disprose (version 0.1.6)

make_blast_DB: 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

Value

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

Details

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

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"))
# }
# NOT RUN {
# }