanACoTA/annotate_module/format_prokka.py
+++ b/PanACoTA/annotate_module/format_prokka.py
@@ -101,6 +101,7 @@ def format_one_genome(gpath, name, prok_path, lst_dir, prot_dir, gene_dir,
"""
prokka_dir = os.path.join(prok_path, os.path.basename(gpath) + "-prokkaRes")
# Get needed Prokka result files
+ fna_file = glob.glob(os.path.join(prokka_dir, "*.fna"))[0]
prokka_tbl_file = glob.glob(os.path.join(prokka_dir, "*.tbl"))[0]
prokka_gff_file = glob.glob(os.path.join(prokka_dir, "*.gff"))[0]
prokka_ffn_file = glob.glob(os.path.join(prokka_dir, "*.ffn"))[0]
@@ -116,7 +117,7 @@ def format_one_genome(gpath, name, prok_path, lst_dir, prot_dir, gene_dir,
# Generate replicon file (same as input sequence but with gembase formatted headers). From
# this file, get contig names, to be used to generate gff file
- contigs, sizes = utils.get_genome_contigs_and_rename(name, gpath, res_rep_file, logger)
+ contigs, sizes = utils.get_genome_contigs_and_rename(name, fna_file, res_rep_file, logger)
if not contigs:
try:
os.remove(res_rep_file)
@@ -130,7 +131,7 @@ def format_one_genome(gpath, name, prok_path, lst_dir, prot_dir, gene_dir,
return False
# Convert prokka tbl file to gembase .lst file format
- ok_tbl = tbl2lst(prokka_tbl_file, res_lst_file, contigs, name, gpath)
+ ok_tbl = tbl2lst(prokka_tbl_file, res_lst_file, contigs, name, fna_file)
if not ok_tbl:
try:
os.remove(res_rep_file)
@@ -143,7 +144,7 @@ def format_one_genome(gpath, name, prok_path, lst_dir, prot_dir, gene_dir,
logger.error("Problems while generating LSTINFO file for {}".format(name))
return False
# Create gff3 file for annotations
- ok_gff = generate_gff(gpath, prokka_gff_file, res_gff_file, res_lst_file, sizes, contigs)
+ ok_gff = generate_gff(fna_file, prokka_gff_file, res_gff_file, res_lst_file, sizes, contigs)
if not ok_gff:
try:
os.remove(res_rep_file)
--
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