Python Vcf.check_info Beispiele

Beispiel #1

Datei: add_on_target.py Projekt: drio/py.analysis

def doHeader(fd):
  vcf = Vcf(fd)
  vcf.load_meta_header()
  ot_already_there = str(vcf.check_info('OT'))
  if ot_already_there == True:
    error("This vcf seems to have an OT INFO already. Bailing out.")
  vcf.add_info('OT', '0', 'Flag', 'The site is on target.')
  # print "Checking if INFO id=OT is there: " + str(vcf.check_info('OT'))
  print vcf.get_meta()
  return vcf

Beispiel #2

def doHeader(fd):
    vcf = Vcf(fd)
    vcf.load_meta_header()
    ot_already_there = str(vcf.check_info('OT'))
    if ot_already_there == True:
        error("This vcf seems to have an OT INFO already. Bailing out.")
    vcf.add_info('OT', '0', 'Flag', 'The site is on target.')
    # print "Checking if INFO id=OT is there: " + str(vcf.check_info('OT'))
    print vcf.get_meta()
    return vcf

Beispiel #3

def doHeader(fd):
  vcf = Vcf(fd)
  vcf.load_meta_header()
  ot_already_there = str(vcf.check_info('RDP'))
  if ot_already_there == True:
    error("This vcf seems to have an RDP INFO already. Bailing out.")
  vcf.add_info('RDP', '1', 'Integer', 'Raw read coverage at locus.')
  # print "Checking if INFO id=OT is there: " + str(vcf.check_info('OT'))
  print vcf.get_meta()
  return vcf