changeset 0:544c5266fc0f draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/pindel.py	Wed Jul 02 04:39:54 2014 -0400
@@ -0,0 +1,144 @@
+
+import argparse, optparse, os, shutil, subprocess, sys, tempfile, time, shlex
+
+parser = argparse.ArgumentParser(description='')
+parser.add_argument('-r', dest='input_reference', required=True, help='the reference file')
+parser.add_argument('-b', dest='input_bam', required=True, help='the bam file')
+parser.add_argument('-s', dest='insert_size', type=int, default='500', required=True, help='the insert size')
+parser.add_argument('-n', dest='sampleTag', default='sample', required=False, help='the sample tag')
+parser.add_argument('-o', dest='output_vcf', help='the output vcf', required=True)
+parser.add_argument('--name', dest='name', default='defaults')
+parser.add_argument('--number_of_threads', dest='number_of_threads', type=int, default='1')
+parser.add_argument('--window_size', dest='window_size', type=int, default='5')
+parser.add_argument('--sequencing_error_rate', dest='sequencing_error_rate', type=float, default='0.01')
+parser.add_argument('--sensitivity', dest='sensitivity', default='0.95', type=float)
+parser.add_argument('--report_long_insertions', dest='report_long_insertions', action='store_true', default=False)
+parser.add_argument('--report_duplications', dest='report_duplications', action='store_true', default=False)
+parser.add_argument('--report_inversions', dest='report_inversions', action='store_true', default=False)
+parser.add_argument('--report_breakpoints', dest='report_breakpoints', action='store_true', default=False)
+
+tmp_dir = tempfile.mkdtemp()
+pindel_dir=tmp_dir+"/pindel"
+errorFile = tmp_dir+"/errorLog"
+
+
+def execute( cmd, output="" ):
+	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 index (args):
+	cmd = "samtools index %s" % (args.input_bam)
+	# print( "commande = "+cmd )
+	# os.system(cmd)
+	execute(cmd)
+
+	cmd = "samtools faidx %s" % (args.input_reference)
+	# print( "commande = "+cmd )
+	# os.system(cmd)
+	execute(cmd)
+
+
+def config( args ):
+	# print("config")
+	config = tmp_dir+"/pindel_config"
+	# cmd = 'echo %s\t%s\t%s > %s' % (bam, size, name, config)
+	# print("commande = "+cmd)
+	# os.system(cmd)
+	fil = open(config, 'w')
+	fil.write("%s\t%s\t%s" % (args.input_bam, args.insert_size, args.name) )
+	fil.close()
+	return config
+
+
+# def pindel( reference, config, output ):
+# 	print("pindel")
+# 	cmd="pindel -f %s -i %s -o %s" % (reference, config, output)
+# 	print("commande = "+cmd)
+# 	os.system(cmd)
+
+# 	os.system("rm %s" % (output))
+# 	if not os.path.exists(output):
+# 		os.makedirs(output)
+# 	os.system("mv %s_* %s" %(output, output) )
+
+
+def pindel( reference, config, temp, args ):
+	cmd = "pindel -f %s -i %s -o %s " % (reference, config, pindel_dir)
+	cmd += "--number_of_threads %d --window_size %d --sequencing_error_rate %f --sensitivity %f" % (args.number_of_threads, args.window_size, args.sequencing_error_rate, args.sensitivity)
+	if args.report_long_insertions:
+		cmd += ' --report_long_insertions '
+	if args.report_duplications:
+		cmd += ' --report_duplications '
+	if args.report_inversions:
+		cmd += ' --report_inversions '
+	if args.report_breakpoints:
+		cmd += ' --report_breakpoints '
+	print("commande = "+cmd)
+	execute( cmd )
+
+
+
+
+
+def move( avant, apres ):
+	if os.path.exists(avant):
+		execute("mv %s %s" %(avant, apres))
+
+
+def pindel2vcf( args ):
+	date = str(time.strftime('%d/%m/%y',time.localtime()))
+	name = "test"
+	cmd = "pindel2vcf -P %s -r %s -R %s -d %s" % (pindel_dir, args.input_reference, name, date )
+	print ("commande = " + cmd)
+	execute(cmd)
+	if os.path.exists(pindel_dir+".vcf"):
+		execute("cp %s %s" %(pindel_dir+".vcf", args.output_vcf))
+
+
+def __main__():
+	
+	args = parser.parse_args()
+
+	# try:
+	# 	cmd = 'pindel'
+	# 	cmd += ' -i1 %s -i2 %s -o %s ' % (args.input1, args.input2, args.output1)
+	# except:
+	# 	sys.stdout.write( 'problem args : %s' % (cmd) )
+	# try:
+	# 	os.system(cmd)
+	# except:
+	# 	sys.stdout.write( 'problem cmd' )
+	# pipeline(args.reference, args.bam, args.output_raw, args.output_vcf, size, name, args)
+
+	reference = args.input_reference
+	bam = args.input_bam
+	temp = args.output_vcf+"_temp/temp"
+	output_vcf = args.output_vcf
+	
+	try:
+		index( args )
+		conf = config( args )
+
+		pindel( reference, conf, temp, args )
+		pindel2vcf(args)
+		
+
+	finally:
+		if os.path.exists( tmp_dir ):
+			shutil.rmtree( tmp_dir )
+
+if __name__=="__main__":
+	__main__()