def run(o_options):
"""The Main function/pipeline for duplication filter.
"""
# Parse options...
options = opt_validate(o_options)
# end of parsing commandline options
info = options.info
warn = options.warn
debug = options.debug
error = options.error
#0 output arguments
assert options.format != 'BAMPE', "Pair-end data with BAMPE option currently doesn't work with pileup command. You can pretend your data to be single-end with -f BAM. Please try again!"
#0 prepare output file
outfile = os.path.join(options.outdir, options.outputfile)
if os.path.isfile(outfile):
info("# Existing file %s will be replaced!" % outfile)
os.unlink(outfile)
#1 Read tag files
info("# read alignment files...")
(tsize, treat) = load_tag_files_options(options)
info("# tag size = %d", tsize)
t0 = treat.total
info("# total tags in alignment file: %d", t0)
if options.bothdirection:
info(
"# Pileup alignment file, extend each read towards up/downstream direction with %d bps"
% options.extsize)
pileup_and_write(treat,
outfile,
options.extsize * 2,
1,
directional=False,
halfextension=False)
else:
info(
"# Pileup alignment file, extend each read towards downstream direction with %d bps"
% options.extsize)
pileup_and_write(treat,
outfile,
options.extsize,
1,
directional=True,
halfextension=False)
info("# Done! Check %s" % options.outputfile)
def run( o_options ):
"""The Main function/pipeline for duplication filter.
"""
# Parse options...
options = opt_validate( o_options )
# end of parsing commandline options
info = options.info
warn = options.warn
debug = options.debug
error = options.error
#0 output arguments
options.PE_MODE = options.format in ('BAMPE','BEDPE')
#assert options.format != 'BAMPE', "Pair-end data with BAMPE option currently doesn't work with pileup command. You can pretend your data to be single-end with -f BAM. Please try again!"
#0 prepare output file
outfile = os.path.join( options.outdir, options.outputfile )
if os.path.isfile( outfile ):
info("# Existing file %s will be replaced!" % outfile )
os.unlink( outfile )
#1 Read tag files
info("# read alignment 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) )
info("# Pileup paired-end alignment file.")
pileup_and_write_pe(treat, outfile )
else:
(tsize, treat) = load_tag_files_options (options)
info("# tag size = %d", tsize)
t0 = treat.total
info("# total tags in alignment file: %d", t0)
if options.bothdirection:
info("# Pileup alignment file, extend each read towards up/downstream direction with %d bps" % options.extsize)
pileup_and_write(treat, outfile, options.extsize * 2, 1, directional=False, halfextension=False)
else:
info("# Pileup alignment file, extend each read towards downstream direction with %d bps" % options.extsize)
pileup_and_write(treat, outfile, options.extsize, 1, directional=True, halfextension=False)
info("# Done! Check %s" % options.outputfile)