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# Time-stamp: <2020-11-24 17:00:16 Tao Liu>
"""Description: Random sample certain number/percentage of tags.
This code is free software; you can redistribute it and/or modify it
under the terms of the BSD License (see the file LICENSE included with
the distribution).
"""
# ------------------------------------
# python modules
# ------------------------------------
import os
import sys
# ------------------------------------
# own python modules
# ------------------------------------
from MACS3.Utilities.Constants import *
from MACS3.Utilities.OptValidator import opt_validate_randsample
# ------------------------------------
# Main function
# ------------------------------------
def run( options0 ):
options = opt_validate_randsample( options0 )
# end of parsing commandline options
info = options.info
warn = options.warn
debug = options.debug
error = options.error
options.PE_MODE = options.format in ('BAMPE','BEDPE')
#0 check output file
if options.outputfile:
outfhd = open( os.path.join( options.outdir, options.outputfile ), "w" )
else:
outfhd = sys.stdout
#1 Read tag files
if options.PE_MODE:
info("# read input file in Paired-end mode.")
treat = load_frag_files_options ( options ) # return PETrackI object
t0 = treat.total # total fragments
info("# total fragments/pairs in alignment file: %d" % (t0) )
else:
info("read tag files...")
treat = load_tag_files_options (options)
info("tag size = %d" % options.tsize)
treat.fw = options.tsize
t0 = treat.total
info(" total tags in alignment file: %d" % (t0))
if options.number:
if options.number > t0:
error(" Number you want is bigger than total number of tags in alignment file! Please specify a smaller number and try again!")
error(" %.2e > %.2e" % (options.number, t0))
sys.exit(1)
info(" Number of tags you want to keep: %.2e" % (options.number))
options.percentage = float(options.number)/t0*100
info(" Percentage of tags you want to keep: %.2f%%" % (options.percentage))
if options.seed >= 0:
info(" Random seed has been set as: %d" % options.seed )
treat.sample_percent(options.percentage/100.0, options.seed )
info(" tags after random sampling in alignment file: %d" % (treat.total))
info("Write to BED file")
treat.print_to_bed(fhd=outfhd)
info("finished! Check %s." % options.outputfile)
def load_tag_files_options ( options ):
"""From the options, load alignment tags.
"""
options.info("# read treatment tags...")
tp = options.parser(options.ifile[0], buffer_size=options.buffer_size)
if not options.tsize: # override tsize if user specified --tsize
ttsize = tp.tsize()
options.tsize = ttsize
treat = tp.build_fwtrack()
#treat.sort()
if len(options.ifile) > 1:
# multiple input
for ifile in options.ifile[1:]:
tp = options.parser(ifile, buffer_size=options.buffer_size)
treat = tp.append_fwtrack( treat )
#treat.sort()
treat.finalize()
options.info("tag size is determined as %d bps" % options.tsize)
return treat
def load_frag_files_options ( options ):
"""From the options, load treatment fragments and control fragments (if available).
"""
options.info("# read treatment fragments...")
tp = options.parser(options.ifile[0], buffer_size=options.buffer_size)
treat = tp.build_petrack()
#treat.sort()
if len(options.ifile) > 1:
# multiple input
for ifile in options.ifile[1:]:
tp = options.parser(ifile, buffer_size=options.buffer_size)
treat = tp.append_petrack( treat )
#treat.sort()
treat.finalize()
return treat
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