virusdetect

This function is used for detect virus in sequencing data.

Note

This this function is calling centrifuge, only used for WGS data.

centrifuge official docs

Kim, Daehwan, et al. “Centrifuge: rapid and sensitive classification of metagenomic sequences.” Genome research 26.12 (2016): 1721-1729.

Parameters

virusdetect(seqInput1=None, seqInput2=None,
            ref=None, outputdir=None,
            threads=1, paired=True,
            other_params={"-q": True, "-N": 1, "--time": True},
            stepNum=None, upstream=None,)

  • seqInput1: list, input _1 fastq files.

  • seqInput2: list, input _2 fastq files, None for single end.

  • ref: bowtie2 reference path.

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

  • threads: int, how many thread to use.

  • paired: True for paired data, False for single end data.

  • other_params: dict, other parameters passing to Bismark.

    “-parameter”: True means “-parameter” in command line. “-parameter”: 1 means “-parameter 1” in command line.

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

  • upstream: upstream output results, used for pipeline. This parameter can be True, which means a new pipeline start.

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

Example usage:

from cfDNApipe import *
import glob

pipeConfigure(
    threads=20,
    genome="hg19",
    refdir=r"path_to_reference/hg19",
    outdir=r"path_to_output/virus_output",
    data="WGS",
    type="paired",
    build=True,
    JavaMem="10g",
)

# Download and Build Virus Genome
Configure.virusGenomeCheck(folder="path_to_reference/virus_database", build=True)

# paired data
fq1 = glob.glob("path_to_unmapped/*.fq.1.gz")
fq2 = glob.glob("path_to_unmapped/*.fq.2.gz")

virusdetect(seqInput1=fq1, seqInput2=fq2, upstream=True)