view pindel.py @ 13:077a2dbd906a draft

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import argparse, optparse, os, shutil, subprocess, sys, tempfile, time, shlex

parser = argparse.ArgumentParser(description='')
parser.add_argument('-r', dest='inputFastaFile', required=True, help='the reference file')
parser.add_argument('-b', dest='inputBamFile', 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('-o1', dest='outputRaw', help='the output raw', required=True)
parser.add_argument('-o2', dest='outputVcfFile', help='the output vcf', required=True)
parser.add_argument('--name', dest='name', default='name')
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)

parser.add_argument('-u', '--maximum_allowed_mismatch_rate', dest='maximum_allowed_mismatch_rate', type=float, default='0.02')
parser.add_argument('--report_close_mapped_reads', dest='report_close_mapped_reads', action='store_true', default=False)
parser.add_argument('--report_only_close_mapped_reads', dest='report_only_close_mapped_reads', action='store_true', default=False)
parser.add_argument('--report_interchromosomal_events', dest='report_interchromosomal_events', action='store_true', default=False)
parser.add_argument('--IndelCorrection', dest='IndelCorrection', action='store_true', default=False)
parser.add_argument('--NormalSamples', dest='NormalSamples', action='store_true', default=False)
parser.add_argument('-a', '--additional_mismatch', dest='additional_mismatch', type=int, default='1')
parser.add_argument('-m', '--min_perfect_match_around_BP', dest='min_perfect_match_around_BP', type=int, default='3')
parser.add_argument('-v', '--min_inversion_size', dest='min_inversion_size', type=int, default='50')
parser.add_argument('-d', '--min_num_matched_bases', dest='min_num_matched_bases', type=int, default='30')
parser.add_argument('-B', '--balance_cutoff', dest='balance_cutoff', type=int, default='0')
parser.add_argument('-A', '--anchor_quality', dest='anchor_quality', type=int, default='0')
parser.add_argument('-M', '--minimum_support_for_event', dest='minimum_support_for_event', type=int, default='3')
parser.add_argument('--detect_DD', dest='detect_DD', action='store_true', default=False)
parser.add_argument('--MAX_DD_BREAKPOINT_DISTANCE', dest='MAX_DD_BREAKPOINT_DISTANCE', type=int, default='350')
parser.add_argument('--MAX_DISTANCE_CLUSTER_READS', dest='MAX_DISTANCE_CLUSTER_READS', type=int, default='100')
parser.add_argument('--MIN_DD_CLUSTER_SIZE', dest='MIN_DD_CLUSTER_SIZE', type=int, default='3')
parser.add_argument('--MIN_DD_BREAKPOINT_SUPPORT', dest='MIN_DD_BREAKPOINT_SUPPORT', type=int, default='3')
parser.add_argument('--MIN_DD_MAP_DISTANCE', dest='MIN_DD_MAP_DISTANCE', type=int, default='8000')
parser.add_argument('--DD_REPORT_DUPLICATION_READS', dest='DD_REPORT_DUPLICATION_READS', action='store_true', default=False)


# def execute(cmd, output=""):
# 	try: 
# 		err = open(tempDir+"/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 execute(cmd, output=None):
	import subprocess, sys, shlex
	# function to execute a cmd and report if an error occur
	print(cmd)
	try: 
		process = subprocess.Popen(args=shlex.split(cmd), stdout=subprocess.PIPE, stderr=subprocess.PIPE)
		process.wait()
		stdout,stderr = process.communicate()
	except Exception, e: # une erreur de ma commande : stderr
		sys.stderr.write("problem doing : %s\n%s\n" %(cmd, e))
		return
	if output:
		output = open(output, 'w')
		output.write(stdout)
		output.close()
	if stderr != '': # une erreur interne au programme : stdout (sinon, souvent des warning arrete les programmes)
		sys.stdout.write("warning or error while doing : %s\n-----\n%s-----\n\n" %(cmd, stderr))


def indexBam(inputFastaFile, inputBamFile):
	cmd = "samtools index %s" %(inputBamFile)
	execute(cmd)
	cmd = "samtools faidx %s" %(inputFastaFile)
	execute(cmd)


def config(inputBamFile, meanInsertSize, name, tempDir):
	configFile = tempDir+"/pindel_configFile"
	# cmd = 'echo %s\t%s\t%s > %s' %(bam, size, name, configFile)
	# print("commande = "+cmd)
	# os.system(cmd)
	fil = open(configFile, 'w')
	fil.write("%s\t%s\t%s" %(inputBamFile, meanInsertSize, name))
	fil.close()
	return configFile


# def pindel(reference, configFile, output):
# 	print("pindel")
# 	cmd="pindel -f %s -i %s -o %s" %(reference, configFile, 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, configFile, args, tempDir):
	pindelTempDir=tempDir+"/pindel" 
	cmd = "pindel -f %s -i %s -o %s " %(reference, configFile, pindelTempDir)
	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)
	cmd += " -u %f -n %d -a %d -m %d -v %d -d %d -B %d -A %d -M %d " %(args.maximum_allowed_mismatch_rate, args.NM, args.additional_mismatch, args.min_perfect_match_around_BP, args.min_inversion_size, args.min_num_matched_bases, args.balance_cutoff, args.anchor_quality, args.minimum_support_for_event)

	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 '

	if args.report_close_mapped_reads:
		cmd += ' --report_close_mapped_reads '
	if args.report_only_close_mapped_reads:
		cmd += ' --report_only_close_mapped_reads '
	if args.report_interchromosomal_events:
		cmd += ' --report_interchromosomal_events '
	if args.IndelCorrection:
		cmd += ' --IndelCorrection '
	if args.NormalSamples:
		cmd += ' --NormalSamples '
	if args.input_SV_Calls_for_assembly:
		cmd += ' --input_SV_Calls_for_assembly %s ' %(args.input_SV_Calls_for_assembly)

	if args.detect_DD:
		cmd += ' -q '
		cmd += ' --MAX_DD_BREAKPOINT_DISTANCE '+str(args.MAX_DD_BREAKPOINT_DISTANCE)
		cmd += ' --MAX_DISTANCE_CLUSTER_READS '+str(args.MAX_DISTANCE_CLUSTER_READS)
		cmd += ' --MIN_DD_CLUSTER_SIZE '+str(args.MIN_DD_CLUSTER_SIZE)
		cmd += ' --MIN_DD_BREAKPOINT_SUPPORT '+str(args.MIN_DD_BREAKPOINT_SUPPORT)
		cmd += ' --MIN_DD_MAP_DISTANCE '+str(args.MIN_DD_MAP_DISTANCE)
		if args.DD_REPORT_DUPLICATION_READS:
			cmd += ' --DD_REPORT_DUPLICATION_READS '

	execute(cmd)
	return pindelTempDir


def move(avant, apres):
	if os.path.exists(avant):
		execute("mv %s %s" %(avant, apres))


def pindel2vcf(outputVcf, inputFastaFile, name, pindelTempDir):
	date = str(time.strftime('%d/%m/%y',time.localtime()))
	cmd = "pindel2vcf -P %s -r %s -R %s -d %s" %(pindelTempDir, inputFastaFile, name, date)
	print("commande = " + cmd)
	execute(cmd)
	if os.path.exists(pindelTempDir+".vcf"):
		execute("cp %s %s" %(pindelTempDir+".vcf", outputVcf))


def getMeanInsertSize(bamFile, tempDir):
	samFile = tempDir+"/sam"
	histogramFile = tempDir+"/histogram"
	outputFile = tempDir+"/output"
	cmd = "samtools view -h -o %s %s" % (bamFile, samFile)
	execute(cmd, )
	cmd = "picard-tools CollectInsertSizeMetrics H=%s O=%s I=%s" % (histogramFile, outputFile, samFile)
	execute(cmd)
	try:
		f = open(outputFile, 'r')
		lignes = f.readlines()
		f.close()
		meanInsertSize = lignes[7].split('\t')[0]
	except:
		sys.stderr.write("problem while opening file %s " %(outputFile))
		return 0
	return meanInsertSize


def __main__():
	
	args = parser.parse_args()
	tempDir = tempfile.mkdtemp()

	# 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.outputVcfFile, size, name, args)
	
	try:
		indexBam(args.inputFastaFile, args.inputBamFile)
		meanInsertSize = int(getMeanInsertSize(args.inputBamFile, tempDir))
		configFile = config(args.inputBamFile, meanInsertSize, args.name, tempDir)
		pindelTempDir = pindel(args.inputFastaFile, configFile, args, tempDir)
		pindel2vcf(args.outputVcfFile, args.inputFastaFile, args.name, pindelTempDir)
		
	finally:
		if os.path.exists(tempDir):
			shutil.rmtree(tempDir)

if __name__=="__main__":
	__main__()