old_contents: from GamTools import corr
  import numpy as np
  import argparse
  
  parser = argparse.ArgumentParser(description='Calculate coverage over different window sizes for a list of bam files.')
  parser.add_argument('npz_frequencies_file', help='An npz file containing co-segregation frequencies to convert to correlations')
  
  args = parser.parse_args()
  
  correlation_file = args.npz_frequencies_file.split('.')
  correlation_file = correlation_file[0] + '.correlations.npz'
  
  freqs = np.load(args.npz_frequencies_file)['freqs']
  
  def flatten_freqs(freqs):
          
      freqs_shape = freqs.shape
      flat_shape = ( freqs_shape[0] * freqs_shape[1], freqs_shape[2], freqs_shape[3])
      return freqs.reshape(flat_shape)
  
  distances = np.array(map(corr, flatten_freqs(freqs))).reshape(freqs.shape[:2])
  
  np.save_compressed(correlation_file, corr=distances)
  
new_contents: from GamTools import corr
  import numpy as np
  import argparse
  
  parser = argparse.ArgumentParser(description='Calculate coverage over different window sizes for a list of bam files.')
  parser.add_argument('npz_frequencies_file', help='An npz file containing co-segregation frequencies to convert to correlations')
  
  args = parser.parse_args()
  
  correlation_file = args.npz_frequencies_file.split('.')
  correlation_file[correlation_file.index('chrom')] = "corr"
  correlation_file = '.'.join(correlation_file)
  
  freqs = np.load(args.npz_frequencies_file)['freqs']
  
  def flatten_freqs(freqs):
          
      freqs_shape = freqs.shape
      flat_shape = ( freqs_shape[0] * freqs_shape[1], freqs_shape[2], freqs_shape[3])
      return freqs.reshape(flat_shape)
  
  distances = np.array(map(corr, flatten_freqs(freqs))).reshape(freqs.shape[:2])
  
  np.savez_compressed(correlation_file, corr=distances)
  
subject: Change how/where to save the file