new_contents: #!/usr/bin/env python
  
  """
  add_metadata_to_delly_manta_vcf.py
  
  ##INFO=<ID=SOMATIC  is automatically added after i) the delly somatic filtering step ii) manta somatic calling
  
  """
  
  import sys
  import argparse
  import re
  import vcf
  
  def add_meta2vcf(vcf_file):
  	try:
  		f = open(vcf_file, 'r')
  	except IOError:
  		sys.exit("Error: Can't open vcf file: {0}".format(vcf_file))
  	else:
  		with f:
  			vcf_header = []
  			vcf_chrom = []
  			vcf_variants = []
  			countline = 0
  			version = ""
  			for line in f:
  				countline = countline + 1
  				line = line.strip('\n')
  				if line.startswith('##'):
  					##Print original vcf meta-information lines##
  					vcf_header.append(line)
  					if line.startswith('##cmdline'):
  						find_manta = re.findall('(manta_\w+\.\w+\.\w+)', line)
  						version = find_manta[0]
  					## print header lines and Add meta-information lines with melter info to vcf
  				elif line.startswith("#CHROM"):
  					vcf_chrom.append(line)
  					countline = 0
  				else:
  					variant = line.split('\t')
  					if countline == 1:
  						find_delly = re.findall('(EMBL.DELLYv\w+\.\w+.\w+)', variant[7])
  						if not version:
  							version = find_delly[0]
  					if not "DELLY" in variant[7]:
  						variant[7] = variant[7]+";SVMETHOD={0}".format(find_manta[0])
  					vcf_variants.append("\t".join(variant))
  					
  					
  			print "\n".join(vcf_header)
  			print "##INFO=<ID=caller={0}".format(version)
  			print "\n".join(vcf_chrom)
  			print "\n".join(vcf_variants)
  
  
  if __name__ == "__main__":
  	parser = argparse.ArgumentParser(description = 'add metadata to a SV VCF file')
  	required_named = parser.add_argument_group('required named arguments')
  	required_named.add_argument('-v', '--vcf_file', help='path/to/file.vcf', required=True)
  	args = parser.parse_args()
  	add_meta2vcf(args.vcf_file)
  
  
subject: Create add_metadata_to_delly_manta_vcf.py