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Subsample sequences

Source: R/vs_fastx_subsample.R
vs_fastx_subsample.Rd

vs_fastx_subsample subsamples sequences in FASTA/FASTQ file or object by randomly extracting sequences based on number or percentage using VSEARCH.

Usage

vs_fastx_subsample(
  fastx_input,
  output_format = "fastq",
  fastx_output = NULL,
  sample_pct = NULL,
  sample_size = NULL,
  sizein = TRUE,
  sizeout = TRUE,
  relabel = NULL,
  relabel_sha1 = FALSE,
  randseed = NULL,
  fasta_width = 0,
  sample = NULL,
  threads = 1,
  vsearch_options = NULL,
  tmpdir = NULL
)

Arguments

fastx_input

(Required). A FASTA/FASTQ file path or FASTA/FASTQ object. See Details.

output_format

(Optional). Desired output format of file or tibble: "fasta" or "fastq" (default). If fastx_input is a FASTA file path or a FASTA object, output_format cannot be "fastq".

fastx_output

(Optional). Name of the output file for subsampled reads from fastx_input. File can be in either FASTA or FASTQ format, depending on output_format. If NULL (default), no sequences are written to file. See Details.

sample_pct

(Optional). Percentage of the input sequences to be subsampled. Numeric value ranging from 0.0 to 100.0. Defaults to NULL.

sample_size

(Optional). The given number of sequences to extract. Must be a positive integer if specified. Defaults to NULL.

sizein

(Optional). If TRUE (default), abundance annotations present in sequence headers are taken into account.

sizeout

(Optional). If TRUE (default), abundance annotations are added to FASTA headers.

relabel

(Optional). Relabel sequences using the given prefix and a ticker to construct new headers. Defaults to NULL.

relabel_sha1

(Optional). If TRUE (default), relabel sequences using the SHA1 message digest algorithm. Defaults to FALSE.

randseed

(Optional). Random seed. Must be a positive integer. A given seed always produces the same output, which is useful for replicability. Defaults to NULL.

fasta_width

(Optional). Number of characters per line in the output FASTA file. Defaults to 0, which eliminates wrapping.

sample

(Optional). Add the given sample identifier string to sequence headers. For instance, if the given string is "ABC", the text ";sample=ABC" will be added to the header. If NULL (default), no identifier is added.

threads

(Optional). Number of computational threads to be used by VSEARCH.Defaults to 1.

vsearch_options

Additional arguments to pass to VSEARCH. Defaults to NULL. See Details.

tmpdir

(Optional). Path to the directory where temporary files should be written when tables are used as input or output. Defaults to NULL, which resolves to the session-specific temporary directory (tempdir()).

Value

A tibble or NULL.

If fastx_output is specified, the subsampled sequences are written to the specified output file, and no tibble is returned.

If fastx_output NULL, a tibble containing the subsampled reads in the format specified by output_format is returned.

Details

Sequences in the input file/object (fastx_input) are subsampled by randomly extracting a specified number or percentage of sequences. Extraction is performed as random sampling with a uniform distribution among the input sequences and without replacement.

fastx_input can either be a FASTA/FASTQ file or a FASTA/FASTQ object. FASTA objects are tibbles that contain the columns Header and Sequence, see readFasta. FASTQ objects are tibbles that contain the columns Header, Sequence, and Quality, see readFastq.

Specify either sample_size or sample_pct to determine the number or percentage of sequences to subsample. Only one of these parameters can be specified at a time. If neither is specified, an error is thrown.

If fastx_output is specified, the sampled sequences are output to this file in format given by output_format. If fastx_output is NULL, the sample sequences are returned as a FASTA or FASTQ object, depending on output_format.

vsearch_options allows users to pass additional command-line arguments to VSEARCH that are not directly supported by this function. Refer to the VSEARCH manual for more details.

References

https://github.com/torognes/vsearch

Examples

if (FALSE) { # \dontrun{
# Define arguments
fastx_input <- file.path(file.path(path.package("Rsearch"), "extdata"),
                         "small_R1.fq")
fastx_output <- NULL
output_format <- "fastq"
sample_size <- 10

# Subsample sequences and return a FASTQ tibble
subsample_R1 <- vs_fastx_subsample(fastx_input = fastx_input,
                                   fastx_output = fastx_output,
                                   output_format = output_format,
                                   sample_size = sample_size)

# Subsample sequences and write subsampled sequences to a file
vs_fastx_subsample(fastx_input = fastx_input,
                   fastx_output = "subsample.fq",
                   output_format = output_format,
                   sample_size = sample_size)
} # }