MACS3/Commands/cmbreps_cmd.py

   1 # Time-stamp: <2024-10-02 16:42:02 Tao Liu>
   2
   3 """Description: combine replicates
   4
   5 This code is free software; you can redistribute it and/or modify it
   6 under the terms of the BSD License (see the file LICENSE included with
   7 the distribution).
   8 """
   9
  10 import os
  11
  12 from MACS3.IO import BedGraphIO
  13 from MACS3.Utilities.OptValidator import opt_validate_cmbreps
  14
  15 # ------------------------------------
  16 # constants
  17 # ------------------------------------
  18
  19 # ------------------------------------
  20 # Misc functions
  21 # ------------------------------------
  22
  23 # ------------------------------------
  24 # Main function
  25 # ------------------------------------
  26
  27
  28 def run(options):
  29     options = opt_validate_cmbreps(options)
  30     info = options.info
  31     # warn = options.warn
  32     # debug = options.debug
  33     # error = options.error
  34
  35     info("Read and build bedGraph for each replicate...")
  36     reps = []
  37     i = 1
  38     for ifile in options.ifile:
  39         info("Read file #%d" % i)
  40         reps.append(BedGraphIO.bedGraphIO(ifile).read_bedGraph())
  41         i += 1
  42
  43     # first two reps
  44     info("combining tracks 1-%i with method '%s'" % (i - 1, options.method))
  45     cmbtrack = reps[0].overlie([reps[j] for j in range(1, i - 1)], func=options.method)
  46
  47     # now output
  48     ofile = BedGraphIO.bedGraphIO(os.path.join(options.outdir, options.ofile), data=cmbtrack)
  49     info("Write bedGraph of combined scores...")
  50     ofile.write_bedGraph(name="%s_combined_scores" % (options.method.upper()), description="Scores calculated by %s" % (options.method.upper()))
  51     info("Finished '%s'! Please check '%s'!" % (options.method, ofile.bedGraph_filename))