extractor: Extract reads and output from Kraken

In rsahmi: Single-Cell Analysis of Host-Microbiome Interactions

Extract reads and output from Kraken

Description

Extract reads and output from Kraken

Usage

extract_taxids(
  kraken_report,
  taxon = c("d__Bacteria", "d__Fungi", "d__Viruses")
)

extract_kraken_output(
  kraken_out,
  taxids,
  odir,
  ofile = "kraken_microbiome_output.txt",
  ...
)

extract_kraken_reads(
  kraken_out,
  reads,
  ofile = NULL,
  odir = getwd(),
  threads = NULL,
  ...,
  envpath = NULL,
  seqkit = NULL
)

Arguments

kraken_report	The path to kraken report file.
taxon	An atomic character specify the taxa name wanted. Should follow the kraken style, connected by rank codes, two underscores, and the scientific name of the taxon (e.g., "d__Viruses")
kraken_out	The path to kraken output file.
taxids	A character specify NCBI taxonony identifier to extract.
odir	A string of directory to save the ofile.
ofile	A string of file save the kraken output of specified taxids.
...	extract_kraken_output: Additional arguments passed to sink_csv(). extract_kraken_reads: Additional arguments passed to cmd_run() method.
reads	The original fastq files (input in kraken2). You can pass two paired-end files directly.
threads	Number of threads to use, see blit::cmd_help(blit::seqkit("grep")).
envpath	A string of path to be added to the environment variable PATH.
seqkit	A string of path to seqkit command.

Value

• extract_taxids: An atomic character vector of taxon identifiers.

• extract_kraken_output: A polars DataFrame.

• extract_kraken_reads: Exit status invisiblely.

See Also

https://github.com/DerrickWood/kraken2/blob/master/docs/MANUAL.markdown

Examples

## Not run: 
# For 10x Genomic data, `fq1` only contain barcode and umi, but the official
# didn't give any information for this. In this way, I prefer using
# `umi-tools` to transform the `umi` into fq2 and then run `rsahmi` with
# only fq2.
blit::kraken2(
    fq1 = fq1,
    fq2 = fq2,
    classified_out = "classified.fq",
    # Number of threads to use
    blit::arg("--threads", 10L, format = "%d"),
    # the kraken database
    blit::arg("--db", kraken_db),
    "--use-names", "--report-minimizer-data",
) |> blit::cmd_run()

# `kraken_report` should be the output of `blit::kraken2()`
taxids <- extract_taxids(kraken_report = "kraken_report.txt")

# 1. `kraken_out` should be the output of `blit::kraken2()`
# 2. `taxids` should be the output of `extract_taxids()`
# 3. `odir`: the output directory
extract_kraken_output(
    kraken_out = "kraken_output.txt",
    taxids = taxids,
    odir = # specify the output directory
)

# 1. `kraken_out` should be the output of `extract_kraken_output()`
# 2. `fq1` and `fq2` should be the same with `blit::kraken2()`
extract_kraken_reads(
    kraken_out = "kraken_microbiome_output.txt",
    reads = c(fq1, fq2),
    threads = 10L, # Number of threads to use
    # try to change `seqkit` argument into your seqkit path. If `NULL`, the
    # internal will detect it in your `PATH` environment variable
    seqkit = NULL
)

## End(Not run)

rsahmi documentation built on April 4, 2025, 1:46 a.m.