fragprofplot

This function is used for computing and plotting the fragmentation profile plot.

Parameters

fragprofplot(casetxtInput=None, ctrltxtInput=None,
             outputdir=None, cytoBandInput=None,
             stepNum=None, caseupstream=None,
             ctrlupstream=None)

• casetxtInput: list, paths of files of input short and long counts for case samples,

  [sample1_short, sample1_long, sample2_short, sample2_long, etc.].

• ctrltxtInput: list, paths of files of input short and long counts for control samples(format is same as casetxtInput).

• cytoBandInput: str, path of the cytoBand file.

• labelInput: list, name of case and control(which will be marked on the output plot), [case_name, control_name]

• outputdir: str, output result folder, None means the same folder as input files.

• stepNum: Step number for folder name.

• caseupstream: Not used parameter, do not set this parameter.

• ctrlupstream: Not used parameter, do not set this parameter.

Warning

We recommend using this function in short long fragmentation analysis.

Example usage:

# an example for short long fragmentation analysis
from cfDNApipe import *
import glob

pipeConfigure2(
    threads=20,
    genome="hg19",
    refdir=r"path_to_genome/hg19",
    outdir=r"path_to_output/pcs_fp",
    data="WGS",
    type="paired",
    JavaMem="8G",
    case="cancer",
    ctrl="normal",
    build=True,
)

verbose = False

# these bed.gz output can be get from bam2bed function in cfDNApipe
case_bedgz = glob.glob("/data/wzhang/pcs_final/HCC/*.bed.gz")
ctrl_bedgz = glob.glob("/data/wzhang/pcs_final/Healthy/*.bed.gz")

# case
switchConfigure("cancer")
case_fragCounter = fpCounter(
    bedgzInput=case_bedgz, upstream=True, verbose=verbose, stepNum="case01", processtype=1
)
case_gcCounter = runCounter(
    filetype=0, binlen=5000000, upstream=True, verbose=verbose, stepNum="case02"
)
case_GCCorrect = GCCorrect(
    readupstream=case_fragCounter,
    gcupstream=case_gcCounter,
    readtype=2,
    corrkey="-",
    verbose=verbose,
    stepNum="case03",
)

# ctrl
switchConfigure("normal")
ctrl_fragCounter = fpCounter(
    bedgzInput=ctrl_bedgz, upstream=True, verbose=verbose, stepNum="ctrl01", processtype=1
)
ctrl_gcCounter = runCounter(
    filetype=0, binlen=5000000, upstream=True, verbose=verbose, stepNum="ctrl02"
)
ctrl_GCCorrect = GCCorrect(
    readupstream=ctrl_fragCounter,
    gcupstream=ctrl_gcCounter,
    readtype=2,
    corrkey="-",
    verbose=verbose,
    stepNum="ctrl03",
)

switchConfigure("cancer")
res_fragprofplot = fragprofplot(
    caseupstream=case_GCCorrect,
    ctrlupstream=ctrl_GCCorrect,
    stepNum="FP",
)