Package 'rBLAST'

Description

Open a BLAST database and execute blastn (blastp or blastx) from blast+ to find sequences matches.

Usage

blast(db = NULL, remote = FALSE, type = "blastn")

blast_help(type = "blastn")

## S3 method for class 'BLAST'
print(x, info = TRUE, ...)

## S3 method for class 'BLAST'
predict(
  object,
  newdata,
  BLAST_args = "",
  custom_format = "",
  verbose = FALSE,
  keep_tmp = FALSE,
  ...
)

has_blast()

Arguments

Value

• blast() returns a BLAST database object which can be used for queries (via predict).

• predict returns a data.frame containing the BLAST results.

• has_blast() returns TRUE if the blast software installation can be found and FALSE otherwise.

Installing BLAST+

The BLAST+ software needs to be installed on your system. Installation instructions are available in this package's INSTALL file and at https://www.ncbi.nlm.nih.gov/books/NBK569861/.

R needs to be able to find the executable. After installing the software, try in R

Sys.which("blastn")

If the command returns "" instead of the path to the executable, then you need to set the environment variable called PATH. In R

Sys.setenv(PATH = paste(Sys.getenv("PATH"),
   "path_to_your_BLAST_installation", sep=.Platform$path.sep))

BLAST Databases

You will also need a database. NCBI BLAST databases are updated daily and may be downloaded via FTP from https://ftp.ncbi.nlm.nih.gov/blast/db/. See blast_db_cache() on how to manage a local cache of database files.

BLAST databases are a set of database files with different extensions. All files start with the same database name. For example, ⁠16S_ribosomal_RNA.tar.gz⁠ contains files starting with ⁠16S_ribosomal_RNA⁠ which is the database name used for calling blast().

Large databases are separated into several archives numbered 00, 01, etc. Download all archives and extract the files in the same directory. All files will have a common name which is the database name used for calling blast().

Author(s)

Michael Hahsler

References

BLAST Help - BLAST+ Executable: https://blast.ncbi.nlm.nih.gov/doc/blast-help/downloadblastdata.html

BLAST Command Line Applications User Manual, https://www.ncbi.nlm.nih.gov/books/NBK279690/

See Also

Other blast: blast_db_cache(), makeblastdb()

Examples

## check if blastn is correctly installed. Should return the path to the
##   executable
Sys.which("blastn")

## only run if blast is installed
if (has_blast()) {
    ## check version you should have version 1.8.1+
    system2("blastn", "-version")

    ## download the latest version of the 16S Microbial
    ##  rRNA data base from NCBI using the local chache
    tgz_file <- blast_db_get("16S_ribosomal_RNA.tar.gz")

    ## extract the database files
    untar(tgz_file, exdir = "./16S_rRNA_DB")

    ## Note the database file can also downloaded without using a
    ##    cache using download.file
    # download.file(paste("https://ftp.ncbi.nlm.nih.gov/blast/db",
    #    "16S_ribosomal_RNA.tar.gz", sep = "/"),
    #    "16S_ribosomal_RNA.tar.gz", mode = "wb")
    # untar("16S_ribosomal_RNA.tar.gz", exdir = "./16S_rRNA_DB")

    ## A BLAST database is just a set of files. It is a good idea to
    ## organize the files in a directory.
    list.files("./16S_rRNA_DB")

    ## load a BLAST database (replace db with the location + name of
    ##   the BLAST DB without the extension)
    bl <- blast(db = "./16S_rRNA_DB/16S_ribosomal_RNA")
    bl

    ## read a single example sequence to BLAST
    seq <- readRNAStringSet(system.file("examples/RNA_example.fasta",
        package = "rBLAST"
    ))[1]
    seq

    ## query a sequence using BLAST
    cl <- predict(bl, seq)
    cl[1:5, ]

    ## Pass on BLAST arguments (99% identity) and use a custom format
    ## (see BLAST documentation)
    fmt <- paste(
        "qaccver saccver pident length mismatch gapopen qstart qend",
        "sstart send evalue bitscore qseq sseq"
    )
    cl <- predict(bl, seq,
        BLAST_args = "-perc_identity 99",
        custom_format = fmt
    )
    cl

    ## cleanup the example: delete the database files
    unlink("./16S_rRNA_DB", recursive = TRUE)
}

Description

Use BiocFileCache::BiocFileCache to manage local copies of BLAST database downloads. NCBI BLAST databases are updated daily and may be downloaded via FTP from https://ftp.ncbi.nlm.nih.gov/blast/db/.

Usage

blast_db_cache()

blast_db_get(
  file = "16S_ribosomal_RNA.tar.gz",
  baseURL = "https://ftp.ncbi.nlm.nih.gov/blast/db/",
  check_update = TRUE,
  verbose = TRUE
)

Arguments

Details

The package maintains its own local cache which can be accessed using blast_db_cache().

Value

• blast_db_cache() returns the path to the local BiocFileCache::BiocFileCache cache.

• blast_db_get() returns the file path to a downloaded BLAST database file.

Author(s)

Michael Hahsler

See Also

Other blast: blast(), makeblastdb()

Examples

## get a database file (will be downloaded if the
##     local copy is not up-to-date)
db_16S <- blast_db_get("16S_ribosomal_RNA.tar.gz")
db_16S

## directly interacting with the local cache
library(BiocFileCache)

## show the package's cache directory
local_cache <- blast_db_cache()
local_cache

## bfc functions can be used to manage the local cache
bfcinfo(local_cache)

Description

Call the makeblastdb utility to create a BLAST database from a FASTA file.

Usage

makeblastdb(
  file,
  db_name = NULL,
  dbtype = "nucl",
  hash_index = TRUE,
  args = "",
  verbose = TRUE
)

Arguments

Details

R needs to be able to find the executable (mostly an issue with Windows). Try Sys.which("makeblastdb") to see if the program is properly installed.

Use blast_help("makeblastdb") to see all possible extra arguments. Arguments need to be formated in exactly the way as they would be used for the command line tool.

Value

Nothing but creates a BLAST database directory.

Author(s)

Michael Hahsler

See Also

Other blast: blast(), blast_db_cache()

Examples

## check if makeblastdb is correctly installed
Sys.which("makeblastdb")

## only run if blast is installed
if (has_blast()) {
    ## see possible arguments
    blast_help("makeblastdb")

    ## read some example sequences
    seq <- readRNAStringSet(system.file("examples/RNA_example.fasta",
        package = "rBLAST"
    ))

    ## 1. write the FASTA file
    writeXStringSet(seq, filepath = "seqs.fasta")

    ## 2. make database
    makeblastdb(file = "seqs.fasta", db_name = "db/small", dbtype = "nucl")

    ## 3. open database
    db <- blast("db/small")
    db

    ## 4. perform search (first sequence in the db should be a perfect match)
    predict(db, seq[1])

    ## clean up
    unlink("seqs.fasta")
    unlink("db", recursive = TRUE)
}