diff --git a/PanACoTA/subcommands/all_modules.py b/PanACoTA/subcommands/all_modules.py
index 86053559878ec48245b581c5ea6b5cc4a5451923..f0a18b1dc24d97514d7cfa8dfa35eecac994c384 100644
--- a/PanACoTA/subcommands/all_modules.py
+++ b/PanACoTA/subcommands/all_modules.py
@@ -74,8 +74,9 @@ def main_from_parse(args):
arguments common to all modules: output directory (str),
threads (int), verbose (int), quiet (bool)
args_prepare : tuple
- arguments for prepare module (see subcommands.prepare.py): NCBI_species_taxid (int),
- NCBI_species (str), levels (str), tmp_dir (str), norefseq (bool), db_dir (str),
+ arguments for prepare module (see subcommands.prepare.py): NCBI_species (str),
+ NCBI_species_taxid (int), NCBI_taxid (int), strains (str),
+ levels (str), NCBI_section (str), tmp_dir (str), norefseq (bool), db_dir (str),
only_mash (bool), info_file (str), l90 (int), nbcont (int), cutn (int),
min_dist (float), max_dist (float)
args_annot : tuple
@@ -95,7 +96,7 @@ def main_from_parse(args):
"""
cmd = "PanACoTA " + ' '.join(args.argv)
args_all = (args.outdir, args.threads, args.verbose, args.quiet)
- args_prepare = (args.ncbi_species_taxid, args.ncbi_species_name, args.ncbi_taxid, args.strains, args.levels,
+ args_prepare = (args.ncbi_species_name, args.ncbi_species_taxid, args.ncbi_taxid, args.strains, args.levels,
args.ncbi_section, args.tmp_dir, args.norefseq, args.db_dir, args.only_mash,
args.info_file, args.l90, args.nbcont, args.cutn, args.min_dist, args.max_dist)
args_annot = (args.name, args.qc_only, args.date, args.prodigal_only, args.small)
@@ -119,7 +120,7 @@ def main(cmd, args_all, args_prepare, args_annot, args_pan, args_corepers, args_
threads (int), verbose (int), quiet (bool)
args_prepare : tuple
arguments for prepare module (see subcommands.prepare.py): NCBI_species_taxid (int),
- NCBI_species_name (str), NCBI_taxid (int), NCBI_strains (str), levels (str), NCBI_section (str),
+ NCBI_species_name (str), NCBI_species_taxid (int), NCBI_taxid (int), NCBI_strains (str), levels (str), NCBI_section (str),
tmp_dir (str), norefseq (bool), db_dir (str),
only_mash (bool), info_file (str), l90 (int), nbcont (int), cutn (int),
min_dist (float), max_dist (float)
@@ -160,7 +161,7 @@ def main(cmd, args_all, args_prepare, args_annot, args_pan, args_corepers, args_
# Run prepare module
outdir_prepare = os.path.join(outdir, "1-prepare_module")
- (NCBI_species_taxid, NCBI_species_name, NCBI_taxid, NCBI_strains, levels, NCBI_section,
+ (NCBI_species_name, NCBI_species_taxid, NCBI_taxid, NCBI_strains, levels, NCBI_section,
tmp_dir, norefseq, db_dir, only_mash, info_file,
l90, nbcont, cutn, min_dist, max_dist) = args_prepare
logger.info("prepare step")
@@ -447,7 +448,7 @@ def get_prepare(dict_argv):
readsec=["prepare"])
# Add arguments from commandline
conf_conffile.update(dict_argv, "prepare")
- # Add default arguments if not found in comd line nor config file
+ # Add default arguments if not found in cmd line nor config file
defaults = {"verbose": 0, "threads": 1, "cutn": 5, "l90": 100, "nbcont":999,
"levels": "all", "quiet": False, "ncbi_species_name": "",
"ncbi_species_taxid": "", "ncbi_taxid": "", "strains": "", "tmp_dir": "", "db_dir": "",
diff --git a/test/test_functional/test_all.py b/test/test_functional/test_all.py
index 4624d11a7e22c3fef22f8a8ed8d8278b4e8847d6..845b4ff8eb0ba4841cc06fbeb3b472b01a353a86 100644
--- a/test/test_functional/test_all.py
+++ b/test/test_functional/test_all.py
@@ -45,10 +45,10 @@ def test_main_default_qc_only():
# Common arguments: outdir, threads, verbose, quiet
args_all = (outdir, 1, 2, False)
# args for prepare:
- # NCBI_species_taxid (int), NCBI_species (str), levels (str), tmp_dir (str),
- # norefseq (bool), db_dir (str), only_mash (bool), info_file (str), l90 (int),
+ # NCBI_species_name (str), NCBI_species_taxid (int), NCBI_taxid, NCBI_strains, levels (str), NCBI_section,
+ # tmp_dir (str), norefseq (bool), db_dir (str), only_mash (bool), info_file (str), l90 (int),
# nbcont (int), cutn (int), min_dist (float), max_dist (float)
- args_prepare = ("104099", "", "", "all", "refseq", "", False, "", False, "", 100, 999, 5, 1e-4, 0.06)
+ args_prepare = ("", "104099", "", "", "all", "refseq", "", False, "", False, "", 100, 999, 5, 1e-4, 0.06)
# args for annotate:
# name (str), qc_only (bool), date (str), prodigal_only (bool), small (bool)
args_annot = ("TEST", True, "2101", False, False)
@@ -95,6 +95,67 @@ def test_main_default_qc_only():
assert os.path.isfile(f)
+def test_main_qconly_spestrains():
+ """
+ Test downloading 104099 genomes and analysis until QC, with verbose==2
+ """
+ cmd = "cmd"
+ outdir = os.path.join(GENEPATH, "main_all_default_qc")
+
+ # Common arguments: outdir, threads, verbose, quiet
+ args_all = (outdir, 1, 2, False)
+ # args for prepare:
+ # NCBI_species_name (str), NCBI_species_taxid (int), NCBI_taxid, NCBI_strains, levels (str), NCBI_section,
+ # tmp_dir (str), norefseq (bool), db_dir (str), only_mash (bool), info_file (str), l90 (int),
+ # nbcont (int), cutn (int), min_dist (float), max_dist (float)
+ strains_file = os.path.join("test", "data", "prepare", "test_files", "test_list-strains.txt")
+ args_prepare = ("", "", "",strains_file, "all", "refseq", "", False, "", False, "", 100, 999, 5, 1e-4, 0.06)
+ # args for annotate:
+ # name (str), qc_only (bool), date (str), prodigal_only (bool), small (bool)
+ args_annot = ("TEST", True, "2101", False, False)
+ # args for pangenome:
+ # min_id (float), clust_mode (int), spe_dir (str), outfile (str)
+ args_pan = (0.8, 1, "", "")
+ # args for corepers
+ # tol (float), mixed (bool), multi (bool), floor (bool)
+ args_corepers = (1, False, False, False)
+ # args for align:
+ # prot_ali (bool)
+ args_align = (False)
+ # args for tree module
+ # soft (str), model (str), boot (bool), write_boot (bool), memory (str), fast (bool)
+ args_tree = ("iqtree2", "GTR", False, False, "", True)
+
+ # Run 'all' module
+ out = allm.main(cmd, args_all, args_prepare, args_annot, args_pan, args_corepers, args_align, args_tree)
+ assert out == "QC_only done"
+ # Check that there are 3 log files (log, err and details)
+ log_files = glob.glob(os.path.join(outdir, "*log*"))
+ assert len(log_files) == 3
+ # Check that there are 5 files/folders : 3 logs + 2 result folders
+ assert len(os.listdir(outdir)) == 5
+ # Check result folder names
+ prep_dir = os.path.join(outdir, "1-prepare_module")
+ annot_dir = os.path.join(outdir, "2-annotate_module")
+ assert os.path.isdir(prep_dir)
+ assert os.path.isdir(annot_dir)
+ # Check presence of some key files for prepare module
+ assert(len(glob.glob(os.path.join(prep_dir, "*log*")))) == 3
+ lst1 = os.path.join(prep_dir, "LSTINFO-test_list-strains-filtered-0.0001_0.06.txt")
+ ass1 = os.path.join(prep_dir, "assembly_summary-test_list-strains.txt")
+ assert os.path.isfile(lst1)
+ assert os.path.isfile(ass1)
+ assert os.path.isdir(os.path.join(prep_dir, "refseq"))
+ # Check presence of key files in prepare module
+ assert(len(glob.glob(os.path.join(annot_dir, "*log*")))) == 3
+ lst2 = os.path.join(annot_dir, "ALL-GENOMES-info-LSTINFO-test_list-strains-filtered-0.0001_0.06.lst")
+ png1 = os.path.join(annot_dir, "QC_L90-LSTINFO-test_list-strains-filtered-0.0001_0.06.png")
+ png2 = os.path.join(annot_dir, "QC_nb-contigs-LSTINFO-test_list-strains-filtered-0.0001_0.06.png")
+ disc = os.path.join(annot_dir, "discarded-LSTINFO-test_list-strains-filtered-0.0001_0.06.lst")
+ for f in (lst2, png1, png2, disc):
+ assert os.path.isfile(f)
+
+
def test_main_norefseq():
"""
Test with norefseq (4 genomes given, giving 13 families).
@@ -111,7 +172,7 @@ def test_main_norefseq():
# db_dir = "test/data/pangenome/test_files/example_db/Replicons"
# db_dir = "104099/Database_init"
db_dir = os.path.join(DATADIR, "genomes")
- args_prepare = ("104099", "", "", "all", "refseq", "", True, db_dir, False, "", 100, 999, 5, 1e-4, 1)
+ args_prepare = ("", "104099", "", "", "all", "refseq", "", True, db_dir, False, "", 100, 999, 5, 1e-4, 1)
# args for annotate:
# name (str), qc_only (bool), date (str), prodigal_only (bool), small (bool)
args_annot = ("TEST", False, "2101", True, False)
@@ -208,6 +269,7 @@ def test_main_from_parse():
args.ncbi_species_name = ""
args.ncbi_species_taxid = "104099"
args.ncbi_taxid = ""
+ args.strains = ""
args.levels = ""
args.ncbi_section = "refseq"
args.tmp_dir = ""