old_contents: #!/usr/bin/env python
  
  import argparse, os.path, sys
  
  from fastq2adjacency import fastq2adjacency
  
  # Set up the command line parameters
  parser = argparse.ArgumentParser(description="Load adjacency list into HDF5 file")
  parser.add_argument("--genome", help="Genome name") #             default="GCA_000001405.22")
  parser.add_argument("--dataset", help="Name of the dataset") #    default="GSE63525")
  parser.add_argument("--sra_id", help="SRA ID") #                  default="SRR1658572")
  parser.add_argument("--library", help="Library") #                default="HIC003")
  parser.add_argument("--enzyme_name", help="Enzyme name (HboI)") # default="HboI")
  parser.add_argument("--resolution", help="Resolution") #          default=1000000)
  parser.add_argument("--tmp_dir", help="Temporary data dir")
  parser.add_argument("--data_dir", help="Data directory; location of SRA FASTQ files")
  
  # Get the matching parameters from the command line
  args = parser.parse_args()
  
  if len(sys.argv) < 9:
      parser.print_help()
      sys.exit(2)
  
  genome      = args.genome
  dataset     = args.dataset
  sra_id      = args.sra_id
  library     = args.library
  enzyme_name = args.enzyme_name
  resolution  = args.resolution
  tmp_dir     = args.tmp_dir
  data_dir    = args.data_dir
  
  
  f2a = fastq2adjacency()
  
  windows1 = ((1,25), (1,50), (1,75),(1,100))
  windows2 = ((1,25), (1,50), (1,75),(1,100))
  #windows2 = ((101,125), (101,150), (101,175),(101,200))
  f2a.set_params(genome, dataset, sra_id, library, enzyme_name, resolution, tmp_dir, data_dir, False, windows1, windows1)
  
  f2a.mapWindows(1)
  f2a.mapWindows(2)
  
  f2a.parseGenomeSeq()
  
  f2a.parseMaps()
  
  f2a.mergeMaps()
  
  f2a.filterReads(conservative=True)
  
  f2a.load_hic_data()
  
  f2a.normalise_hic_data()
  
  f2a.save_hic_data()
  
new_contents: #!/usr/bin/env python
  
  import argparse, os.path, sys
  
  from fastq2adjacency import fastq2adjacency
  
  # Set up the command line parameters
  parser = argparse.ArgumentParser(description="Load adjacency list into HDF5 file")
  parser.add_argument("--genome", help="Genome name") #             default="GCA_000001405.22")
  parser.add_argument("--dataset", help="Name of the dataset") #    default="GSE63525")
  parser.add_argument("--sra_id", help="SRA ID") #                  default="SRR1658572")
  parser.add_argument("--library", help="Library") #                default="HIC003")
  parser.add_argument("--enzyme_name", help="Enzyme name (HboI)") # default="HboI")
  parser.add_argument("--resolution", help="Resolution") #          default=1000000)
  parser.add_argument("--tmp_dir", help="Temporary data dir")
  parser.add_argument("--data_dir", help="Data directory; location of SRA FASTQ files")
  
  # Get the matching parameters from the command line
  args = parser.parse_args()
  
  if len(sys.argv) < 9:
      parser.print_help()
      sys.exit(2)
  
  genome      = args.genome
  dataset     = args.dataset
  sra_id      = args.sra_id
  library     = args.library
  enzyme_name = args.enzyme_name
  resolution  = args.resolution
  tmp_dir     = args.tmp_dir
  data_dir    = args.data_dir
  
  
  f2a = fastq2adjacency()
  
  windows1 = ((1,25), (1,50), (1,75),(1,100))
  windows2 = ((1,25), (1,50), (1,75),(1,100))
  #windows2 = ((101,125), (101,150), (101,175),(101,200))
  f2a.set_params(genome, dataset, sra_id, library, enzyme_name, resolution, tmp_dir, data_dir, False, windows1, windows1)
  
  map(f2a.mapWindows, [1, 2])
  #f2a.mapWindows(1)
  #f2a.mapWindows(2)
  
  f2a.parseGenomeSeq()
  
  f2a.parseMaps()
  
  f2a.mergeMaps()
  
  f2a.filterReads(conservative=True)
  
  f2a.load_hic_data()
  
  f2a.normalise_hic_data()
  
  f2a.save_hic_data()
  
subject: Change to test runnig this as a map call, which is able to get parellelised via COMPS