make_blast_DB {disprose}

Builds local database for BLAST

Description

Builds a BLAST database with local sequences using FASTA file.

Usage

make_blast_DB(
  makeblastdb.way,
  fasta.way,
  db.way,
  db.type = "nucl",
  db.title,
  delete.fasta = FALSE,
  verbose = TRUE
)

Arguments

makeblastdb.way

character; name and path to makeblastdb executable file

fasta.way

character; name and path to FASTA file

db.way

character; name and path to local BLAST database

db.type

character; type of BLAST database

db.title

character; BLAST data base title

delete.fasta

logical; delete FASTA file

verbose

logical; show messages

Details

This function is using BLAST applications. BLAST+ (UNIX or Windows) should be installed.

Value

The function creates local BLAST data base. No additional data is returned.

Author(s)

Elena N. Filatova

References

Camacho C., Coulouris G., Avagyan V. et al. (2009). BLAST+: architecture and applications. BMC Bioinformatics 10, 421. https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-10-421.

Examples

## Not run: 
# This function is using BLAST applications. BLAST+ should be installed.
# FASTA file with sequences for local data base should be downloaded first (see get_seq_for_DB ())
path <- tempdir()
dir.create (path)
# load metadata for target sequences of Chlamydia pneumoniae
(meta.target)
# load sequences, it will take about 3 minutes
get_seq_for_DB (ids = meta.target$gi, db = "nucleotide", check.result = TRUE,
              return="fasta", fasta.file = paste0 (path, "/seq.fasta"), verbose = TRUE)
# create local data base, it will take 0.235217 seconds
make_blast_DB (makeblastdb.way = "D:/Blast/blast-2.11.0+/bin/makeblastdb.exe",
              fasta.way = paste0 (path, "/seq.fasta"), db.title = "Cl_pneumoniae",
              db.way = paste0 (path, "/DB"), db.type = "nucl", delete.fasta = FALSE)
# delete FASTA file (also can set delete.fasta = TRUE)
file.remove (paste0 (path, "/seq.fasta"))

## End(Not run)