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Cluster FASTA sequences

Source: R/vs_cluster_subseq.R
vs_cluster_subseq.Rd

vs_cluster_subseq clusters FASTA sequences from a given file or object using VSEARCH´s cluster_fast method and 100 identity. The function automatically sorts sequences by decreasing length before clustering.

Usage

vs_cluster_subseq(
  fasta_input,
  centroids = NULL,
  strand = "plus",
  sizein = TRUE,
  fasta_width = 0,
  log_file = NULL,
  threads = 1,
  vsearch_options = NULL,
  tmpdir = NULL
)

Arguments

fasta_input

(Required). A FASTA file path or a FASTA object containing reads to cluster. See Details.

centroids

(Optional). A character string specifying the name of the FASTA output file for the cluster centroid sequences. If NULL (default), no output is written to a file and the centroid sequences are returned as a FASTA object. See Details.

strand

(Optional). Specifies which strand to consider when comparing sequences. Can be either "plus" (default) or "both".

sizein

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

fasta_width

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

log_file

(Optional). Name of the log file to capture messages from VSEARCH. If NULL (default), no log file is created.

threads

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

vsearch_options

(Optional). 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 centroids is specified the centroid sequences are written to the specified file, and no tibble is returned.

If centroids is not specified, a FASTA object is returned. This is a tibble with columns Header and Sequence, and also the additional column(s) members and, if sizein = TRUE, size.

Details

After merging/dereplication some sequences may be sub-sequences of longer sequences. This function will cluster such sequences at 100 (terminal gaps ignored), and keep the longest in each cluster as the centroid.

fasta_input can either be a file path to a FASTA file or a FASTA object. FASTA objects are tibbles that contain the columns Header and Sequence, see readFasta.

If sizein = TRUE (default) the FASTA headers must contain text matching the regular expression "size=[0-9]+" indicating the copy number (=size) of each input sequence. This is then summed for each cluster and added to the output. This text is typically added by de-replication, see vs_fastx_uniques.

The number of distinct sequences in each cluster is output as members.

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
fasta_input <- file.path(file.path(path.package("Rsearch"), "extdata"),
                                   "small.fasta")

# De-replicating
derep.tbl <- vs_fastx_uniques(fasta_input, output_format = "fasta")

# Clustering subsequences
cluster.tbl <- vs_cluster_subseq(fasta_input = derep.tbl)

# Cluster sequences and write centroids to a file
vs_cluster_subseq(fasta_input = derep.tbl,
                  centroids = "distinct.fa")
} # }