old_contents: import numpy as np
  import h5py
  
  def get_1000G_snps(sumstats, out_file):
      sf = np.loadtxt(sumstats,dtype=str,skiprows=1)
      h5f = h5py.File('ref/1000G_SNP_info.h5','r')
      rf = h5f['snp_chr'][:]
      h5f.close()
      ind1 = np.in1d(sf[:,1],rf[:,2])
      ind2 = np.in1d(rf[:,2],sf[:,1])
      sf1 = sf[ind1]
      rf1 = rf[ind2]
      ### check order ###
      if sum(sf1[:,1]==rf1[:,2])==len(rf1[:,2]):
          print 'Good!'
      else:
          print 'Shit happens, sorting sf1 to have the same order as rf1'
          O1 = np.argsort(sf1[:,1])
          O2 = np.argsort(rf1[:,2])
          O3 = np.argsort(O2)
          sf1 = sf1[O1][O3]
      out = ['hg19chrc snpid a1 a2 bp or p'+'\n']
      for i in range(len(sf1[:,1])):
          out.append(sf1[:,0][i]+' '+sf1[:,1][i]+' '+sf1[:,2][i]+' '+sf1[:,3][i]+' '+rf1[:,1][i]+' '+sf1[:,5][i]+' '+sf1[:,6][i]+'\n')
      ff = open(out_file,"w")
      ff.writelines(out)
      ff.close()
  
  
  
new_contents: import numpy as np
  import h5py
  
  def get_1000G_snps(sumstats, out_file):
      sf = np.loadtxt(sumstats,dtype=str,skiprows=1)
      h5f = h5py.File('ref/Misc/1000G_SNP_info.h5','r')
      rf = h5f['snp_chr'][:]
      h5f.close()
      ind1 = np.in1d(sf[:,1],rf[:,2])
      ind2 = np.in1d(rf[:,2],sf[:,1])
      sf1 = sf[ind1]
      rf1 = rf[ind2]
      ### check order ###
      if sum(sf1[:,1]==rf1[:,2])==len(rf1[:,2]):
          print 'Good!'
      else:
          print 'Shit happens, sorting sf1 to have the same order as rf1'
          O1 = np.argsort(sf1[:,1])
          O2 = np.argsort(rf1[:,2])
          O3 = np.argsort(O2)
          sf1 = sf1[O1][O3]
      out = ['hg19chrc snpid a1 a2 bp or p'+'\n']
      for i in range(len(sf1[:,1])):
          out.append(sf1[:,0][i]+' '+sf1[:,1][i]+' '+sf1[:,2][i]+' '+sf1[:,3][i]+' '+rf1[:,1][i]+' '+sf1[:,5][i]+' '+sf1[:,6][i]+'\n')
      ff = open(out_file,"w")
      ff.writelines(out)
      ff.close()
  
  
  
subject: Update pre_sumstats.py