, R package version 0.99.4.
119 |
120 | @Misc{,
121 | title = {{rBLAST:} {R} Interface for the Basic Local Alignment Search Tool},
122 | author = {Michael Hahsler and Annurag Nagar},
123 | year = {2024},
124 | doi = {10.18129/B9.bioc.rBLAST},
125 | note = {R package version 0.99.4},
126 | howpublished = {Bioconductor version: Release (3.19)},
127 | }
128 |
129 | ## Acknowledgments
130 |
131 | This work was partially supported by grant no. R21HG005912 from the
132 | [National Human Genome Research Institute](https://www.genome.gov/).
133 |
--------------------------------------------------------------------------------
/vignettes/blast.Rmd:
--------------------------------------------------------------------------------
1 | ---
2 | title: "rBLAST: R Interface for the Basic Local Alignment Search Tool"
3 | author: "Michael Hahsler and Anurag Nagar"
4 | vignette: >
5 | %\VignetteIndexEntry{rBLAST: R Interface for the Basic Local Alignment Search Tool}
6 | %\VignetteEngine{knitr::rmarkdown}
7 | %\VignetteEncoding{UTF-8}
8 | output:
9 | rmarkdown::html_vignette
10 | ---
11 |
12 |
13 | ```{r, include = FALSE}
14 | knitr::opts_chunk$set(
15 | collapse = TRUE,
16 | comment = "#>"
17 | )
18 | ```
19 |
20 | ```{r setup}
21 | library("rBLAST")
22 | ```
23 |
24 |
25 | ```{r, include = FALSE}
26 | # only run code if blast+ is installed
27 | run <- has_blast()
28 | ```
29 |
30 | ```{r, echo = FALSE, eval = !run, results='asis'}
31 | cat("**Note: BLAST was not installed when this vignette was built. Some output is not available in this vignette!**")
32 | ```
33 |
34 | # Introduction
35 |
36 | This package provides an R interface to use
37 | a local installation of
38 | the Basic Local Alignment Search Tool (BLAST) executable. This allows the user
39 | to download BLAST databases for querying or to create their own database from
40 | sets of sequences.
41 | The interface integrates BLAST search directly with the Bioconductor
42 | infrastructure by using
43 | the `XStringSet` (e.g., `RNAStringSet`) from the package `Biostrings`.
44 |
45 | This package complements the function in `blastSequences()` in package `annotate`
46 | that runs a BLAST query not locally but by connecting to the NCBI server.
47 |
48 | # System requirements
49 | The BLAST+ software needs to be installed on your system. Installation
50 | instructions are available in this package's
51 | [INSTALL](https://github.com/mhahsler/rBLAST/blob/devel/INSTALL) file and
52 | at \url{https://www.ncbi.nlm.nih.gov/books/NBK569861/}.
53 |
54 | R needs to be able to find the executable. After installing the software,
55 | try in R
56 | ```{r, eval=run}
57 | Sys.which("blastn")
58 | ```
59 |
60 | If the command returns "" instead of the path to the executable,
61 | then you need to set the environment variable called PATH. In R
62 | ```{r, eval=run}
63 | Sys.setenv(PATH = paste(Sys.getenv("PATH"),
64 | "path_to_your_BLAST_installation", sep=.Platform$path.sep))
65 | ```
66 |
67 | # Examples
68 |
69 | ## Use an existing database
70 |
71 | You can download pretrained databases from NCBI at https://ftp.ncbi.nlm.nih.gov/blast/db/.
72 | Here we download the 16S rRNA database. To avoid multiple downloads of the same file, we
73 | use BiocFileCache in function `blast_db_cache` for download. The database compressed and
74 | needs to be expanded.
75 |
76 | ```{r, eval=run}
77 | ## download the 16S Microbial rRNA data base from NCBI
78 | tgz_file <- blast_db_get("16S_ribosomal_RNA.tar.gz")
79 | untar(tgz_file, exdir = "16S_rRNA_DB")
80 | ```
81 |
82 | The extracted database consists of a folder with a set of database files.
83 |
84 | ```{r, eval=run}
85 | list.files("./16S_rRNA_DB/")
86 | ```
87 |
88 | Next, we open the database for querying using the `blast()` function which
89 | returns a BLAST database object.
90 | ```{r, eval=run}
91 | bl <- blast(db = "./16S_rRNA_DB/16S_ribosomal_RNA")
92 | bl
93 | ```
94 |
95 | To demonstrate how to query the database, we read one sequence from an example
96 | FASTA file that
97 | is shipped with the package. Queries are performed using the `predict()` function. The result is a
98 | `data.frame` with one row per match. We will show the first 5 matches.
99 |
100 | ```{r, eval=run}
101 | seq <- readRNAStringSet(system.file("examples/RNA_example.fasta",
102 | package = "rBLAST"
103 | ))[1]
104 | seq
105 |
106 | cl <- predict(bl, seq)
107 | nrow(cl)
108 | cl[1:5, ]
109 | ```
110 |
111 | Additional arguments for BLAST can be passed on using the `BLAST_args`
112 | parameter for `predict()`.
113 | The output format
114 | can be specified using `custom_format`. In the following, we specify a custom format and
115 | that the sequences need to have 99% identity.
116 | See the BLAST Command Line Applications User Manual for details
117 | (https://www.ncbi.nlm.nih.gov/books/NBK279690/).
118 |
119 | ```{r, eval=run}
120 | fmt <- paste(
121 | "qaccver saccver pident length mismatch gapopen qstart qend",
122 | "sstart send evalue bitscore qseq sseq"
123 | )
124 | cl <- predict(bl, seq,
125 | BLAST_args = "-perc_identity 99",
126 | custom_format = fmt
127 | )
128 | cl
129 | ```
130 |
131 |
132 | ```{r, include = FALSE, eval=run}
133 | ## clean up
134 | unlink("16S_rRNA_DB", recursive = TRUE)
135 | ```
136 |
137 | ## Create a custom BLAST database
138 |
139 | The `makeblastdb` utility can be used to create a BLAST database from a
140 | FASTA file with sequences.
141 | The package provides an R interface function of the same name. As an example,
142 | we will create a searchable database from a sequence FASTA file shipped with the package.
143 |
144 | ```{r}
145 | seq <- readRNAStringSet(system.file("examples/RNA_example.fasta",
146 | package = "rBLAST"
147 | ))
148 | seq
149 | ```
150 |
151 | First, we write a FASTA file that will be used by blast to create the database.
152 | ```{r}
153 | writeXStringSet(seq, filepath = "seqs.fasta")
154 | ```
155 |
156 | Next, we create a BLAST database from the file. We need to specify that
157 | the sequences contains RNA and thus nucleotides.
158 | ```{r, eval=run}
159 | makeblastdb("seqs.fasta", db_name = "db/small", dbtype = "nucl")
160 | ```
161 |
162 | Note that it is convenient to specify a folder and a name separated by
163 | a `/` to organize all index files in a folder.
164 |
165 | We can now open the database and use it for queries.
166 | ```{r, eval=run}
167 | db <- blast("db/small")
168 | db
169 | ```
170 |
171 | Check if it finds a 100 nucleotide long fragment from the first sequence
172 | in the training data.
173 |
174 | ```{r, eval=run}
175 | fragment <- subseq(seq[1], start = 101, end = 200)
176 | fragment
177 |
178 | predict(db, fragment)
179 | ```
180 |
181 | We see that the found sequence ID (`ssequid`) matches the query sequence ID
182 | (`qsequid`) and that it matches the correct region in the sequence
183 | (see `sstart` and `send`).
184 |
185 | To permanently remove a database, the folder can be deleted.
186 | ```{r}
187 | unlink("seqs.fasta")
188 | unlink("db", recursive = TRUE)
189 | ```
190 |
191 | # SessionInfo
192 |
193 | ```{r}
194 | sessionInfo()
195 | ```
196 |
--------------------------------------------------------------------------------
/man/blast.Rd:
--------------------------------------------------------------------------------
1 | % Generated by roxygen2: do not edit by hand
2 | % Please edit documentation in R/BLAST.R
3 | \name{blast}
4 | \alias{blast}
5 | \alias{BLAST}
6 | \alias{blast_help}
7 | \alias{print.BLAST}
8 | \alias{predict.BLAST}
9 | \alias{has_blast}
10 | \title{Basic Local Alignment Search Tool (BLAST)}
11 | \usage{
12 | blast(db = NULL, remote = FALSE, type = "blastn")
13 |
14 | blast_help(type = "blastn")
15 |
16 | \method{print}{BLAST}(x, info = TRUE, ...)
17 |
18 | \method{predict}{BLAST}(
19 | object,
20 | newdata,
21 | BLAST_args = "",
22 | custom_format = "",
23 | verbose = FALSE,
24 | keep_tmp = FALSE,
25 | ...
26 | )
27 |
28 | has_blast()
29 | }
30 | \arguments{
31 | \item{db}{the database file to be searched (without file extension).}
32 |
33 | \item{remote}{logical execute the query remotely on a NCBI server. \code{db}
34 | needs to be the name of a database available in the server.
35 | Note: This is very slow since it uses a shared resource at NCBI where jobs
36 | may be queued for execution.}
37 |
38 | \item{type}{BLAST program to use (e.g., \code{blastn}, \code{blastp}, \code{blastx}).}
39 |
40 | \item{info}{show additional data base information.}
41 |
42 | \item{...}{additional arguments are ignored.}
43 |
44 | \item{object, x}{An open BLAST database as a BLAST object created
45 | with \code{\link[=blast]{blast()}}.}
46 |
47 | \item{newdata}{the query as an object of class \link[Biostrings:XStringSet-class]{Biostrings::XStringSet}.}
48 |
49 | \item{BLAST_args}{additional arguments in command-line style.}
50 |
51 | \item{custom_format}{custom format specified by space delimited format
52 | specifiers.}
53 |
54 | \item{verbose}{logical; print progress and debugging information.}
55 |
56 | \item{keep_tmp}{logical; keep temporary files for debugging.}
57 | }
58 | \value{
59 | \itemize{
60 | \item \code{blast()} returns a BLAST database object which can be used for
61 | queries (via \code{predict}).
62 | \item \code{predict} returns a data.frame containing
63 | the BLAST results.
64 | \item \code{has_blast()} returns \code{TRUE} if the blast software installation can be
65 | found and \code{FALSE} otherwise.
66 | }
67 | }
68 | \description{
69 | Open a BLAST database and execute blastn (blastp or blastx)
70 | from blast+ to find sequences matches.
71 | }
72 | \section{Installing BLAST+}{
73 | The BLAST+ software needs to be installed on your system. Installation
74 | instructions are available in this package's
75 | \href{https://github.com/mhahsler/rBLAST/blob/devel/INSTALL}{INSTALL} file and
76 | at \url{https://www.ncbi.nlm.nih.gov/books/NBK569861/}.
77 |
78 | R needs to be able to find the executable. After installing the software,
79 | try in R
80 |
81 | \if{html}{\out{}}\preformatted{Sys.which("blastn")
82 | }\if{html}{\out{
}}
83 |
84 | If the command returns "" instead of the path to the executable,
85 | then you need to set the environment variable called PATH. In R
86 |
87 | \if{html}{\out{}}\preformatted{Sys.setenv(PATH = paste(Sys.getenv("PATH"),
88 | "path_to_your_BLAST_installation", sep=.Platform$path.sep))
89 | }\if{html}{\out{
}}
90 | }
91 |
92 | \section{BLAST Databases}{
93 | You will also need a database. NCBI BLAST databases are updated daily and
94 | may be downloaded via FTP from \url{https://ftp.ncbi.nlm.nih.gov/blast/db/}.
95 | See \code{\link[=blast_db_cache]{blast_db_cache()}} on how to manage a local cache of database files.
96 |
97 | BLAST databases are a set of database files with different extensions.
98 | All files start with the same database name. For example,
99 | \verb{16S_ribosomal_RNA.tar.gz} contains
100 | files starting with \verb{16S_ribosomal_RNA} which is the database name used
101 | for calling \code{blast()}.
102 |
103 | Large databases are separated into several archives numbered \code{00}, \code{01}, etc.
104 | Download all archives and extract the files in the same directory.
105 | All files will have a common name which is the database name used for calling
106 | \code{blast()}.
107 | }
108 |
109 | \examples{
110 | ## check if blastn is correctly installed. Should return the path to the
111 | ## executable
112 | Sys.which("blastn")
113 |
114 | ## only run if blast is installed
115 | if (has_blast()) {
116 | ## check version you should have version 1.8.1+
117 | system2("blastn", "-version")
118 |
119 | ## download the latest version of the 16S Microbial
120 | ## rRNA data base from NCBI using the local chache
121 | tgz_file <- blast_db_get("16S_ribosomal_RNA.tar.gz")
122 |
123 | ## extract the database files
124 | untar(tgz_file, exdir = "./16S_rRNA_DB")
125 |
126 | ## Note the database file can also downloaded without using a
127 | ## cache using download.file
128 | # download.file(paste("https://ftp.ncbi.nlm.nih.gov/blast/db",
129 | # "16S_ribosomal_RNA.tar.gz", sep = "/"),
130 | # "16S_ribosomal_RNA.tar.gz", mode = "wb")
131 | # untar("16S_ribosomal_RNA.tar.gz", exdir = "./16S_rRNA_DB")
132 |
133 | ## A BLAST database is just a set of files. It is a good idea to
134 | ## organize the files in a directory.
135 | list.files("./16S_rRNA_DB")
136 |
137 | ## load a BLAST database (replace db with the location + name of
138 | ## the BLAST DB without the extension)
139 | bl <- blast(db = "./16S_rRNA_DB/16S_ribosomal_RNA")
140 | bl
141 |
142 | ## read a single example sequence to BLAST
143 | seq <- readRNAStringSet(system.file("examples/RNA_example.fasta",
144 | package = "rBLAST"
145 | ))[1]
146 | seq
147 |
148 | ## query a sequence using BLAST
149 | cl <- predict(bl, seq)
150 | cl[1:5, ]
151 |
152 | ## Pass on BLAST arguments (99\% identity) and use a custom format
153 | ## (see BLAST documentation)
154 | fmt <- paste(
155 | "stitle staxid qaccver saccver pident length mismatch",
156 | "gapopen qstart qend",
157 | "sstart send evalue bitscore qseq sseq"
158 | )
159 | cl <- predict(bl, seq,
160 | BLAST_args = "-perc_identity 99",
161 | custom_format = fmt
162 | )
163 | cl
164 |
165 | ## cleanup the example: delete the database files
166 | unlink("./16S_rRNA_DB", recursive = TRUE)
167 | }
168 | }
169 | \references{
170 | BLAST Help - BLAST+ Executable:
171 | https://blast.ncbi.nlm.nih.gov/doc/blast-help/downloadblastdata.html
172 |
173 | BLAST Command Line Applications User Manual,
174 | https://www.ncbi.nlm.nih.gov/books/NBK279690/
175 | }
176 | \seealso{
177 | Other blast:
178 | \code{\link{blast_db_cache}()},
179 | \code{\link{makeblastdb}()}
180 | }
181 | \author{
182 | Michael Hahsler
183 | }
184 | \concept{blast}
185 | \keyword{model}
186 |
--------------------------------------------------------------------------------
/inst/examples/RNA_example.fasta:
--------------------------------------------------------------------------------
1 | >1675 AB015560.1 deep-sea sediment clone BD4-10 k__Bacteria; p__Proteobacteria; c__Deltaproteobacteria; o__Desulfobacterales; f__Nitrospinaceae; g__Nitrospina; otu_3187
2 | AGAGUUUGAUCCUGGCUCAGAACGAACGCUGGCGGCGUGCCUAACACAUGCAAGUCGAACGAGAAAGUCCCUUCGGGGGC
3 | UAGUAAAGUGGCGCAAGGGUGAGUAACACGUGAAUAAUCUGCCCUCAAACCUGGGAUAACUUCGCGAAAGUGAAGCUAAU
4 | ACCGGAUAAGACCACGUUUCGCAAGAAACGCGGUAAAAGGAGCCUCAAACUUCAUUUGAGGAUGAGUUCGCGGACCAUUA
5 | GCUUGUUGGCGGGAUAAAAGCCCACCAAGGCUUCGAUGGUUAGCCGGCCUGAGAGGGUGAUCGGCCACACUGGAACUGAG
6 | ACACGGUCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGCGCAAUGGGCGAAAGCCUGACGCAGCAACGCCGCGUG
7 | AGGGAUGAAGGCUUUAGGGUUGUAAACCUCUGUCGAAUGGGAAGAAUUAUGACGGUACCAUUAAAGGAAGCCCCGGCUAA
8 | CUCCGUGCCAGCAGCCGCGGUAAUACGGAGGGGGCAAGCGUUGUUCGGAAUUAUUGGGCGUAAAGCGUAUGUAGGCGGUU
9 | AAAUAAGUCAGGUGUGUAAGCCCAGGGCUCAACCCUGGAAUUGCAUUUGAAACUAUUUGACUUGAGGUCGGGAGAGGAAA
10 | GCGGAAUUCCCAGUGUAGCGGUGAAAUGCAUUGAUAUUGGGAAGAACAUCGGUGGCGAAGGCGGCUUUCUGGUCCGAUUC
11 | UGACGCUGAGAUACGAAAGCUAGGGGAGCAAACGGGAUUAGAUACCCCGGUAGUCCUAGCCGUAAACGAUGGGUACUAGG
12 | UGUAGGGGGUAUCGAUCCCCUCUGUGUCGCAGCUAACGCAUUAAGUACCCCGCCUGGGGAGUACGGUCGCAAGGCUGAAA
13 | CUCAAAGGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGACGCAACGCGAAGAACCUUACCUGGA
14 | UUUGACAUGCAUGGGAAAGCUCUAGAGAUAGAGCCCUCUUCGGACUCAUGUGCAGGUGCUGCAUGGCUGUCGUCAGCUCG
15 | UGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCCUACCUUUAGUUGCCAGCGAGUCAUGUCGGGAACUCUA
16 | GAGGGACUGCCGGUGAUAAACCGGAGGAAGGUGGGGAUGACGUCAAGUCCUCAUGGCCUUUAUAUCCAGGGCUACACACG
17 | UGCUACAAUGGUCGGUACAAAGAGUUGCAAUACCGCGAGGUUGAGCUAAUCUCAAAAAACCGAUCUCAGUUCGGAUUGGA
18 | GUCUGCAACUCGACUCCAUGAAGCUGGAAUCGCUAGUAAUCGUGGAUCAGCAUGCCACGGUGAAUACGUUCCCGGGCCUU
19 | GUACACACCGCCCGUCACACCAUGAAAGCUGGUCGUACCAGAAGUCAACAAGCCAACCCUCACGGGAGGCUACUGCCUAA
20 | GGUAUGGCUGGUGAUCGGGGUGAAGUCGUAACAAGGUAACC
21 | >4399 D14432.1 Rhodovibrio salinarum str. NCIMB2243 k__Bacteria; p__Proteobacteria; c__Alphaproteobacteria; o__Rhodospirillales; f__Rhodospirillaceae; g__Rhodovibrio; s__Rhodovibrio salinarum; otu_2816
22 | GCUGGCGGCAGGCCUAACACAUGCAAGUCGAACGGGGACCUUCGGGUCUUACGUGGCGCACGGGUGAGUAACGCGUGGGA
23 | AUCUACCCUAAAGUCGGGGAUAACCGCUGGAAACGGCGGCUAAUACCGGAUACGCCCUGAGGGGCAAAGCUUUUGCGCUU
24 | UAGGAGGAGCCCGCGUCCGAUUAGCUAGUUGGUGGGGUAAAGGCCUACCAAGGCUGCGAUCGGUAGCUGGUCUGAGAGGA
25 | UGAUCAGCCACACUGGGACUGAGACACGGCCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUCUUGGACAAUGGGGGCAA
26 | CCCUGAUCCAGCCAUGCCGCGUGGGUGAAGAAGGCCUUAGGGUUGUAAAGCCCUUUCGGCGGGGAAGAUGAUGACGGUAC
27 | CCGCAGAAGAAGCCCCGGCUAACUCCGUGCCAGCAGCNNNGGUAAUACGGAGGGGGCNAGCGUUGUUCGGAAUCACUGGG
28 | CGUAAAGGGCGCGUAGGCGGACCAGCAAGUCAGGGGUGAAAGCCCUGGGCUCAACCUAGGAAGUGCCCUUGAAACUGCAG
29 | GUCUUGAGUCCGGGAGAGGAGAGCGGAAUUCCCAGUGUAGAGGUGAAAUUCGUAGAUAUUGGGAAGAACACCGGUGGCGA
30 | AGGCGGCUCUCUGGACCGGCACUGACGCUGAGGCGCGAAAGCGUGGGGAGCAAACAGGAUUAGAUACCCUGGUAGUCCAC
31 | GCCGUAAACGAUGUGCGCUAGCCGUUGGGCAACCUAGUUGUUCAGUGGCGCAGCCAACGCAUUAAGCGCACCGCCUGGGG
32 | AGUACGGCCGCAAGGCUAAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGAAGCA
33 | ACGCGCAGAACCUUACCAGCCCUUGACAUGUCCGUCGCGCACGGGAGACCGAGGCUUUCAGUUCGGCUGGACGGAACACA
34 | GGUGCUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCCUGUCCUUAGUU
35 | GCUAUCGGUUCGGUUGAGCACUCUAGGGAGACUGCCGGUGAUAAGCCGGAGGAAGGCGGGGAUGACGUCAAGUCCUCAUG
36 | GCCCUUAUGGGCUGGGCUACACACGUGCUACAAUGGCGGCGACAGAGGGAAGCAAGCCCGCGAGGGUGCGCGAAUCUCCA
37 | AACGCCGUCUCAGUUCGGAUCGCAGUCUGCAACUCGACUGCGUGAAGCCGGAAUCGCUAGUAAUCGCGGAUCAGAAUGCC
38 | GCGGUGAAUACGUUCCCGGGCCUUGUACACACNGCCCGUCACACCAUGGGAGUUGGCUUUACCCGAAGCCGGUGCGCUAA
39 | CCCGCAAGGGAGGCAGCCGACCACGGUAAGGUCAGCGACUGGGG
40 | >4403 X72908.1 Roseococcus thiosulfatophilus str. RB-3 Yurkov strain Drews k__Bacteria; p__Proteobacteria; c__Alphaproteobacteria; o__Rhodospirillales; f__Acetobacteraceae; g__Roseococcus; otu_2785
41 | GGAAUGCUNAACACAUGCAAGUCGCACGGGCAGCAAUGUCAGUGGCGGACGGGUGAGUAACGCGUAGGAACGUGUCCGAG
42 | GGUGGGGGAUAACGCUGGGAAACUGGCGCUAAUACCGCAUAUCUCCUGAGGGAGAAAGCAGCGAUGCGCCCAUGGAGCGG
43 | CCUGCGUCCGAUUAGCUAGUUGGUGGGGUAAAGGCUUACCAAGGCGACGAUCGGUAGCUGGUCUGAGAGGAUGAUCAGCC
44 | ACACUGGGACUGAGACACGGCCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGGACAAUGGGCGCAAGCCUGAUCC
45 | AGCAAUUCCGCGUGGGUGAAGAAGGUCUUCGGAUUGUAAAGCCCUUUCGACAGGGACGAUGAUGACGGUACCUGUAGAAG
46 | AAGCCCCGGCUAACUUCGUGCCAGCAGCCGCGGUAAUACGAAGGGGGCUAGCGUUGCUCGGAAUGACUGGGCGUAAAGGG
47 | CGCGUAGGCGGCACACACAGUCAGGCGUGAAAUUCCCGGGCUUAACCUGGGGACUGCGCUUGAUACAUGUGAGCUAGAGG
48 | AUGGAAGAGGCUCGUGGAAUUCCCAGUGUAGAGGUGAAAUUCGUAGAUAUUGGGAGGAACACCGGUGGCGAAGGCGGCGA
49 | ACUGGUCCAUUACUGACGCUGAGGCGCGAAAGCGUGGGGAGAAAACAGGAUUAGAUACCCUGGUAGUCCACNCUGUAAAC
50 | GAUGUUCGCUGGAUGUUGGGUGACNUANUCACUCAGUGUCGUAACUAACGCGAUAANCGCNCCGCCUGGGGAGUACGGCC
51 | NCAAGGUUAAAACUCAAAGGAAUUGNCGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGACGCAACGCGCAGA
52 | ACCUUACCAGCUCUUGACAUCUGUCGGACAUCGCAGAGAUGCGUUGGUGUUCCGCAAGGGACGGCAAGACAGGUGCUGCA
53 | UGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUCGCCUCUAGUUGCCAGCAUG
54 | UUUGGGUGGGCACUCUAGAGGAGCUCCCGGUGACAAACCGGAGGAAGGUGGGGAUGACGUCAAGUCCUCAUGGCCCUUAU
55 | GAGCUGGGCUACACACGUGCUACAAUGGCGGUGACAAUGGGAAGCCAGGUCGCGAGNCCGAGCGGAUCCCAAAAAGCCGU
56 | CUCAGUUCAGAUUGCACUCUGCAACUCGGGUGCAUGAAGGUGGAAUCGCUAGUAAUCGCGGAUCAGCAUGCCGCGGUGAA
57 | UACGUUCCCGGGCCUUGUNCACACCGCCCGUCACACCAUGGGAGUUGGUUCUACCUUAAGCCGAUGUGGCAUCCGCAAGG
58 | AGCUAGUCGACCACGGUAGGGUCAGCGACUGGGGUGUAGUCGNAACAAGGUAGCCGUAGGGGAACC
59 | >4404 AF173825.1 Antarctic clone LB3-94 k__Bacteria; p__Proteobacteria; c__Alphaproteobacteria; o__Rhodospirillales; f__Acetobacteraceae; g__Roseococcus; otu_2785
60 | GCUGGCGGAAUGCUUAACACAUGCAAGUCGCACGGGGGUUUCGGCCUUAGUGGCGGACGGGUGAGUAACGCGUAGGAAUG
61 | UGUCCGAGGGUGGGGGACAACGUUGGGAAACNGACGCUAAUACCGCAUAUCUCCUGAGGGAGAAAGCCGUGAGGCGCCCA
62 | UGGAGCAGCCUGCGUACGAUUAGCUUGUUGGUGGGGUAAAGGCUUACCAAGGCUACGAUCGUUAGCUGGUCUGAGAGGAU
63 | GAUCAGCCACACUGGAACUGAGACACGGUCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGGACAAUGGGCGCAAG
64 | CCUGAUCCAGCAAUUCCGCGUGGGUGAAGAAGGUCUUCGGAUUGUAAAGCCCUUUCGUUGGGGACGAUGAUGACGGUACC
65 | CAAAGAAGAAGCCCCGGCUAACUUCGUGCCAGCAGCCGCGGUAAUACGAAGGGGGCUAGCGUUGCUCGGAAUGACUGGGC
66 | GUAAAGGGUGCGUAGGCGGCAUAACUAGUCAGGCGUGAAAUUCCUGGGCUUAACCUGGGGACUGCGUUUGAUACGGUUGG
67 | GCUAGAGGAUGGAAGAGGCUCGUGGAAUUCCCAGUGUAGAGGUGAAAUUCGUAGAUAUUGGGAAGAACACCGGUGGCGAA
68 | GGCGGCGAGCUGGUCCAUUACUGACGCUGAGGCACGAAAGCGUGGGGAGCAAACAGGAUUAGAUACCCUGGUAGUCCACG
69 | CUGUAAACGAUGUGCGCUGGAUGUUGGGUAACUUAGUUACUCAGUGUCGUAGCUAACGCGAUAAGCGCACCGCCUGGGGA
70 | GUACGGCCGCAAGGUUGAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUNGAAGCAA
71 | CGCGCAGAACCUUACCAGCUCUUGACAUCUGUCGGAGUUCUCGGAGACGAGAAUGUGCCCGCAAGGGAACGGCAAGACAG
72 | GUGCUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUCGCCUUUAGUUG
73 | CCAGCACGUUUGGGUGGGCACUCUAGAGGAACUGCCGGUGACAAGCCGGAGGAAGGUGGGGAUGACGUCAAGUCCUCAUG
74 | GCCCUUAUGAGCUGGGCUACACACGUGCUACAAUGGCGGUGACAAUGGGAAGCCAGGUCGCGANGCCGAGCGGAUCCCAA
75 | AAAGCCGUCUCAGUUCAGAUUGCACUCUGCAACUCGGGUGCAUGAANGUGGAAUUGCUAGUAAUCGCGGAUCAGCAUGCC
76 | GCGGUGAAUACGUUCCCGGGCCUUGUACACCACGCCCGUCACACCAUGGGAGUUGGUUUUACCUUAGGUGUCUAGGCUAA
77 | CC
78 | >4411 Y07647.2 Drentse grassland soil clone vii k__Bacteria; p__Proteobacteria; c__Alphaproteobacteria; o__Rhodospirillales; f__Acetobacteraceae; Unclassified; otu_2752
79 | AGAGUUUGAUUAUGGCUCAGAGCGAACGCUGGCGGCAUGCUUAACACAUGCAAGUCGCACGGGCAGGGGCAACCCUGUCA
80 | GUGGCGGACGGGUGAGUAACGCGUAGGUAUCUAUCCUUGGGUGGGGGACAACUGUGGGAAACUACAGCUAAUACCGCAUG
81 | AUGACCGAGGUCCAAAGCUCGCGAGAGCGCCUGGGGAGGAGCCUGCGUACGAUUAGCUAGUUGGUGGGGUAAAGGCCUAC
82 | CAAGGCGACGAUCGUUAGCUGGUCUGAGAGGAUGAUCAGCCACAUUGGGACUGAGACACGGCCCAAACUCCUACGGGAGG
83 | CAGCAGUGGGGAAUAUUGGACAAUGGGCGCAAGCCUGAUCCAGCAAUGCCGCGUGUGUGAAGAAGUCUUCGGAUUGUAAA
84 | GCACUUUCGACGGGGACGAUGAUGACCGUACCCGUUAAAAAAACCCCCGGCUAACUUCGUGCCAGCAGCCGCGGUAAUAC
85 | GAAGGGGGGUAGCGUUGCUCGGAUUGACUGGGCGUAAAGGGCGCGUAGGCGGUUUGCACAGUCAGGCGUGAAAUUCCUGG
86 | GCUCAACCUGGGGGCUGCGCCUGAUACAUGCAAACUUGAGUUCGGAAGAGGGUCGUGGAAUUCCCAGUGUAGAGGUGAAA
87 | UUCGUAGAUAUUGGGAAGAACACCGGUGGCGAAGGCGGCGACCCGGUCCGUUACUGACGCUGAGGCGCGAAAGCGUGGGG
88 | AGCAAACAGGAUUAGAUACCCUGGUAGUCCACGCUGUAAACGAUGUGUGCUGGAUGUUGGGCGACGUAGUCGUUCAGUGU
89 | CGUAGCUAACGCGAUAAGCACACCGCCUGGGGAGUACGGCCGCAAGGUUGAAACUCAAAGGAAUUGACGGGGGCCCGGAC
90 | AAGCGGUGGAGCAUGUGGUUUAAUUCAAAGCAACGCGCAGAACCUUACCAGGAUUUGACAUGGAGCGGACGUGUCGAGAG
91 | AUCGACAUUCCCGCAAGGGCCGCUCGCACAGGUGCUGCAUGGCUGUCGUCAGCUCGUUUCGUGAGAUGUUGGGUUAAGUC
92 | CCGCAACGAGCGUCACCCUCGCUUUCAGUUGCCAUCAGGUUUGGCUGGGCACCCUGAAGGAACUGCCGGUGACAAGCCGG
93 | AGGAAGGUGGGGAUGACGUCAAGUCCUCAUGGCCCUUAUGUCCUGGGCUACACACGUGCUACAAUGGCGGUGACAGUGGG
94 | AAGCCAGGUCGCGAGACCGAGCUGAUCCCGAAAAGCCGUCUCAGUUCGGAUUGCACUCUGCAACUCGAGUGCAUGAAGGU
95 | GGAAUCGCUAGUAAUCGCGGAUCAGCACGCCGCGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACACCAUGG
96 | CAGUUGGUUUGACCUUAAGCNGGUGCGCCAACCCGCAAGGGGGGCAGCCAACCACGGUCGGGUCAGCGACUGGGGUGAAG
97 | UCGUAACAAGGUAACCGU
98 |
--------------------------------------------------------------------------------
/R/BLAST.R:
--------------------------------------------------------------------------------
1 | #######################################################################
2 | # rBLAST - Interface to BLAST
3 | # Copyright (C) 2015 Michael Hahsler and Anurag Nagar
4 | #
5 | # This program is free software; you can redistribute it and/or modify
6 | # it under the terms of the GNU General Public License as published by
7 | # the Free Software Foundation; either version 2 of the License, or
8 | # any later version.
9 | #
10 | # This program is distributed in the hope that it will be useful,
11 | # but WITHOUT ANY WARRANTY; without even the implied warranty of
12 | # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
13 | # GNU General Public License for more details.
14 | #
15 | # You should have received a copy of the GNU General Public License along
16 | # with this program; if not, write to the Free Software Foundation, Inc.,
17 | # 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
18 |
19 |
20 | #' Basic Local Alignment Search Tool (BLAST)
21 | #'
22 | #' Open a BLAST database and execute blastn (blastp or blastx)
23 | #' from blast+ to find sequences matches.
24 | #'
25 | #' # Installing BLAST+
26 | #' The BLAST+ software needs to be installed on your system. Installation
27 | #' instructions are available in this package's
28 | #' [INSTALL](https://github.com/mhahsler/rBLAST/blob/devel/INSTALL) file and
29 | #' at \url{https://www.ncbi.nlm.nih.gov/books/NBK569861/}.
30 | #'
31 | #' R needs to be able to find the executable. After installing the software,
32 | #' try in R
33 | #' ```
34 | #' Sys.which("blastn")
35 | #' ```
36 | #'
37 | #' If the command returns "" instead of the path to the executable,
38 | #' then you need to set the environment variable called PATH. In R
39 | #' ```
40 | #' Sys.setenv(PATH = paste(Sys.getenv("PATH"),
41 | #' "path_to_your_BLAST_installation", sep=.Platform$path.sep))
42 | #' ```
43 | #' # BLAST Databases
44 | #' You will also need a database. NCBI BLAST databases are updated daily and
45 | #' may be downloaded via FTP from \url{https://ftp.ncbi.nlm.nih.gov/blast/db/}.
46 | #' See [blast_db_cache()] on how to manage a local cache of database files.
47 | #'
48 | #' BLAST databases are a set of database files with different extensions.
49 | #' All files start with the same database name. For example,
50 | #' `16S_ribosomal_RNA.tar.gz` contains
51 | #' files starting with `16S_ribosomal_RNA` which is the database name used
52 | #' for calling `blast()`.
53 | #'
54 | #' Large databases are separated into several archives numbered `00`, `01`, etc.
55 | #' Download all archives and extract the files in the same directory.
56 | #' All files will have a common name which is the database name used for calling
57 | #' `blast()`.
58 | #' @name blast
59 | #' @aliases blast BLAST
60 | #' @family blast
61 | #' @param db the database file to be searched (without file extension).
62 | #' @param type BLAST program to use (e.g., `blastn`, `blastp`, `blastx`).
63 | #' @param object,x An open BLAST database as a BLAST object created
64 | #' with [blast()].
65 | #' @param newdata the query as an object of class [Biostrings::XStringSet].
66 | #' @param remote logical execute the query remotely on a NCBI server. `db`
67 | #' needs to be the name of a database available in the server.
68 | #' Note: This is very slow since it uses a shared resource at NCBI where jobs
69 | #' may be queued for execution.
70 | #' @param BLAST_args additional arguments in command-line style.
71 | #' @param custom_format custom format specified by space delimited format
72 | #' specifiers.
73 | #' @param info print information about the database (needs the executable
74 | #' `blastdbcmd` in the
75 | #' path).
76 | #' @param verbose logical; print progress and debugging information.
77 | #' @param keep_tmp logical; keep temporary files for debugging.
78 | #' @param info show additional data base information.
79 | #' @param ... additional arguments are ignored.
80 | #' @return
81 | #' * `blast()` returns a BLAST database object which can be used for
82 | #' queries (via `predict`).
83 | #' * `predict` returns a data.frame containing
84 | #' the BLAST results.
85 | #' * `has_blast()` returns `TRUE` if the blast software installation can be
86 | #' found and `FALSE` otherwise.
87 | #' @author Michael Hahsler
88 | #' @references BLAST Help - BLAST+ Executable:
89 | #' https://blast.ncbi.nlm.nih.gov/doc/blast-help/downloadblastdata.html
90 | #'
91 | #' BLAST Command Line Applications User Manual,
92 | #' https://www.ncbi.nlm.nih.gov/books/NBK279690/
93 | #' @keywords model
94 | #' @examples
95 | #' ## check if blastn is correctly installed. Should return the path to the
96 | #' ## executable
97 | #' Sys.which("blastn")
98 | #'
99 | #' ## only run if blast is installed
100 | #' if (has_blast()) {
101 | #' ## check version you should have version 1.8.1+
102 | #' system2("blastn", "-version")
103 | #'
104 | #' ## download the latest version of the 16S Microbial
105 | #' ## rRNA data base from NCBI using the local chache
106 | #' tgz_file <- blast_db_get("16S_ribosomal_RNA.tar.gz")
107 | #'
108 | #' ## extract the database files
109 | #' untar(tgz_file, exdir = "./16S_rRNA_DB")
110 | #'
111 | #' ## Note the database file can also downloaded without using a
112 | #' ## cache using download.file
113 | #' # download.file(paste("https://ftp.ncbi.nlm.nih.gov/blast/db",
114 | #' # "16S_ribosomal_RNA.tar.gz", sep = "/"),
115 | #' # "16S_ribosomal_RNA.tar.gz", mode = "wb")
116 | #' # untar("16S_ribosomal_RNA.tar.gz", exdir = "./16S_rRNA_DB")
117 | #'
118 | #' ## A BLAST database is just a set of files. It is a good idea to
119 | #' ## organize the files in a directory.
120 | #' list.files("./16S_rRNA_DB")
121 | #'
122 | #' ## load a BLAST database (replace db with the location + name of
123 | #' ## the BLAST DB without the extension)
124 | #' bl <- blast(db = "./16S_rRNA_DB/16S_ribosomal_RNA")
125 | #' bl
126 | #'
127 | #' ## read a single example sequence to BLAST
128 | #' seq <- readRNAStringSet(system.file("examples/RNA_example.fasta",
129 | #' package = "rBLAST"
130 | #' ))[1]
131 | #' seq
132 | #'
133 | #' ## query a sequence using BLAST
134 | #' cl <- predict(bl, seq)
135 | #' cl[1:5, ]
136 | #'
137 | #' ## Pass on BLAST arguments (99% identity) and use a custom format
138 | #' ## (see BLAST documentation)
139 | #' fmt <- paste(
140 | #' "stitle staxid qaccver saccver pident length mismatch",
141 | #' "gapopen qstart qend",
142 | #' "sstart send evalue bitscore qseq sseq"
143 | #' )
144 | #' cl <- predict(bl, seq,
145 | #' BLAST_args = "-perc_identity 99",
146 | #' custom_format = fmt
147 | #' )
148 | #' cl
149 | #'
150 | #' ## cleanup the example: delete the database files
151 | #' unlink("./16S_rRNA_DB", recursive = TRUE)
152 | #' }
153 | #' @importFrom utils read.table
154 | #' @importFrom methods is
155 | #' @import Biostrings
156 | #' @export
157 | blast <- function(db = NULL, remote = FALSE, type = "blastn") {
158 | if (is.null(db)) {
159 | stop("No BLAST database specified!")
160 | }
161 |
162 | if (remote) {
163 | return(structure(list(db = db, type = type, remote = TRUE),
164 | class = "BLAST"))
165 | }
166 |
167 | db <- file.path(normalizePath(dirname(db)), basename(db))
168 | dbfiles <- Sys.glob(paste0(db, "*"))
169 | if (length(dbfiles) < 1) {
170 | stop("BLAST database does not exist! (tried to open: ", db, ")")
171 | }
172 |
173 | ### check for spaces
174 | if (length(grep(" ", db)) > 0) {
175 | stop(
176 | "Database name or path contains spaced.",
177 | " Rename or move database to remove spaces (current path: ",
178 | db,
179 | ")"
180 | )
181 | }
182 |
183 | ### check if executable is available
184 | .findExecutable(type)
185 |
186 | ### check database
187 | status <-
188 | try(system2(
189 | .findExecutable("blastdbcmd"),
190 | args = c("-db", db, "-info"),
191 | stdout = FALSE
192 | ))
193 | if (status != 0) {
194 | stop("Problem loading the database! (trying to execute: blastdbcmd)")
195 | }
196 |
197 | structure(list(db = db, remote = FALSE, type = type), class = "BLAST")
198 | }
199 |
200 | #' @rdname blast
201 | #' @export
202 | blast_help <- function(type = "blastn") {
203 | system2(.findExecutable(c(type)), args = c("-help"))
204 | }
205 |
206 | #' @rdname blast
207 | #' @export
208 | print.BLAST <- function(x, info = TRUE, ...) {
209 | cat("BLAST Database\nLocation:", x$db, "\n")
210 | cat("BLAST Type:", x$type, "\n")
211 |
212 | if (info) {
213 | out <- system2(
214 | .findExecutable("blastdbcmd"),
215 | args = c(
216 | "-db", x$db,
217 | "-info"
218 | ),
219 | stdout = TRUE
220 | )
221 | cat(paste(out, collapse = "\n"))
222 | cat("\n")
223 | }
224 | }
225 |
226 | #' @rdname blast
227 | #' @export
228 | predict.BLAST <-
229 | function(object,
230 | newdata,
231 | BLAST_args = "",
232 | custom_format = "",
233 | verbose = FALSE,
234 | keep_tmp = FALSE,
235 | ...) {
236 | db <- object$db
237 | remote <- object$remote
238 | if (is.null(remote)) {
239 | remote <- FALSE
240 | }
241 | exe <- object$type
242 | x <- newdata
243 |
244 | ## get temp files and change working directory
245 | wd <- tempdir()
246 | dir <- getwd()
247 | temp_file <- basename(tempfile(tmpdir = wd))
248 | on.exit({
249 | if (!keep_tmp) {
250 | file.remove(Sys.glob(paste(temp_file, "*", sep = "")))
251 | } else {
252 | cat("Temporary BLAST files kept in", wd, "\n")
253 | }
254 | setwd(dir)
255 | })
256 |
257 | if (verbose) {
258 | cat("Starting BLAST\n * all files are written to:", wd, "\n")
259 | }
260 | setwd(wd)
261 |
262 | infile <- paste(temp_file, ".fasta", sep = "")
263 | outfile <- paste(temp_file, "_BLAST_out.txt", sep = "")
264 |
265 | if (verbose) {
266 | cat(" * writing FASTA query sequences to", infile, "\n")
267 | }
268 | writeXStringSet(x, infile, append = FALSE, format = "fasta")
269 |
270 | cmd <- .findExecutable(exe)
271 | args <- c(
272 | "-db",
273 | db,
274 | ifelse(remote, "-remote", ""),
275 | "-query",
276 | infile,
277 | "-out",
278 | outfile,
279 | '-outfmt "10 delim=@ ',
280 | ### 10 is CSV
281 | custom_format,
282 | '"',
283 | BLAST_args
284 | )
285 |
286 | if (verbose) {
287 | cat(
288 | " * running", .findExecutable(exe),
289 | args, "\n"
290 | )
291 | }
292 |
293 | system2(
294 | command = cmd,
295 | args = args
296 | )
297 |
298 | ## rdp output column names
299 | if (custom_format == "") {
300 | c_names <- c(
301 | "qseqid",
302 | "sseqid",
303 | "pident",
304 | "length",
305 | "mismatch",
306 | "gapopen",
307 | "qstart",
308 | "qend",
309 | "sstart",
310 | "send",
311 | "evalue",
312 | "bitscore"
313 | )
314 | } else {
315 | c_names <- unlist(strsplit(custom_format, split = " +"))
316 | }
317 |
318 | ## read and parse BLAST output
319 | hits <- length(readLines(outfile))
320 | if (verbose) {
321 | cat(" * reading results from", outfile, "\n")
322 | cat(" * number of lines in results file:", hits, "\n")
323 | }
324 |
325 | if (length(readLines(outfile)) == 0L) {
326 | return(data.frame(matrix(ncol = length(c_names), nrow = 0)))
327 | }
328 |
329 | cl_tab <-
330 | read.table(outfile,
331 | sep = "@",
332 | quote = "",
333 | col.names = c_names
334 | )
335 |
336 |
337 | if (verbose) {
338 | cat(" * found", nrow(cl_tab), "matches.\n")
339 | }
340 |
341 | cl_tab
342 | }
343 |
344 | #' @rdname blast
345 | #' @export
346 | has_blast <- function() {
347 | length(.findExecutable("blastn",
348 | interactive = FALSE
349 | )) != 0
350 | }
351 |
--------------------------------------------------------------------------------
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--------------------------------------------------------------------------------
6 |
7 | ```{r echo=FALSE, results = 'asis'}
8 | pkg <- "rBLAST"
9 |
10 | source("https://raw.githubusercontent.com/mhahsler/pkg_helpers/main/pkg_helpers.R")
11 | pkg_title(pkg, CRAN = FALSE, Bioc = TRUE)
12 | ```
13 |
14 | Interfaces the Basic Local Alignment Search Tool (BLAST) to search genetic sequence data bases with the Bioconductor infrastructure. This includes
15 | interfaces to `blastn`, `blastp`, `blastx`, and `makeblastdb`.
16 | The BLAST software needs to be downloaded and installed separately.
17 |
18 | Other R interfaces for bioinformatics are also available:
19 |
20 | * [rRDP](https://bioconductor.org/packages/rRDP): Interface to the RDP Classifier
21 | * [rMSA](https://mhahsler.r-universe.dev/rMSA): Interface for Popular Multiple
22 | Sequence Alignment Tools including ClustalW, MAFFT, MUSCLE, and Kalign
23 |
24 |
25 | ## Installation
26 |
27 | 1. Install the BLAST software by following the instructions in the
28 | [INSTALL](https://github.com/mhahsler/rBLAST/blob/devel/INSTALL) file.
29 |
30 | 2. Install the latest version of the R package
31 | ```{r eval = FALSE}
32 | if (!require("BiocManager", quietly = TRUE)) {
33 | install.packages("BiocManager")
34 | }
35 |
36 | # The following initializes usage of Bioc devel
37 | BiocManager::install(version='devel')
38 |
39 | BiocManager::install("rBLAST")
40 | ```
41 |
42 | ## Usage
43 |
44 | ```{r, message=FALSE}
45 | library(rBLAST)
46 | ```
47 |
48 | Download the prebuilt 16S Microbial data base from NCBI's ftp server at:
49 | https://ftp.ncbi.nlm.nih.gov/blast/db/
50 |
51 | ```{r}
52 | tgz_file <- blast_db_get("16S_ribosomal_RNA.tar.gz")
53 | untar(tgz_file, exdir = "16S_rRNA_DB")
54 | ```
55 |
56 | Load the downloaded BLAST database.
57 | ```{r}
58 | bl <- blast(db = "./16S_rRNA_DB/16S_ribosomal_RNA")
59 | bl
60 | ```
61 |
62 | Load some test sequences shipped with the package.
63 |
64 | ```{r}
65 | seq <- readRNAStringSet(system.file("examples/RNA_example.fasta",
66 | package = "rBLAST"
67 | ))
68 | seq
69 | ```
70 |
71 | Query the BLAST database to find matches for the first test sequence
72 | with a 99% percent identity or higher.
73 |
74 | ```{r}
75 | cl <- predict(bl, seq[1, ], BLAST_args = "-perc_identity 99")
76 | cl
77 | ```
78 |
79 | ```{r, include=FALSE}
80 | unlink("./16S_rRNA_DB", recursive = TRUE)
81 | ```
82 |
83 | ## Citation Request
84 |
85 | ```{r, echo=FALSE, results='asis', comment= ""}
86 | pkg_citation(pkg)
87 | ```
88 |
89 | ## Acknowledgments
90 | This work was partially supported by grant no. R21HG005912 from the [National Human Genome Research Institute](https://www.genome.gov/).
91 |
92 |
--------------------------------------------------------------------------------
/R/makeblastdb.R:
--------------------------------------------------------------------------------
1 | #######################################################################
2 | # rBLAST - Interface to BLAST
3 | # Copyright (C) 2015 Michael Hahsler and Anurag Nagar
4 | #
5 | # This program is free software; you can redistribute it and/or modify
6 | # it under the terms of the GNU General Public License as published by
7 | # the Free Software Foundation; either version 2 of the License, or
8 | # any later version.
9 | #
10 | # This program is distributed in the hope that it will be useful,
11 | # but WITHOUT ANY WARRANTY; without even the implied warranty of
12 | # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
13 | # GNU General Public License for more details.
14 | #
15 | # You should have received a copy of the GNU General Public License along
16 | # with this program; if not, write to the Free Software Foundation, Inc.,
17 | # 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
18 |
19 | #' Create BLAST Databases
20 | #'
21 | #' Call the `makeblastdb` utility to create a BLAST database from a FASTA file.
22 | #'
23 | #' R needs to be able to find the executable (mostly an issue with Windows).
24 | #' Try `Sys.which("makeblastdb")` to see if the program is properly
25 | #' installed.
26 | #'
27 | #' Use `blast_help("makeblastdb")` to see all possible extra arguments.
28 | #' Arguments need to be formated in exactly the way as they would be used for
29 | #' the command line tool.
30 | #'
31 | #' @family blast
32 | #' @param file input file/database name. **Note** that the filename and path
33 | #' cannot contain whitespaces.
34 | #' @param dbtype molecule type of target db (`"nucl"` or `"prot"`).
35 | #' @param db_name name of the database (files).
36 | #' @param hash_index logical; create index of sequence hash values.
37 | #' @param args string including additional arguments passed on
38 | #' to `makeblastdb`.
39 | #' @param verbose logical; show the progress report produced by `makeblastdb`?
40 | #' @author Michael Hahsler
41 | #' @returns Nothing but creates a BLAST database directory.
42 | #' @keywords model
43 | #' @examples
44 | #' ## check if makeblastdb is correctly installed
45 | #' Sys.which("makeblastdb")
46 | #'
47 | #' ## only run if blast is installed
48 | #' if (has_blast()) {
49 | #' ## see possible arguments
50 | #' blast_help("makeblastdb")
51 | #'
52 | #' ## read some example sequences
53 | #' seq <- readRNAStringSet(system.file("examples/RNA_example.fasta",
54 | #' package = "rBLAST"
55 | #' ))
56 | #'
57 | #' ## 1. write the FASTA file
58 | #' writeXStringSet(seq, filepath = "seqs.fasta")
59 | #'
60 | #' ## 2. make database
61 | #' makeblastdb(file = "seqs.fasta", db_name = "db/small", dbtype = "nucl")
62 | #'
63 | #' ## 3. open database
64 | #' db <- blast("db/small")
65 | #' db
66 | #'
67 | #' ## 4. perform search (first sequence in the db should be a perfect match)
68 | #' predict(db, seq[1])
69 | #'
70 | #' ## clean up
71 | #' unlink("seqs.fasta")
72 | #' unlink("db", recursive = TRUE)
73 | #' }
74 | #' @export
75 | makeblastdb <- function(file, db_name = NULL, dbtype = "nucl",
76 | hash_index = TRUE,
77 | args = "", verbose = TRUE) {
78 | system2(
79 | .findExecutable("makeblastdb"),
80 | paste(
81 | "-in",
82 | file,
83 | "-dbtype",
84 | dbtype,
85 | ifelse(!is.null(db_name), paste("-out", db_name), ""),
86 | ifelse(hash_index, "-hash_index", ""),
87 | args
88 | ),
89 | stdout = ifelse(verbose, "", FALSE)
90 | )
91 | }
92 |
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/R/BiocFileCache.R:
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1 | #######################################################################
2 | # rBLAST - Interface to BLAST
3 | # Copyright (C) 2015 Michael Hahsler and Anurag Nagar
4 | #
5 | # This program is free software; you can redistribute it and/or modify
6 | # it under the terms of the GNU General Public License as published by
7 | # the Free Software Foundation; either version 2 of the License, or
8 | # any later version.
9 | #
10 | # This program is distributed in the hope that it will be useful,
11 | # but WITHOUT ANY WARRANTY; without even the implied warranty of
12 | # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
13 | # GNU General Public License for more details.
14 | #
15 | # You should have received a copy of the GNU General Public License along
16 | # with this program; if not, write to the Free Software Foundation, Inc.,
17 | # 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
18 |
19 | #' Manage BLAST Database Downloads using BioCFileCache
20 | #'
21 | #' Use [BiocFileCache::BiocFileCache] to manage local copies of BLAST database downloads.
22 | #' NCBI BLAST databases are updated daily and
23 | #' may be downloaded via FTP from \url{https://ftp.ncbi.nlm.nih.gov/blast/db/}.
24 | #'
25 | #' The package maintains its own local cache which can be accessed using
26 | #' `blast_db_cache()`.
27 | #'
28 | #' @family blast
29 | #' @param file the filename of the database.
30 | #' @param baseURL URL to download blast databases from. The default is NCBI's
31 | #' ftp server.
32 | #' @param check_update logical; update the local cache if there is a newer
33 | #' version of the file available on the server. This may take some time.
34 | #' @param verbose logical; display download information.
35 | #' @returns
36 | #' * `blast_db_cache()` returns the path to the local [BiocFileCache::BiocFileCache] cache.
37 | #' * `blast_db_get()` returns the file path to a downloaded BLAST database
38 | #' file.
39 |
40 | #' @author Michael Hahsler
41 | #' @examples
42 | #' ## get a database file (will be downloaded if the
43 | #' ## local copy is not up-to-date)
44 | #' db_16S <- blast_db_get("16S_ribosomal_RNA.tar.gz")
45 | #' db_16S
46 | #'
47 | #' ## directly interacting with the local cache
48 | #' library(BiocFileCache)
49 | #'
50 | #' ## show the package's cache directory
51 | #' local_cache <- blast_db_cache()
52 | #' local_cache
53 | #'
54 | #' ## bfc functions can be used to manage the local cache
55 | #' bfcinfo(local_cache)
56 | #' @export
57 | blast_db_cache <-
58 | function() {
59 | cache <- tools::R_user_dir("rBLAST", which = "cache")
60 | BiocFileCache::BiocFileCache(cache)
61 | }
62 |
63 | #' @rdname blast_db_cache
64 | #' @export
65 | blast_db_get <-
66 | function(file = "16S_ribosomal_RNA.tar.gz",
67 | baseURL = "https://ftp.ncbi.nlm.nih.gov/blast/db/",
68 | check_update = TRUE,
69 | verbose = TRUE) {
70 | fileURL <-
71 | paste0("https://ftp.ncbi.nlm.nih.gov/blast/db/", file)
72 |
73 | bfc <- blast_db_cache()
74 | rid <-
75 | BiocFileCache::bfcquery(bfc, file, "rname")$rid
76 | if (!length(rid)) {
77 | rid <-
78 | names(BiocFileCache::bfcadd(bfc, file, fileURL))
79 | }
80 |
81 | if (check_update && !isFALSE(BiocFileCache::bfcneedsupdate(bfc, rid))) {
82 | if (verbose)
83 | message("Downloading latest version of ", file, " from ",
84 | baseURL)
85 | BiocFileCache::bfcdownload(bfc, rid)
86 | } else
87 | if (verbose)
88 | message("Returning local copy of ", file)
89 |
90 | BiocFileCache::bfcrpath(bfc, rids = rid)
91 | }
92 |
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/README.md:
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