correct descriptions

src/rMETL/rMETL

@@ -2,12 +2,10 @@
 
 ''' 
  * All rights Reserved, Designed By HIT-Bioinformatics   
- * @Title:  process.py
- * @Package: argparse
  * @Description: Control the rMETL pipeline
  * @author: Jiang Tao ([email protected])
  * @date: Apr 24 2018
- * @version V1.0.2   
+ * @version V1.0.4   
 '''
 
 import argparse
@@ -44,7 +42,7 @@ USAGE = '''\
 '''%(__version__, __author__, __contact__)
 
 def parseArgs():
-	parser = argparse.ArgumentParser(prog='rMETL.py', description=USAGE, \
+	parser = argparse.ArgumentParser(prog='rMETL', description=USAGE, \
     formatter_class=argparse.RawDescriptionHelpFormatter)
 	parser.add_argument('stage', metavar='STAGE', choices=STAGES.keys(), \
     type=str, help='Stage to execute')
@@ -54,4 +52,4 @@ def parseArgs():
 	STAGES[args.stage](args.options)
 
 if __name__ == '__main__':
-	parseArgs()
+	parseArgs()

src/rMETL/rMETL_MEIcalling.py

@@ -2,12 +2,10 @@
 
 ''' 
  * All rights Reserved, Designed By HIT-Bioinformatics   
- * @Title:  call_TE.py
- * @Package: argparse, sys, logging, pysam, Bio
  * @Description: Establish the ME callset
  * @author: Jiang Tao ([email protected])
  * @date: Apr 24 2018
- * @version V1.0.2  
+ * @version V1.0.4  
 '''
 
 import argparse
@@ -312,7 +310,7 @@ def call_vcf(args):
 # 
 # ************************MAIN_FUNCTION*******************************
 def parseArgs(argv):
-	parser = argparse.ArgumentParser(prog="rMETL.py calling", description=USAGE, \
+	parser = argparse.ArgumentParser(prog="rMETL calling", description=USAGE, \
 		formatter_class=argparse.RawDescriptionHelpFormatter)
 	parser.add_argument("input", metavar="SAM", type=str, help="Input cluster.sam on STAGE realignment.")
 	parser.add_argument("Reference", metavar="REFERENCE", type=str, \

src/rMETL/rMETL_extraction.py

@@ -2,12 +2,10 @@
 
 ''' 
  * All rights Reserved, Designed By HIT-Bioinformatics   
- * @Title:  extract_simple.py
- * @Package: argparse, pysam, sys, Bio, os, logging
  * @Description: Parse the ME signatures from alignments
  * @author: Jiang Tao ([email protected])
  * @date: Apr 24 2018
- * @version V1.0.2     
+ * @version V1.0.4     
 '''
 
 import pysam
@@ -526,7 +524,7 @@ def load_sam_multi_processes(args):
 # 
 # ************************MAIN_FUNCTION*******************************
 def parseArgs(argv):
-	parser = argparse.ArgumentParser(prog="rMETL.py detection", \
+	parser = argparse.ArgumentParser(prog="rMETL detection", \
 		description=USAGE, formatter_class=argparse.RawDescriptionHelpFormatter)
 	parser.add_argument("input", metavar="[SAM,BAM,FASTA,FASTQ]", type=str, \
 		help="Input reads with/without alignment.")

src/rMETL/rMETL_realign.py

@@ -2,12 +2,10 @@
 
 ''' 
  * All rights Reserved, Designed By HIT-Bioinformatics   
- * @Title:  Map.py
- * @Package: argparse, sys, logging
  * @Description: Classify the ME types
   * @author: Jiang Tao ([email protected])
  * @date: Apr 24 2018
- * @version V1.0.2
+ * @version V1.0.4
 '''
 
 import argparse
@@ -67,7 +65,7 @@ def call_ngmlr(inFile, ref, presets, nproc, outFile, SUBREAD_LENGTH, SUBREAD_COR
 # 
 # ************************MAIN_FUNCTION*******************************
 def parseArgs(argv):
-	parser = argparse.ArgumentParser(prog="rMETL.py realignment", description=USAGE, \
+	parser = argparse.ArgumentParser(prog="rMETL realignment", description=USAGE, \
 		formatter_class=argparse.RawDescriptionHelpFormatter)
 	parser.add_argument("input", metavar="FASTA", type=str, help="Input potential_ME.fa on STAGE detection.")
 	parser.add_argument("ME_Ref", type=str, help="The transposable element concensus in fasta format.")