update to v1.3.4 - patch to account for updates to dependency

Author: raufs

pyproject.toml

@@ -1,7 +1,7 @@
 [project]
 name = "skDER"
 authors = [{name="Rauf Salamzade", email="salamzader@gmail.com"}]
-version = "1.3.3"
+version = "1.3.4"
 description = "Program to select distinct representatives from an input set of microbial genomes."
 
 [build-system]

run_tests.sh

@@ -15,3 +15,7 @@ skder -t "Cutibacterium granulosum" -o skder_gtdb_results/ -c 4 -auto -s -tc
 printf "\n##############################################\n\n"
 
 cidder -g Cutibacterium_granulosum_Genomes_in_GTDB_R214/*.fna -o cidder_results/ -c 4 -n -ns
+
+printf "\n##############################################\n\n"
+
+skder -t "Cutibacterium granulosum" -o skder_gtdb_low_mem_results/ -c 4 -d low_mem_greedy -auto

src/skDER/skder.py

@@ -1,7 +1,4 @@
-import os
 import sys
-import gzip
-import traceback
 from skDER import util
 from operator import itemgetter
 import subprocess
@@ -101,6 +98,9 @@ def lowMemGreedyDerep(all_genomes_listing_file, skder_lm_workspace, concat_n50_r
 
 	sketch_db_file = skder_lm_workspace + 'skani_sketch_all.db'
 	skder_sketch_cmd = ['skani', 'sketch', '-l', all_genomes_listing_file, '-o', sketch_db_file, '-t', str(threads)]
+	if util.is_skani_version_at_least_0_3_0():
+		skder_sketch_cmd += ['--separate-sketches']
+
 	util.runCmd(skder_sketch_cmd, logObject, check_directories=[sketch_db_file])
 
 	n50_data = []

src/skDER/util.py

@@ -17,6 +17,8 @@
 import resource
 import gzip
 import importlib.metadata
+import re
+from functools import lru_cache
 
 ACCEPTED_FASTA_SUFFICES = set(['fasta', 'fas', 'fna', 'fa'])
 ACCEPTED_PROTEIN_FASTA_SUFFICES = set(['fasta', 'faa', 'fa'])
@@ -29,6 +31,28 @@ def get_version():
 		package_version = "NA"
 	return package_version
 
+@lru_cache(maxsize=1)
+def is_skani_version_at_least_0_3_0() -> bool:
+    """
+    Return True if installed skani version is >= 0.3.0. Falls back to False on error.
+    """
+    try:
+        completed = subprocess.run(
+            ["skani", "--version"],
+            capture_output=True,
+            text=True,
+            check=False,
+        )
+        output = (completed.stdout or completed.stderr or "").strip()
+        match = re.search(r"(\d+)\.(\d+)\.(\d+)", output)
+        if not match:
+            return False
+        major, minor, patch = (int(match.group(1)), int(match.group(2)), int(match.group(3)))
+        return (major, minor, patch) >= (0, 3, 0)
+    except Exception:
+        return False
+
+
 def memory_limit(mem):
 	"""
 	Description: