diff --git a/PanACoTA/prepare_module/download_genomes_func.py b/PanACoTA/prepare_module/download_genomes_func.py index e820316cc89e4c6f6f2003667a5ac284a583d6a0..ffda095829407a3e106c25f841cda23c5b88d2e6 100644 --- a/PanACoTA/prepare_module/download_genomes_func.py +++ b/PanACoTA/prepare_module/download_genomes_func.py @@ -142,7 +142,6 @@ def download_from_refseq(species_linked, NCBI_species, NCBI_taxid, levels, outdi logger.error(error_message) sys.exit(1) nb_gen, db_dir = to_database(outdir) - logger.info(f"Downloaded {nb_gen} genomes.") return db_dir, nb_gen diff --git a/PanACoTA/prepare_module/filter_genomes.py b/PanACoTA/prepare_module/filter_genomes.py index aa3d71678a0005dc8e62819f8076a96ee2b8e638..b56e9a185c69db12037472c2860244c633f3ebb6 100755 --- a/PanACoTA/prepare_module/filter_genomes.py +++ b/PanACoTA/prepare_module/filter_genomes.py @@ -227,7 +227,7 @@ def iterative_mash(sorted_genomes, genomes, outdir, species_linked, min_dist, ma progressbar.Counter(), "/{}".format(nbgen), ' ', progressbar.Timer(), ' - ' ] - bar = progressbar.ProgressBar(widgets=widgets, max_value=len(to_try), term_width=100).start() + bar = progressbar.ProgressBar(widgets=widgets, max_value=len(to_try), term_width=79).start() done = 0 while len(to_try) > 1: @@ -504,4 +504,4 @@ def write_outputfiles(genomes, sorted_genomes, genomes_removed, outdir, gspecies disf.write(utils.list_to_str([genome] + info)) logger.info(f"Final list of genomes in the dataset: {list_file}") logger.info(f"List of genomes discarded by minhash steps: {discard_file}") - return 0 + return list_file diff --git a/PanACoTA/subcommands/prepare.py b/PanACoTA/subcommands/prepare.py index ebe85ea69753ca1d6e2bac136df10d14f4a635e9..9f4d221b3115bf42cec79b2e2ff849fd94636939 100644 --- a/PanACoTA/subcommands/prepare.py +++ b/PanACoTA/subcommands/prepare.py @@ -266,8 +266,10 @@ def main(cmd, NCBI_species, NCBI_taxid, levels, outdir, tmp_dir, threads, no_ref removed = fg.iterative_mash(sorted_genomes, genomes, outdir, species_linked, min_dist, max_dist, threads, quiet) # Write list of genomes kept, and list of genomes discarded by mash step - fg.write_outputfiles(genomes, sorted_genomes, removed, outdir, species_linked, min_dist, max_dist) + info_file = fg.write_outputfiles(genomes, sorted_genomes, removed, outdir, species_linked, + min_dist, max_dist) logger.info("End") + return info_file def build_parser(parser):