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Search for exact full-length matches

Source: R/vs_search_exact.R
vs_search_exact.Rd

vs_search_exact searches for exact full-length matches of query sequences in a database of target sequences using VSEARCH.

Usage

vs_search_exact(
  fastx_input,
  database,
  userout = NULL,
  otutabout = NULL,
  userfields = "query+target+id+alnlen+mism+opens+qlo+qhi+tlo+thi+evalue+bits",
  strand = "plus",
  threads = 1,
  vsearch_options = NULL,
  tmpdir = NULL
)

Arguments

fastx_input

(Required). A FASTA/FASTQ file path or FASTA/FASTQ tibble object containing the query sequences. See Details.

database

(Required). A FASTA/FASTQ file path or FASTA/FASTQ tibble object containing the target sequences.

userout

(Optional). A character string specifying the name of the output file for the alignment results. If NULL (default), no output is written to a file and the results are returned as a tibble with the columns specified in userfields. See Details.

otutabout

(Optional). A character string specifying the name of the output file in an OTU table format. If NULL (default), no output is written to a file. If TRUE, the output is returned as a tibble. See Details.

userfields

(Optional). Fields to include in the output file. Defaults to "query+target+id+alnlen+mism+opens+qlo+qhi+tlo+thi+evalue+bits". See Details.

strand

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

threads

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

vsearch_options

(Optional). A character string of 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 userout is NULL a tibble containing the alignment results with the fields specified by userfields is returned. If userout is specified the alignment results are written to the specified file, and no tibble is returned.

If otutabout is TRUE, an OTU table is returned as a tibble. If otutabout is a character string, the output is written to the file, and no tibble is returned.

If neither userout nor otutabout is specified, a tibble containing the alignment results is returned.

Details

Identifies exact full-length matches between query and target sequences using VSEARCH. Only 100 specificity and making this command much faster than vs_usearch_global.

fastx_input and database can either be file paths to a FASTA/FASTQ files or FASTA/FASTQ objects. 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.

userfields specifies the fields to include in the output file. Fields must be given as a character string separated by "+". The default value of userfields equals "query+target+id+alnlen+mism+opens+qlo+qhi+tlo+thi+evalue+bits", which gives a blast-like tab-separated format of twelve fields. See the 'Userfields' section in the VSEARCH manual for more information.

otutabout gives the option to output the results in an OTU table format with tab-separated columns. When writing to a file, the first line starts with the string "#OTU ID", followed by a tab-separated list of all sample identifiers (formatted as "sample=X"). Each subsequent line, corresponding to an OTU, begins with the OTU identifier and is followed by tab-separated abundances for that OTU in each sample. If otutabout is a character string, the output is written to the specified file. If otutabout is TRUE, the function returns the OTU table as a tibble, where the first column is named otu_id instead of "#OTU ID".

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

See also

vs_usearch_global

Examples

if (FALSE) { # \dontrun{
# You would typically use something else as database
query_file <- file.path(file.path(path.package("Rsearch"), "extdata"),
                        "small.fasta")
db <- query_file

# Search for exact full-length matches with default parameters, with file as output
vs_search_exact(fastx_input = query_file,
                database = db,
                userout = "delete_me.txt")

# Read results, and give column names
result.tbl <- read.table("delete_me.txt",
                         sep = "\t",
                         header = FALSE,
                         col.names = c("query", "target", "id", "alnlen",
                                       "mism", "opens", "qlo", "qhi",
                                       "tlo", "thi", "evalue", "bits"))
} # }