MACS3/Commands/bdgbroadcall_cmd.py

   1 # Time-stamp: <2024-10-02 15:55:43 Tao Liu>
   2
   3 """Description: Fine-tuning script to call broad peaks from a single
   4 bedGraph track for scores.
   5
   6 This code is free software; you can redistribute it and/or modify it
   7 under the terms of the BSD License (see the file LICENSE included with
   8 the distribution).
   9
  10 """
  11
  12 # ------------------------------------
  13 # python modules
  14 # ------------------------------------
  15
  16 import os
  17 from MACS3.IO import BedGraphIO
  18 # ------------------------------------
  19 # constants
  20 # ------------------------------------
  21
  22 # ------------------------------------
  23 # Misc functions
  24 # ------------------------------------
  25 from MACS3.Utilities.Logger import logging
  26
  27 logger = logging.getLogger(__name__)
  28 debug = logger.debug
  29 info = logger.info
  30 error = logger.critical
  31 warn = logger.warning
  32
  33 # ------------------------------------
  34 # Classes
  35 # ------------------------------------
  36
  37 # ------------------------------------
  38 # Main function
  39 # ------------------------------------
  40
  41
  42 def run(options):
  43     info("Read and build bedGraph...")
  44     bio = BedGraphIO.bedGraphIO(options.ifile)
  45     btrack = bio.read_bedGraph(baseline_value=0)
  46
  47     info("Call peaks from bedGraph...")
  48
  49     bpeaks = btrack.call_broadpeaks(options.cutoffpeak, options.cutofflink, options.minlen, options.lvl1maxgap, options.lvl2maxgap)
  50
  51     info("Write peaks...")
  52
  53     if options.ofile:
  54         bf = open(os.path.join(options.outdir, options.ofile), "w")
  55         options.oprefix = options.ofile
  56     else:
  57         bf = open(os.path.join(options.outdir, "%s_c%.1f_C%.2f_l%d_g%d_G%d_broad.bed12" % (options.oprefix,options.cutoffpeak, options.cutofflink, options.minlen, options.lvl1maxgap, options.lvl2maxgap)), "w")
  58     bpeaks.write_to_gappedPeak(bf, name_prefix=(options.oprefix+"_broadRegion").encode(), score_column="score", trackline=options.trackline)
  59     info("Done")