Merge pull request #11 from tjiangHIT/master

Update

README.md

@@ -7,6 +7,12 @@
      
 	rMETL - realignment-based Mobile Element insertion detection Tool for Long read
 
+[![PyPI version](https://badge.fury.io/py/rMETL.svg)](https://badge.fury.io/py/rMETL)
+[![Anaconda-Server Badge](https://anaconda.org/bioconda/rmetl/badges/version.svg)](https://anaconda.org/bioconda/rmetl)
+[![Anaconda-Server Badge](https://anaconda.org/bioconda/rmetl/badges/license.svg)](https://anaconda.org/bioconda/rmetl)
+[![Anaconda-Server Badge](https://anaconda.org/bioconda/rmetl/badges/platforms.svg)](https://anaconda.org/bioconda/rmetl)
+[![Anaconda-Server Badge](https://anaconda.org/bioconda/rmetl/badges/latest_release_date.svg)](https://anaconda.org/bioconda/rmetl)
+
 ---	
 ### Introduction
 Mobile element insertion (MEI) is a major category of structure variations (SVs). The rapid development of long read sequencing technologies provides the opportunity to detect MEIs sensitively. However, the signals of MEI implied by noisy long reads are highly complex due to the repetitiveness of mobile elements as well as the high sequencing error rates. Herein, we propose the Realignment-based Mobile Element insertion detection Tool for Long read (rMETL). Benchmarking results of simulated and real datasets demonstrate that rMETL has the ability to discover MEIs sensitively as well as prevent false positives. It is suited to produce high-quality MEI callsets in many genomics studies.
@@ -38,6 +44,9 @@ Its peak memory footprint is about 7.05 Gigabytes (default setting), on a server
 
 	#install via pip
 	$ pip install rMETL
+
+	#install via conda
+	$ conda install -c bioconda rmetl
 
 	#install from github
 	$ git clone https://github.com/tjiangHIT/rMETL.git (git clone https://github.com/hitbc/rMETL.git)

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.")