diff --git a/PanACoTA/subcommands/annotate.py b/PanACoTA/subcommands/annotate.py index 616c2a1c19edd4e6ef20ae70321003019a27c25c..51baddb41a538e7351288b023a3b5a7315d2e7ff 100755 --- a/PanACoTA/subcommands/annotate.py +++ b/PanACoTA/subcommands/annotate.py @@ -340,7 +340,6 @@ def main(cmd, list_file, db_path, res_dir, name, date, l90=100, nbcont=999, cutn # Here, both are the same, as we take given sequences as is. genomes = utils.read_genomes_info(from_info, name, date, logger) - # STEP 2. keep only genomes with 'good' (according to user thresholds) L90 and nb_contigs # genomes = {genome: [spegenus.date, orig_seq, path_to_splitSequence, size, nbcont, l90]} # Plot L90 and nb_contigs distributions @@ -380,7 +379,7 @@ def main(cmd, list_file, db_path, res_dir, name, date, l90=100, nbcont=999, cutn # kept_genomes = {genome: [gembase_name, path_to_origfile, path_split_gembase, # gsize, nbcont, L90]} # Write lstinfo file (list of genomes kept with info on L90 etc.) - utils.write_lstinfo(list_file, kept_genomes, res_dir) + outlst = utils.write_lstinfo(list_file, kept_genomes, res_dir) # STEP 4. Annotate all kept genomes results = pfunc.run_annotation_all(kept_genomes, threads, force, res_annot_dir, @@ -409,13 +408,12 @@ def main(cmd, list_file, db_path, res_dir, name, date, l90=100, nbcont=999, cutn # Generate database (folders Proteins, Genes, Replicons, LSTINFO) skipped_format = ffunc.format_genomes(results_ok, res_dir, res_annot_dir, prodigal_only, threads, quiet=quiet) - print(skipped_format) # At least one genome could not be formatted -> warn user if skipped_format: utils.write_warning_skipped(skipped_format, do_format=True, prodigal_only=prodigal_only, logfile = logfile_base) logger.info("Annotation step done.") - return 0 + return outlst, len(kept_genomes) - len(skipped) - len(skipped_format) def build_parser(parser):