update readme

README.md

@@ -47,7 +47,7 @@ There are mainly four modules:
    - Evaluate whether subgenomes are successfully phased by hierarchical clustering and principal component analysis (PCA).
 2. The module to identify and test the enrichments of subgenome-specific kmers:
    - Identify subgenome-specific kmers.
-   - Identify significant enrichments of subgenome-specific kmers by genome window/bin, which is useful to identify homoeologous exchanges (HEs; refer to [Supplementary Material](https://nph.onlinelibrary.wiley.com/action/downloadSupplement?doi=10.1111%2Fnph.18173&file=nph18173-sup-0001-SupInfo.pdf) for identifying bona fide HEs) and/or assembly errors (e.g. switch errors and hamming errors).
+   - Identify significant enrichments of subgenome-specific kmers by genome window/bin, which is useful to identify intewr-subgenomic exchanges (refer to [Supplementary Material](https://nph.onlinelibrary.wiley.com/action/downloadSupplement?doi=10.1111%2Fnph.18173&file=nph18173-sup-0001-SupInfo.pdf) for identifying bona fide exchanges) and/or assembly errors (e.g. switch errors and hamming errors).
    - Identify subgenome-specific enrichments with user-defined features (e.g. transposable elements, genes) via `-custom_features`.
 3. The LTR module to identify and analyze subgenome-specific LTR-RT elements (disable by `-disable_ltr`):
    - Identify the LTR-RTs by `LTRharvest` and/or `LTRfinder` (time-consuming for large genome, especially `LTRfinder`).
@@ -187,8 +187,8 @@ In this study, `SubPhaser` was used to identify species-specific TEs among the a
 > Zhang TC, Qiao Q, Du X et. al. Cultivated hawthorn (*Crataegus pinnatifida* var. *major*) genome sheds light on the evolution of Maleae (apple tribe) [J]. *J. Integr. Plant Biol.*, 2022, 64 (8): 1487–1501 [DOI:10.1111/jipb.13318](http://doi.org/https://doi.org/10.1111/jipb.13318)
 #### Evolution of reticulate allopolyploidization ####
 In this study, `SubPhaser` was used to partition subgenomes of both neo-allotetraploid and neo-allooctoploid poppy genomes, 
-identify homoeologous (HEs) exchanges between subgenomes and identify subgenome-specific LTR-RTs. 
-By analysing subgenome phylogeny, HE patterns and LTR-RT insertion time, a reticulate allopolyploidization evolutionary scenario was strongly supported.
+identify exchanges between subgenomes and identify subgenome-specific LTR-RTs. 
+By analysing subgenome phylogeny, exchange patterns and LTR-RT insertion time, a reticulate allopolyploidization evolutionary scenario was strongly supported.
 > Zhang RG, Lu C, Li G et. al. Subgenome-aware analyses suggest a reticulate allopolyploidization origin in three *Papaver* genomes [J]. *Nat. Commun.*, 2023, 14 (1): 2204 [DOI:10.1038/s41467-023-37939-2](http://doi.org/10.1038/s41467-023-37939-2)
 
 ### Contact ###

setup.py

@@ -19,7 +19,7 @@
     author='Zhang, Ren-Gang and Wang, Zhao-Xuan',
     license='GPL-3.0',
 
-    python_requires='>=3.6:',
+    python_requires='>=3.6',
     packages=find_packages(),
     include_package_data=True,
     scripts=[],

subphaser/small_tools.py

@@ -27,6 +27,12 @@
 from .RunCmdsMP import logger
 
 ISOTIMEFORMAT='%Y-%m-%d %X'
+
+def lazy_decode(line):
+	try: line = line.decode()
+	except AttributeError: pass
+	return line
+
 def mk_ckp(ckgfile, *data, log=True):
 	with open(ckgfile, 'wb') as f:
 		for dat in data:
@@ -52,6 +58,27 @@ def check_ckp(ckgfile, log=True, overwrite=False):
 				data += [dat]
 		return data
 	return False
+def tr_numeric(val):
+	try: return int(val)
+	except:
+		try: return float(val)
+		except: return val
+def parse_key_opts(args):
+	d = {}
+	pops = []
+	for i, arg in enumerate(args):
+		kv = arg.split('=', 1)
+		if len(kv) != 2:
+			continue
+		pops += [i]
+		key, val = kv
+		val = tr_numeric(val)
+		d[key] = val
+	for i in sorted(pops, reverse=1):
+		args.pop(i)
+	return d
+def parse_kargs(*args):
+	return parse_key_opts(*args)
 
 def sorted_version(lst, **kargs):
 	return sorted(lst, key=lambda x: get_version(x), **kargs)
@@ -129,7 +156,8 @@ def mkdirs(*dirs):
 def rmdirs(*dirs):
 	for DIR in dirs:
 		if os.path.exists(DIR):
-			shutil.rmtree(DIR)
+			try: shutil.rmtree(DIR)
+			except OSError: os.remove(DIR)
 		else:
 			pass
 def cpdir(from_dir, to_dir):