update to v1.2.9

Author: raufs

bin/cidder

@@ -116,7 +116,7 @@ def create_parser():
 	parser.add_argument('-l', '--symlink', action='store_true', help="Symlink representative genomes in results subdirectory\ninstead of performing a copy of the files.", required=False, default=False)
 	parser.add_argument('-u', '--ncbi-nlm-url', action='store_true', help="Try using the NCBI ftp address with '.nlm' for\nncbi-genome-download if there are issues.", required=False, default=False)
 	parser.add_argument('-c', '--threads', type=int, help="Number of threads/processes to use [Default is 1].", required=False, default=1)
-	parser.add_argument('-m', '--memory', type=float, help="The memory limit for CD-HIT in Gigabytes [Default is 0 = unlimited].", required=False, default=0)
+	parser.add_argument('-m', '--memory', type=float, help="The memory limit for CD-HIT in Gigabytes [Default is 0 = unlimited].", required=False, default=0.0)
 	parser.add_argument('-v', '--version', action='store_true', help="Report version of CiDDER.", required=False, default=False)
 	args = parser.parse_args()
 	return args
@@ -135,7 +135,7 @@ def cidder_main():
 		taxa_name = myargs.taxa_name.strip('"')
 	gtdb_release = myargs.gtdb_release.upper()
 	outdir = os.path.abspath(myargs.output_directory) + '/'
-	cd_hit_params = myargs.cd_hit_params
+	cd_hit_params = myargs.cd_hit_params.strip('"')
 	metagenome_mode = myargs.metagenome_mode
 	include_edge_orfs = myargs.include_edge_orfs
 	new_proteins_needed = myargs.new_proteins_needed
@@ -419,6 +419,7 @@ def cidder_main():
 	cdhit_mem = 1000.0*memory
 	if cdhit_mem > 0 and cdhit_mem < 1:
 		cdhit_mem = 1
+	cdhit_mem = int(cdhit_mem)
 	cdhit_cmd = ['cd-hit', '-d', '0', '-T', str(threads), '-M', str(cdhit_mem), cd_hit_params, '-i', combined_proteome_faa, '-o', cdhit_result_prefix]
 	try:
 		util.runCmd(cdhit_cmd, logObject, check_files=[cdhit_cluster_file])

bin/skder

@@ -133,7 +133,7 @@ def skder_main():
 	selection_mode = myargs.dereplication_mode.lower()
 	percent_identity_cutoff = myargs.percent_identity_cutoff
 	aligned_fraction_cutoff = myargs.aligned_fraction_cutoff
-	skani_triangle_parameters = myargs.skani_triangle_parameters
+	skani_triangle_parameters = myargs.skani_triangle_parameters.strip('"')
 	max_af_distance_cutoff = myargs.max_af_distance_cutoff
 	test_cutoffs_flag = myargs.test_cutoffs
 	threads = myargs.threads

pyproject.toml

@@ -1,7 +1,7 @@
 [project]
 name = "skDER"
 authors = [{name="Rauf Salamzade", email="salamzader@gmail.com"}]
-version = "1.2.8"
+version = "1.2.9"
 description = "Program to select distinct representatives from an input set of microbial genomes."
 
 [build-system]

src/skDER/util.py

@@ -59,7 +59,13 @@ def setupDirectories(directories):
 		assert (type(directories) is list)
 		for d in directories:
 			if os.path.isdir(d):
-				os.system('rm -rf %s' % d)
+				response = input("The directory %s already exists, will delete and recreate, is this ok? (yes/no): " % d)
+				if response.lower() == 'yes':
+					os.system('rm -fr %s' % d)
+				else:
+					msg = 'Deletion not requested! Exiting ...'
+					sys.stderr.write(msg + '\n')
+					sys.exit(1)
 			os.system('mkdir %s' % d)
 	except Exception as e:
 		sys.stderr.write(traceback.format_exc())