def run_scorebed(args):
#Verbosity is 0 if output is written to stdout
if args.output == None:
args.verbosity = 0
#Start logger
logger = TobiasLogger("ScoreBed", args.verbosity)
logger.begin()
parser = add_scorebed_arguments(argparse.ArgumentParser())
logger.arguments_overview(parser, args)
logger.output_files([args.output])
#Check input
check_required(args, ["bed", "bigwigs"])
check_files([getattr(args, arg) for arg in ["bed", "bigwigs", "subset"]],
"r")
check_files([getattr(args, "output")], "w")
#Setup output file/stdout
if args.output != None:
sys.stdout = open(args.output, 'w')
no_bigwigs = len(args.bigwigs)
#----------------------------------------------------------------------#
#----------------------- Overlap bed if needed ------------------------#
#----------------------------------------------------------------------#
if args.subset != None:
logger.info("Overlapping {0} to regions in {1}".format(
args.bed, args.subset))
#Make overlap
pb_bed = pb.BedTool(args.bed)
pb_region = pb.BedTool(args.subset)
overlap = pb_bed.intersect(pb_region, c=True)
args.bed = overlap.fn
# Setup score function
score_func = get_score_func(args)
#----------------------------------------------------------------------#
#---------------------- Open bw and run scoring -----------------------#
#----------------------------------------------------------------------#
pybw = {bigwig_f: pyBigWig.open(bigwig_f)
for bigwig_f in args.bigwigs} #open filehandles for all bigwigs
#Get chrom/start/stop from pybw objects
pybw_headers = {bigwig_f: pybw[bigwig_f].chroms() for bigwig_f in pybw}
logger.debug(pybw_headers)
logger.info("Starting scoring...")
#buff = [""]*args.buffer
#buff_idx = 0
count = 0
with open(args.bed) as f:
for line in f:
columns = line.strip().split("\t")
outline = "\t".join(columns) if args.subset == None else "\t".join(
columns[:-1]) #don't save overlap count
chrom, start, end = columns[0], int(columns[1]), int(columns[2])
#Decide whether to get signal or not
overlap = 1 if args.subset == None else int(columns[-1])
if overlap != 0:
for bigwig_f in args.bigwigs: #preserves order of bigwigs
if chrom in pybw_headers[
bigwig_f]: #only get score if chromosome is in bigwig; to prevent error from pybigwig.values
try:
signal = pybw[bigwig_f].values(chrom,
start,
end,
numpy=True)
except:
logger.error(
"Error reading signal for site: {0}".format(
line))
sys.exit()
if len(signal) > 0:
signal = np.nan_to_num(signal)
score = round(score_func(signal), 5)
else:
score = args.null
else:
score = args.null
#Format line with score
outline += "\t" + "{0:.5f}".format(score)
else:
outline += "\t" + "\t".join([args.null] * no_bigwigs)
#outline += "\n"
#buff[buff_idx] = outline
#buff_idx += 1
print(outline)
#if buff_idx == args.buffer: #eg. if idx is 100 (already 0-99 lines in buffer) and args.buffer is 100, this will be out of bounds for next line > write out
# fout.write("\n".join(buff) + "\n")
# #Init
# buff = [""]*args.buffer
# buff_idx = 0
for bigwig_f in pybw:
pybw[bigwig_f].close()
logger.end()
#buff[buff_idx] = outline
#buff_idx += 1
print(outline)
#if buff_idx == args.buffer: #eg. if idx is 100 (already 0-99 lines in buffer) and args.buffer is 100, this will be out of bounds for next line > write out
# fout.write("\n".join(buff) + "\n")
# #Init
# buff = [""]*args.buffer
# buff_idx = 0
for bigwig_f in pybw:
pybw[bigwig_f].close()
logger.end()
#--------------------------------------------------------------------------------------------------------#
if __name__ == '__main__':
parser = argparse.ArgumentParser()
parser = add_scorebed_arguments(parser)
args = parser.parse_args()
if len(sys.argv[1:]) == 0:
parser.print_help()
sys.exit()
run_scorebed(args)