old_contents: import math
  import argparse
  import os
  
  parser = argparse.ArgumentParser()
  parser.add_argument('-i', '--input', required=True, default='./output/sample.bam_ratio.BedGraph', type=str)
  parser.add_argument('-o', '--output', required=True, default='./output/sample.bam_ratio_log2_circos.txt', type=str)
  parser.add_argument('-p', '--ploidy', required=True, default=2, type=int)
  args = parser.parse_args()
  
  path = os.path.dirname(args.input)
  output = os.path.join(path, args.output)
  
  with open(args.input) as file:
      for line in file.readlines():
          ls = line.split()
          if ls[0] != "track" and float(ls[3]) > 0:
              log2_ratio = math.log2(float(ls[3]) / args.ploidy)
              with open(output, "a") as out:
                  out.write("{}\t{}\t{}\t{}\n".format(ls[0], ls[1], ls[2], log2_ratio))
  
new_contents: import argparse
  import os
  import math
  
  parser = argparse.ArgumentParser()
  parser.add_argument('-i', '--input', required=True, default='./output/sample.bam_ratio.BedGraph', type=str)
  parser.add_argument('-o', '--output', required=True, default='./output/sample.bam_ratio_log2_circos.txt', type=str)
  parser.add_argument('-p', '--ploidy', required=True, default=2, type=int)
  args = parser.parse_args()
  
  path = os.path.dirname(args.input)
  output = os.path.join(path, args.output)
  
  with open(args.input) as file:
      for line in file.readlines():
          ls = line.split()
          if ls[0] != "track" and float(ls[3]) > 0:
              log2_ratio = math.log2(float(ls[3]) / args.ploidy)
              with open(output, "a") as out:
                  out.write("{}\t{}\t{}\t{}\n".format(ls[0], ls[1], ls[2], log2_ratio))
  
subject: Fix failed linting