runCounter¶
This function is used for transforming fasta files or bam files into wig files.
Parameters¶
runCounter(fileInput=None, outputdir=None,
filetype=None, stepNum=None,
upstream=None)
fileInput: list, paths of input files waiting to be transformed.
outputdir: str, output result folder, None means the same folder as input files.
filetype: int, 0 for GC counter (which indicates fasta input), 1 for read counter (which indicates bam inputs).
binlen: int, length of the dividing bins of the wig file.
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 arm-level CNV detection.
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,
)