Fragmentomics

The Following example shows how to perform OCF and fragmentation profile analysis. For up- and down-stream relationship, please see “Up Down Stream Flowchart” part.

OCF Example usage

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_bed = glob.glob("path_to_data/HCC/*.bed")
ctrl_bed = glob.glob("path_to_data/CTR/*.bed")

switchConfigure("cancer")

res_computeOCF = computeOCF(
   casebedInput=case_bed,
   ctrlbedInput=ctrl_bed,
   caseupstream=True,
   verbose=verbose,
)
res_OCFplot = OCFplot(upstream=res_computeOCF, verbose=verbose)

fragmentation profile Example usage

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_bedgz = glob.glob("path_to_data/HCC/*.bed.gz")
ctrl_bedgz = glob.glob("path_to_data/CTR/*.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",
)