nuc_tools/nuc_tools.py at master · tjs23/nuc_tools · GitHub

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import sys, importlib
from core import nuc_util as util
from core import nuc_io as io
from core import nuc_parallel as parallel

import formats
import tools

PROG_NAME = 'nuc_tools'
VERSION = '0.1.1'
DESCRIPTION = 'Informatics tools for genome structure and Hi-C analysis'
EPILOG = 'For further help email tjs23@cam.ac.uk or wb104@cam.ac.uk'
TOOLS = {'adapt': 'tools.nuc_adapt',
         'ab_kmeans': 'tools.nuc_ab_kmeans',
         'contact_map': 'tools.contact_map',
         'contact_compare': 'tools.contact_compare',
         'contact_insulation': 'tools.contact_insulation',
         'contact_probability': 'tools.contact_probability',
         'contact_report': 'tools.contact_report',
         'contact_density': 'tools.contact_density',
         'contact_pair_points': 'tools.contact_pair_points',
         'ncc_filter': 'tools.ncc_filter',
         'ncc_bin': 'tools.ncc_bin',
         'ncc_convert': 'tools.ncc_convert',
         'ncc_update':'tools.ncc_update',
         'chip-seq_process': 'tools.chip-seq_process',
         'sequence_properties': 'tools.sequence_properties',
         'structure_data_coords': 'tools.structure_data_coords',
         'structure_data_density': 'tools.structure_data_density',
         'structure_compare': 'tools.structure_compare',
         'structure_report': 'tools.structure_report',
         'data_track_filter': 'tools.data_track_filter',
         'data_track_compare': 'tools.data_track_compare',
         }

def main(argv=None):
  from argparse import ArgumentParser

  if argv is None:
    argv = sys.argv[1:]

  tools = sorted(TOOLS)
  sub_commands = ', '.join(tools)

  if not argv or argv[0] not in TOOLS:

    msg = 'AVAILABLE TOOLS: %s' % ' '.join(sorted(TOOLS))
    print(msg)

    arg_parse = ArgumentParser(prog='nuc_tools', description=DESCRIPTION,
                              epilog=EPILOG, add_help=True)

    arg_parse.add_argument('cmd', metavar='TOOL_NAME', choices=tools,
                            help='The tool to run. Available: %s' % sub_commands)

    arg_parse.add_argument('remainder', nargs='*', metavar='ARGUMENT',
                            help='Arguments for the specified tool')

    args = vars(arg_parse.parse_args(argv))

  module_name = TOOLS[argv[0]]
  module = importlib.import_module(module_name)
  module.main(argv[1:])


if __name__ == '__main__':
  main()