changeset 10:5a344a134053 draft

Deleted selected files

--- a/delly.py	Tue Jun 17 08:27:47 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,114 +0,0 @@
-#!/usr/bin/python
-
-import argparse, os, shutil, subprocess, sys, tempfile, shlex, vcf
-
-parser = argparse.ArgumentParser(description='')
-parser.add_argument ( '-b', dest='bam', help='the bam file', required=True )	
-parser.add_argument ( '-t', dest='types', help='SV analysis type (DEL, DUP, INV, TRA)', nargs='+', required=True )
-parser.add_argument ( '-q', dest='map_qual', help='min. paired-end mapping quality', default='0' )
-parser.add_argument ( '-s', dest='mad_cutoff', help='insert size cutoff, median+s*MAD (deletions only)', default=5 )
-parser.add_argument ( '-g', dest='genome', help='genome fasta file' )
-parser.add_argument ( '-m', dest='min_flank', help='minimum flanking sequence size', default=13 )
-parser.add_argument ( '-e', dest='epsilon', help='allowed epsilon deviation of PE vs. SR deletion', default=0.1 )
-parser.add_argument ( '-o', dest='output', help='output file' )
-
-dellyPath="delly_v0.5.5"
-
-def execute( cmd, output="" ):
-	tmp_dir = tempfile.mkdtemp()
-	try: 
-		err = open(tmp_dir+"/errorLog", 'a')
-		if output != "":
-			out = open(output, 'w')
-		else:
-			out = subprocess.PIPE
-		process = subprocess.Popen( args=shlex.split(cmd), stdout=out, stderr=err )
-		process.wait()
-		err.close()
-		if out != subprocess.PIPE:
-			out.close()
-	except Exception, e:
-		sys.stderr.write("problem doing : %s\n" %(cmd))
-		sys.stderr.write( '%s\n\n' % str(e) )
-
-
-def delly(args, tempDir):
-	tempOutputs=[];
-	for typ in args.types:
-		output=str(tempDir)+"/"+str(typ)
-		tempOutputs.append(output)
-		cmd = "%s %s -t %s -o %s -q %s -s %s -m %s -e %s " % (dellyPath, args.bam, typ, output, args.map_qual, args.mad_cutoff, args.min_flank, args.epsilon)
-		if (args.genome!="" and args.genome!=None):
-			cmd += "-g %s" % (args.genome)
-		# print ("commande = "+cmd)
-		execute( cmd )
-	return tempOutputs
-
-
-def merge(outputs, outputFile):
-	template = vcf.Reader(filename=outputs[0])
-	vcfWriter = vcf.Writer(open(outputFile, 'w'), template)
-	for output in outputs:
-		vcfReader = vcf.Reader(filename=output)
-		for record in vcfReader:
-			vcfWriter.write_record(record)
-	return 0
-
-
-def getVersion(program):
-	try:
-		tmp = tempfile.NamedTemporaryFile().name
-		tmp_stdout = open( tmp, 'wb' )
-		proc = subprocess.Popen( args=program, shell=True, stdout=tmp_stdout )
-		tmp_stdout.close()
-		returncode = proc.wait()
-		stdout = None
-		for line in open( tmp_stdout.name, 'rb' ):
-			if line.lower().find( 'version' ) >= 0:
-				stdout = line.strip()
-				break
-		if stdout:
-			sys.stdout.write( '%s\n' % stdout )
-	except:
-		sys.stdout.write( 'Could not determine %s version\n' % (program) )
-
-
-def __main__():
-	
-	args = parser.parse_args()
-
-	tempDir = tempfile.mkdtemp();
-	getVersion(dellyPath)
-
-	try:
-		execute("samtools index " + args.bam)
-	except Exception, e:
-		print("problem while indexing bam file " + str(e))
-
-	try:
-		tempOutputs = delly(args, tempDir)
-	except Exception, e:
-		sys.stdout.write("problem while runing delly " + str(e))
-
-	try:	
-		if args.output:
-			outputs=[]
-			for output in tempOutputs:
-				if os.path.exists(output):
-					if os.path.getsize(output)>0:
-						outputs.append(output)
-			if len(outputs)>0:
-				merge(outputs, args.output)
-	except Exception, e:
-		sys.stdout.write("problem while merging files " + str(e))
-
-	finally:
-		try:
-			if os.path.exists(tempDir):
-				shutil.rmtree(tempDir)
-			os.system("rm "+str(args.bam)+".bai")
-		except:
-			pass
-
-if __name__=="__main__":
-	__main__()