old_contents: import glob
  import subprocess
  import os
  import argparse
  import shutil
  
  input_parser = argparse.ArgumentParser(
      description="Run RegTools stats script",
  )
  input_parser.add_argument(
      'tag',
      help="Variant tag parameter used to run RegTools.",
  )
  
  args = input_parser.parse_args()
  
  tag = args.tag
  cwd = os.getcwd()
  
  lines_per_file = 1000
  smallfile = None
  num_small_file = 0
  with open(f'all_splicing_variants_{tag}.bed', 'r') as bigfile:
      num_small_file +=1
      for lineno, line in enumerate(bigfile):
          if lineno % lines_per_file == 0:
              if smallfile:
                  smallfile.close()
              small_filename = 'small_file_{}.txt'.format(lineno + lines_per_file)
              smallfile = open(small_filename, "w")
          smallfile.write(line)
      if smallfile:
          num_small_file += 1
          smallfile.close()
  #get chunks
  files = glob.glob('small_file_*')
  files.sort()
  for file in files:
      subprocess.run(f'Rscript --vanilla ~/Git/regtools/scripts/compare_junctions_hist_v2.R {tag} {file}', shell=True, check=False)
  output_files = glob.glob("*_out.tsv")
  output_files.sort()  # glob lacks reliable ordering, so impose your own if output order matters
  with open(f'junction_pvalues_{tag}.tsv', 'wb') as outfile:
      for i, fname in enumerate(output_files):
          with open(fname, 'rb') as infile:
              if i != 0:
                  infile.readline()  # Throw away header on all but first file
              # Block copy rest of file from input to output without parsing
              shutil.copyfileobj(infile, outfile)
              print(fname + " has been imported.")
  for file in files:
      os.remove(file)
  
  
new_contents: import glob
  import subprocess
  import os
  import argparse
  import shutil
  
  input_parser = argparse.ArgumentParser(
      description="Run RegTools stats script",
  )
  input_parser.add_argument(
      'tag',
      help="Variant tag parameter used to run RegTools.",
  )
  
  args = input_parser.parse_args()
  
  tag = args.tag
  cwd = os.getcwd()
  
  lines_per_file = 50000
  smallfile = None
  num_small_file = 0
  with open(f'all_splicing_variants_{tag}.bed', 'r') as bigfile:
      num_small_file +=1
      for lineno, line in enumerate(bigfile):
          if lineno % lines_per_file == 0:
              if smallfile:
                  smallfile.close()
              small_filename = 'small_file_{}.txt'.format(lineno + lines_per_file)
              smallfile = open(small_filename, "w")
          smallfile.write(line)
      if smallfile:
          num_small_file += 1
          smallfile.close()
  #get chunks
  files = glob.glob('small_file_*')
  files.sort()
  for file in files:
      subprocess.run(f'Rscript --vanilla ~/Git/regtools/scripts/compare_junctions_hist_v2.R {tag} {file}', shell=True, check=False)
  output_files = glob.glob("*_out.tsv")
  output_files.sort()  # glob lacks reliable ordering, so impose your own if output order matters
  with open(f'junction_pvalues_{tag}.tsv', 'wb') as outfile:
      for i, fname in enumerate(output_files):
          with open(fname, 'rb') as infile:
              if i != 0:
                  infile.readline()  # Throw away header on all but first file
              # Block copy rest of file from input to output without parsing
              shutil.copyfileobj(infile, outfile)
              print(fname + " has been imported.")
  for file in files:
      os.remove(file)
  
  
subject: change chunk value in stats wrapper script