calculate_methyl

This function is used for computing methylation level from indexed methylation coverage file.

Parameters

calculate_methyl(tbxInput=None, bedInput=None,
                 outputdir=None, threads=1,
                 stepNum=None, upstream=None,)

• tbxInput: list, input indexed methylation coverage files.

• bedInput: str, bed file contains genome regions which will be computed for methylation level.

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

• threads: int, how many thread to use.

• stepNum: int or str, step flag for folder name.

• upstream: upstream output results, used for pipeline.

• verbose: bool, True means print all stdout, but will be slow; False means black stdout verbose, much faster.

Warning

We recommend using this function with bismark related functions.

Example usage:

from cfDNApipe import *

pipeConfigure(
    threads=60,
    genome="hg19",
    refdir=r"path_to_reference/hg19_bismark",
    outdir=r"path_to_output/WGBS",
    data="WGBS",
    type="paired",
    build=True,
    JavaMem="10g",
)

fq1 = ["test1_1.fq", "test2_1.fq"]
fq2 = ["test1_2.fq", "test2_2.fq"]

res_bismark = bismark(seqInput1=fq1, seqInput2=fq2,
                      ref="path_to_bismark_genome",
                      upstream=True, threads=30, paired=True)

res_deduplicate = bismark_deduplicate(
    upstream=res_bismark, other_params=dudupOP, verbose=verbose
)

res_methyextract = bismark_methylation_extractor(
    upstream=res_deduplicate, other_params=extractMethyOP, verbose=verbose
)

res_compressMethy = compress_methyl(upstream=res_methyextract, verbose=verbose)

res_calMethy = calculate_methyl(
    upstream=res_compressMethy, bedInput=methyRegion, verbose=verbose
)