new_contents: import numpy as np
  import VertexCut as vc
  from optparse import OptionParser
  import time
  import scipy.linalg.blas as blas
  import leapUtils
  np.set_printoptions(precision=3, linewidth=200)
  
  parser = OptionParser()
  parser.add_option('--bfilesim', metavar='bfilesim', default=None, help='Binary plink file')
  parser.add_option('--extractSim', metavar='extractSim', default=None, help='extractSim file')
  parser.add_option('--cutoff', metavar='cutoff', type=float, default=0.05, help='Relationship cutoff (default 0.05)')
  parser.add_option('--out', metavar='out', default=None, help='output file')
  
  parser.add_option('--pheno', metavar='pheno', default=None, help='Phenotypes file (optional), only used for identifying unphenotyped individuals')
  parser.add_option('--missingPhenotype', metavar='missingPhenotype', type=float, default=-9, help='identifier for missing values (default: -9)')
  (options, args) = parser.parse_args()
  
  if (options.bfilesim is None): raise Exception('bfilesim must be supplied')
  if (options.out is None):   raise Exception('output file name must be supplied')
  
  bed, _ = leapUtils.loadData(options.bfilesim, options.extractSim, options.pheno, options.missingPhenotype, loadSNPs=True, standardize=True)
  keepArr = leapUtils.findRelated(bed, options.cutoff)
  
  f = open(options.out, 'w')
  for i, (fid,iid) in enumerate(bed.iid):
  	if (keepArr[i]): f.write(fid + ' ' + iid + ' 0\n')
  	else: f.write(fid + ' ' + iid + ' 1\n')
  f.close()
  	
  
subject: Create findRelated.py