def main():
### make bin with specified window length and step size
core.make_bin(chromSize=args.chromsize,
binLength=args.length,
stepSize=args.step,
blackList=args.blacklist,
fileOut=args.prefix + ".bin.bed")
### process covariates
core.proc_cov(bwFiles=args.cov,
bedFile=args.prefix + ".bin.bed",
fileOut=args.prefix + ".cov.tsv")
### process input, output bam
core.proc_bam(bamFiles=[args.input, args.output],
bedFile=args.prefix + ".bin.bed",
chromSize=args.chromsize,
fileOut=args.prefix + ".bam.bct",
minSize=args.min,
maxSize=args.max,
normalize=True,
pseudocount=args.pseudocount)
### call peaks
core.call_peak(prefix=args.prefix,
bedFile=args.prefix + ".bin.bed",
bctFile=args.prefix + ".bam.bct",
covFile=args.prefix + ".cov.tsv",
bwFile=args.prefix + ".bam.bct.1.bw",
chromSize=args.chromsize,
threshold=args.threshold,
minInputQuantile=args.minquantile,
mode=args.mode)
def main():
### make genomic bin with specified window length and step size
core.make_bin(prefix=args.prefix,
chromSize=args.chromsize,
binLength=args.length,
stepSize=args.step,
blackList=args.blacklist)
### process covariates
if args.cov:
core.proc_cov(prefix=args.prefix,
bedFile=args.prefix + ".bin.bed",
bwFiles=args.cov)
### process input, output bam files
core.proc_bam(prefix=args.prefix,
chromSize=args.chromsize,
bedFile=args.prefix + ".bin.bed",
bamFiles=[args.input, args.output],
minSize=args.min,
maxSize=args.max,
readStart=args.readstart,
strand=args.strand,
singleEnd=args.se)
### call peaks
if args.cov:
core.call_peak(prefix=args.prefix,
chromSize=args.chromsize,
bedFile=args.prefix + ".bin.bed",
covFile=args.prefix + ".cov.tsv",
bctFile=args.prefix + ".bam.bct",
bwFile=args.prefix + ".output.bw",
threshold=args.threshold,
mode=args.mode,
minCoverage=args.mincov,
extQuantile=args.eq)
else:
core.call_peak(prefix=args.prefix,
chromSize=args.chromsize,
bedFile=args.prefix + ".bin.bed",
covFile=None,
bctFile=args.prefix + ".bam.bct",
bwFile=args.prefix + ".output.bw",
threshold=args.threshold,
mode=args.mode,
minCoverage=args.mincov,
extQuantile=args.eq)
### LOAD ARGs ###
parser = argparse.ArgumentParser(description='Call Peaks')
### required args
parser.add_argument('--prefix', help='Output File Prefix', required=True)
parser.add_argument('--chromsize', help='Chrom Sizes', required=True)
parser.add_argument('--bed', help='BED File', required=True)
parser.add_argument('--bct', help='BCT File', required=True)
parser.add_argument('--bw', help='BigWig File of STARR-seq Coverage', required=True)
### optional args
parser.add_argument('--cov', help='Covariate File', required=False)
parser.add_argument('--threshold', help='Adjusted P-value Threshold', required=False, type=float, default=0.05)
parser.add_argument('--mode', help='Mode', required=False, type=int, default=1)
parser.add_argument('--mincov', help='Minimum Coverage', required=False, type=int, default=10)
parser.add_argument('--eq', help='Extreme Quantile to Remove', required=False, type=float, default=1e-5)
args = parser.parse_args()
if __name__ == "__main__": core.call_peak(prefix=args.prefix,
chromSize=args.chromsize,
bedFile=args.bed,
covFile=args.cov,
bctFile=args.bct,
bwFile=args.bw,
threshold=args.threshold,
mode=args.mode,
minCoverage=args.mincov,
extQuantile=args.eq)
import argparse
import core
### LOAD ARGs ###
parser = argparse.ArgumentParser(description='Call Peaks')
### required args
parser.add_argument('--prefix', help='Output File Prefix', required=True)
parser.add_argument('--chromsize', help='Chrom Sizes', required=True)
### optional args
parser.add_argument('--threshold',
help='Adjusted P-value Threshold',
required=False,
default=0.05)
parser.add_argument('--mode', help='Mode', required=False, default=1)
args = parser.parse_args()
if __name__ == "__main__":
core.call_peak(prefix=args.prefix,
bedFile=args.prefix + ".bin.bed",
bctFile=args.prefix + ".bam.bct",
covFile=args.prefix + ".cov.tsv",
bwFile=args.prefix + ".bam.bct.1.bw",
chromSize=args.chromsize,
threshold=args.threshold,
mode=args.mode)
parser.add_argument('--bw',
help='STARR-seq Output Coverage BigWig File',
required=True)
parser.add_argument('-c', '--chromsize', help='Chrom Sizes', required=True)
### optional args
parser.add_argument('-t',
'--threshold',
help='Adjusted P-value Threshold',
required=False,
default=0.05)
parser.add_argument('-q',
'--minquantile',
help='Minimum Input Quantile',
required=False,
default=0.2)
parser.add_argument('-m', '--mode', help='Mode', required=False, default=1)
args = parser.parse_args()
if __name__ == "__main__":
core.call_peak(prefix=args.prefix,
bedFile=args.bed,
bctFile=args.bct,
covFile=args.cov,
bwFile=args.bw,
chromSize=args.chromsize,
threshold=args.threshold,
minInputQuantile=args.minquantile,
mode=args.mode)