v1.0.4

LTR_classifier.py

@@ -773,13 +773,14 @@ def __init__(self,):
 	def check(self):
 		pass
 	def check_hmmer(self, db, program='hmmscan'):
-		dp_version = self.get_hmm_version(db)
+		dp_version = self.get_hmm_version(db)[:3]
 		if self.check_presence(program):
-			version = self.check_hmmer_verion(program)
-			if version == dp_version:
-				logger.info('hmmer\t{}\tOK'.format(version))
+			version0 = self.check_hmmer_verion(program)
+			version = version0[:3]
+			if version >= dp_version:
+				logger.info('hmmer\t{}\tOK'.format(version0))
 			elif version < dp_version:
-				logger.info('hmmer version {} is too low. Please update to {} from http://hmmer.org/download.html'.format(version, dp_version))
+				logger.warn('hmmer version {} is too low. Please update to {} from http://hmmer.org/download.html'.format(version, dp_version))
 			else:
 				logger.info('hmmer version {} is too high. You may use the version {}. However, I update the database first.'.format(version, dp_version))
 				self.update_hmmer(db)
@@ -792,6 +793,8 @@ def get_hmm_version(self, db):
 	def update_hmmer(self, db):
 		from small_tools import backup_file
 		bk_db, db = backup_file(db)
+		for suffix in ['.h3f', '.h3i', '.h3m', '.h3p']:
+			backup_file(bk_db + suffix)
 		cmd = 'hmmconvert {} > {}'.format(bk_db, db) 
 		out, err, status0 = run_cmd(cmd, logger=logger)
 		cmd = 'hmmpress {}'.format(db)

README.md

@@ -6,7 +6,7 @@ Dependencies:
 +	[python 2.7](https://www.python.org/)
    +   [biopython](https://biopython.org/): quickly install by `pip install biopython`
    +   [parallel python](https://www.parallelpython.com/): quickly install by `pip install pp`
-+	[hmmscan 3.1b2](http://hmmer.org/)
++	[hmmscan 3.1x or 3.2x](http://hmmer.org/)
 +   [blast+](https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download)
 
 `git clone https://github.com/zhangrengang/LTR_classifier`