Title: | R Interface for the Basic Local Alignment Search Tool |
---|---|
Description: | Seamlessly interfaces the Basic Local Alignment Search Tool (BLAST) to search genetic sequence data bases. This work was partially supported by grant no. R21HG005912 from the National Human Genome Research Institute. |
Authors: | Michael Hahsler [aut, cre] |
Maintainer: | Michael Hahsler <[email protected]> |
License: | GPL-3 |
Version: | 1.1.1 |
Built: | 2024-08-28 05:07:13 UTC |
Source: | https://github.com/mhahsler/rBLAST |
Open a BLAST database and execute blastn (blastp or blastx) from blast+ to find sequences matches.
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()
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()
db |
the database file to be searched (without file extension). |
remote |
logical execute the query remotely on the NCBI server. |
type |
BLAST program to use (e.g., |
info |
show additional data base information. |
... |
additional arguments are ignored. |
object , x
|
An open BLAST database as a BLAST object created
with |
newdata |
the query as an object of class Biostrings::XStringSet. |
BLAST_args |
additional arguments in command-line style. |
custom_format |
custom format specified by space delimited format specifiers. |
verbose |
logical; print progress and debugging information. |
keep_tmp |
logical; keep temporary files for debugging. |
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.
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))
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()
.
Michael Hahsler
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/
Other blast:
blast_db_cache()
,
makeblastdb()
## 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) }
## 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) }
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/.
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 )
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 )
file |
the filename of the database. |
baseURL |
URL to download blast databases from. The default is NCBI's ftp server. |
check_update |
logical; update the local cache if there is a newer version of the file available on the server. This may take some time. |
verbose |
logical; display download information. |
The package maintains its own local cache which can be accessed using
blast_db_cache()
.
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.
Michael Hahsler
Other blast:
blast()
,
makeblastdb()
## 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)
## 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)
Call the makeblastdb
utility to create a BLAST database from a FASTA file.
makeblastdb( file, db_name = NULL, dbtype = "nucl", hash_index = TRUE, args = "", verbose = TRUE )
makeblastdb( file, db_name = NULL, dbtype = "nucl", hash_index = TRUE, args = "", verbose = TRUE )
file |
input file/database name. Note that the filename and path cannot contain whitespaces. |
db_name |
name of the database (files). |
dbtype |
molecule type of target db ( |
hash_index |
logical; create index of sequence hash values. |
args |
string including additional arguments passed on
to |
verbose |
logical; show the progress report produced by |
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.
Nothing but creates a BLAST database directory.
Michael Hahsler
Other blast:
blast()
,
blast_db_cache()
## 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) }
## 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) }