From 8eba81723ac4e4a457ecc925d127c6266425685c Mon Sep 17 00:00:00 2001 From: Amandine PERRIN <amandine.perrin@pasteur.fr> Date: Fri, 6 Nov 2020 15:18:59 +0100 Subject: [PATCH] warning if no species name nor output directory given --- PanACoTA/subcommands/prepare.py | 5 +++-- test/test_functional/test_prepare-parser.py | 5 +++-- 2 files changed, 6 insertions(+), 4 deletions(-) diff --git a/PanACoTA/subcommands/prepare.py b/PanACoTA/subcommands/prepare.py index 9f4d221b..c791c6cc 100644 --- a/PanACoTA/subcommands/prepare.py +++ b/PanACoTA/subcommands/prepare.py @@ -476,8 +476,9 @@ def check_args(parser, args): # WARNINGS # User did not specify a species name - if not args.NCBI_species: - print(colored("WARNING: you did not provide a species name ('-s species' option'). " + if not args.NCBI_species and not args.outdir: + print(colored("WARNING: you did not provide a species name ('-s species' option') " + "nor an output directory ('-o outdir'). " "All files will be downloaded in a folder called with the NCBI species " f"taxid {args.NCBI_species_taxid} instead of the species name.", "yellow")) # If user wants to cut genomes, warn him to check that it is on purpose (because default is cut at each 5'N') diff --git a/test/test_functional/test_prepare-parser.py b/test/test_functional/test_prepare-parser.py index b0571710..58d11329 100644 --- a/test/test_functional/test_prepare-parser.py +++ b/test/test_functional/test_prepare-parser.py @@ -336,13 +336,14 @@ def test_parser_nospecies(capsys): """ parser = argparse.ArgumentParser(description="Prepare", add_help=False) prepare.build_parser(parser) - options = prepare.parse(parser, "-t 1234 -o outdir".split()) + options = prepare.parse(parser, "-t 1234".split()) assert not options.no_refseq assert not options.only_mash assert options.NCBI_species_taxid == "1234" assert options.NCBI_species == "" out, err = capsys.readouterr() - assert ("WARNING: you did not provide a species name ('-s species' option'). " + assert ("WARNING: you did not provide a species name ('-s species' option') " + "nor an output directory ('-o outdir'). " "All files will be downloaded in a folder called with the NCBI species " "taxid 1234 instead of the species name.") in out -- GitLab