bamCounter¶
This function is used for counting counts in each dividing bin of the input bam files.
Parameters¶
bamCounter(bamInput=None, chromsizeInput=None,
binlen=None, outputdir=None, threads=1,
stepNum=None, upstream=None, verbose=True)
bamInput: list, paths of input bedgz files waiting to be processed.
chromsizeInput: str, path of chromsize file.
binlen: int, length of each bin; default is 5000000(5Mb) for fragmentation profile, or 100000(100kb) for CNV.
outputdir: str, output result folder, None means the same folder as input files.
threads: int, how many thread to use.
stepNum: Step number for folder name.
upstream: Not used parameter, do not set this parameter.
verbose: bool, True means print all stdout, but will be slow; False means black stdout verbose, much faster.
Warning
We recommend using this function in a specific analysis like CNV.
Example usage:
# an example for compute arm-level CNV
from cfDNApipe import *
import glob
pipeConfigure2(
threads=20,
genome="hg19",
refdir=r"reference_genome/hg19",
outdir=r"output/pcs_armCNV",
data="WGS",
type="paired",
JavaMem="8G",
case="cancer",
ctrl="normal",
build=True,
)
verbose = False
case_bam = glob.glob("path_to_data/HCC/*.bam")
ctrl_bam = glob.glob("path_to_data/CTR/*.bam")
# case
switchConfigure("cancer")
case_bamCounter = bamCounter(
bamInput=case_bam, upstream=True, verbose=verbose, stepNum="case01"
)
case_gcCounter = runCounter(
filetype=0, upstream=True, verbose=verbose, stepNum="case02"
)
case_GCCorrect = GCCorrect(
readupstream=case_bamCounter,
gcupstream=case_gcCounter,
verbose=verbose,
stepNum="case03",
)
# ctrl
switchConfigure("normal")
ctrl_bamCounter = bamCounter(
bamInput=ctrl_bam, upstream=True, verbose=verbose, stepNum="ctrl01"
)
ctrl_gcCounter = runCounter(
filetype=0, upstream=True, verbose=verbose, stepNum="ctrl02"
)
ctrl_GCCorrect = GCCorrect(
readupstream=ctrl_bamCounter,
gcupstream=ctrl_gcCounter,
verbose=verbose,
stepNum="ctrl03",
)
switchConfigure("cancer")
res_computeCNV = computeCNV(
caseupstream=case_GCCorrect,
ctrlupstream=ctrl_GCCorrect,
stepNum="ARMCNV",
verbose=verbose,
)