old_contents: import sys
  
  import numpy as np
  
  def predict_loci(phi_values, cutoff_percent):
  	average_phi_values = np.mean(axis=1)
  
  	sortable = []
  	for loci, phi in enumerate(average_phi_values):
  		sortable.append((phi, loci))
  	sortable.sort()
  	sortable.reverse()
  
  	cutoff_idx = int(len(sortable) * cutoff_percent)
  
  	return sortable[:cutoff_idx]
  
  def write_predicted(flname, predicted_loci):
  	fl = open(flname, "w")
  	for phi, loci in predicted_loci:
  		fl.write("%s %s\n" % (loci, phi))
  	fl.close()
  
  if __name__ == "__main__":
  	npy_flname = sys.argv[1]
  	cutoff_percent = float(sys.argv[2])
  	predicted_flname = sys.argv[3]
  
  	phi_values = np.load(npy_flname)
  	predicted_loci = predicted_loci(phi_values)
  	write_predicted(predicted_flname, predicted_loci)
  	
  
  	
new_contents: import sys
  
  import numpy as np
  
  def predict_loci(phi_values, cutoff_percent):
  	average_phi_values = np.mean(axis=1)
  
  	sortable = []
  	for loci, phi in enumerate(average_phi_values):
  		sortable.append((phi, loci))
  	sortable.sort()
  	sortable.reverse()
  
  	cutoff_idx = int(len(sortable) * cutoff_percent)
  
  	return sortable[:cutoff_idx]
  
  def write_predicted(flname, predicted_loci):
  	fl = open(flname, "w")
  	for phi, loci in predicted_loci:
  		fl.write("%s %s\n" % (loci, phi))
  	fl.close()
  
  if __name__ == "__main__":
  	npy_flname = sys.argv[1]
  	cutoff_percent = float(sys.argv[2])
  	predicted_flname = sys.argv[3]
  
  	phi_values = np.load(npy_flname)
  	predicted_loci = predict_loci(phi_values)
  	write_predicted(predicted_flname, predicted_loci)
  	
  
  	
subject: Fix syntax error