Download parts of NCBI's GenBank to a local folder and create a simple SQL-like database. Use 'get' tools to query the database by accession IDs. rentrez wrappers are available, so that if sequences are not available locally they can be searched for online through Entrez.
See the detailed tutorials for more information.
Vous entrez, vous rentrez et, maintenant, vous .... restez!
Downloading sequences and sequence information from GenBank and related NCBI taxonomic databases is often performed via the NCBI API, Entrez. Entrez, however, has a limit on the number of requests and downloading large amounts of sequence data in this way can be inefficient. For programmatic situations where multiple Entrez calls are made, downloading may take days, weeks or even months.
This package aims to make sequence retrieval more efficient by allowing a user to download large sections of the GenBank database to their local machine and query this local database either through package specific functions or Entrez wrappers. This process is more efficient as GenBank downloads are made via NCBI's FTP using compressed sequence files. With a good internet connection and a middle-of-the-road computer, a database comprising 20 GB of sequence information can be generated in less than 10 minutes.
You can install restez
from GitHub with:
# install.packages("devtools")
devtools::install_github("ropensci/restez")
For more detailed information on the package's functions and detailed guides on downloading, constructing and querying a database, see the detailed tutorials.
# Warning: running these examples may take a few minutes
library(restez)
#> -------------
#> restez v1.0.0
#> -------------
#> Remember to restez_path_set() and, then, restez_connect()
# choose a location to store GenBank files
restez_path_set(rstz_pth)
# Run the download function
db_download()
# after download, create the local database
db_create()
# connect, ensure safe disconnect after finishing
restez_connect()
#> Remember to run `restez_disconnect()`
# get a random accession ID from the database
id <- sample(list_db_ids(), 1)
#> Warning in list_db_ids(): Number of ids returned was limited to [100].
#> Set `n=NULL` to return all ids.
# you can extract:
# sequences
seq <- gb_sequence_get(id)[[1]]
str(seq)
#> chr "GATCCGGCCGCAGCCGCAGTGTCGGCATTGTTCCCGCTGGGCGAGACGGAGATCACCCTCACGGTCTTCTCGGGCGATCAGTCCGACGCCGAGACGACGACGGTGACGATC"| __truncated__
# definitions
def <- gb_definition_get(id)[[1]]
print(def)
#> [1] "Unidentified clone B15 DNA sequence from ocean beach sand"
# organisms
org <- gb_organism_get(id)[[1]]
print(org)
#> [1] "unidentified"
# or whole records
rec <- gb_record_get(id)[[1]]
cat(rec)
#> LOCUS AF298094 581 bp DNA linear UNA 23-NOV-2000
#> DEFINITION Unidentified clone B15 DNA sequence from ocean beach sand.
#> ACCESSION AF298094
#> VERSION AF298094.1
#> KEYWORDS .
#> SOURCE unidentified
#> ORGANISM unidentified
#> unclassified sequences.
#> REFERENCE 1 (bases 1 to 581)
#> AUTHORS Naviaux,R.K.
#> TITLE Sand DNA: a multigenomic library on the beach
#> JOURNAL Unpublished
#> REFERENCE 2 (bases 1 to 581)
#> AUTHORS Naviaux,R.K.
#> TITLE Direct Submission
#> JOURNAL Submitted (21-AUG-2000) Medicine, University of California, San
#> Diego School of Medicine, 200 West Arbor Drive, San Diego, CA
#> 92103-8467, USA
#> FEATURES Location/Qualifiers
#> source 1..581
#> /organism="unidentified"
#> /mol_type="genomic DNA"
#> /db_xref="taxon:32644"
#> /clone="B15"
#> /note="anonymous environmental sample sequence from ocean
#> beach sand"
#> ORIGIN
#> 1 gatccggccg cagccgcagt gtcggcattg ttcccgctgg gcgagacgga gatcaccctc
#> 61 acggtcttct cgggcgatca gtccgacgcc gagacgacga cggtgacgat cgaggacacg
#> 121 accgcgccga cgttcaccca cgcactgggt gatgtccttc cgatggtgac gaaggaggca
#> 181 acggagcccg gagggcatga cttcagcccg gccacgccgg acgcctggga ccatggagac
#> 241 agcgacctcg acatcgcttg cggtacggaa ctcccgcatc tcttcccgat cggggataca
#> 301 gagatcacct ggacggcgac ggacgatcag gacctttcga cgacggcaac gcagatcatc
#> 361 cggatcgagg acaacacgcc gccgaccttc atccagcgcg atgatcaggt cgtggcgacc
#> 421 acgtacgatc cggtcggtct caggaaggag cacgttccgc tcgcgggcac cgtcatcgcg
#> 481 gtggacttcg gacagcccgt accgctcacg aacaccgccc cggacgtntt tcggttgggg
#> 541 agcacggaga tncctggacc gcgacggtgc gtncgggaac t
#> //
# use the entrez_* wrappers to access GB data
res <- entrez_fetch(db = 'nucleotide', id = id, rettype = 'fasta')
cat(res)
#> >AF298094.1 Unidentified clone B15 DNA sequence from ocean beach sand
#> GATCCGGCCGCAGCCGCAGTGTCGGCATTGTTCCCGCTGGGCGAGACGGAGATCACCCTCACGGTCTTCT
#> CGGGCGATCAGTCCGACGCCGAGACGACGACGGTGACGATCGAGGACACGACCGCGCCGACGTTCACCCA
#> CGCACTGGGTGATGTCCTTCCGATGGTGACGAAGGAGGCAACGGAGCCCGGAGGGCATGACTTCAGCCCG
#> GCCACGCCGGACGCCTGGGACCATGGAGACAGCGACCTCGACATCGCTTGCGGTACGGAACTCCCGCATC
#> TCTTCCCGATCGGGGATACAGAGATCACCTGGACGGCGACGGACGATCAGGACCTTTCGACGACGGCAAC
#> GCAGATCATCCGGATCGAGGACAACACGCCGCCGACCTTCATCCAGCGCGATGATCAGGTCGTGGCGACC
#> ACGTACGATCCGGTCGGTCTCAGGAAGGAGCACGTTCCGCTCGCGGGCACCGTCATCGCGGTGGACTTCG
#> GACAGCCCGTACCGCTCACGAACACCGCCCCGGACGTNTTTCGGTTGGGGAGCACGGAGATNCCTGGACC
#> GCGACGGTGCGTNCGGGAACT
# if the id is not in the local database
# these wrappers will search online via the rentrez package
res <- entrez_fetch(db = 'nucleotide', id = c('S71333.1', id),
rettype = 'fasta')
#> [1] id(s) are unavailable locally, searching online.
cat(res)
#> >AF298094.1 Unidentified clone B15 DNA sequence from ocean beach sand
#> GATCCGGCCGCAGCCGCAGTGTCGGCATTGTTCCCGCTGGGCGAGACGGAGATCACCCTCACGGTCTTCT
#> CGGGCGATCAGTCCGACGCCGAGACGACGACGGTGACGATCGAGGACACGACCGCGCCGACGTTCACCCA
#> CGCACTGGGTGATGTCCTTCCGATGGTGACGAAGGAGGCAACGGAGCCCGGAGGGCATGACTTCAGCCCG
#> GCCACGCCGGACGCCTGGGACCATGGAGACAGCGACCTCGACATCGCTTGCGGTACGGAACTCCCGCATC
#> TCTTCCCGATCGGGGATACAGAGATCACCTGGACGGCGACGGACGATCAGGACCTTTCGACGACGGCAAC
#> GCAGATCATCCGGATCGAGGACAACACGCCGCCGACCTTCATCCAGCGCGATGATCAGGTCGTGGCGACC
#> ACGTACGATCCGGTCGGTCTCAGGAAGGAGCACGTTCCGCTCGCGGGCACCGTCATCGCGGTGGACTTCG
#> GACAGCCCGTACCGCTCACGAACACCGCCCCGGACGTNTTTCGGTTGGGGAGCACGGAGATNCCTGGACC
#> GCGACGGTGCGTNCGGGAACT
#>
#> >S71333.1 alpha 1,3 galactosyltransferase [New World monkeys, mermoset lymphoid cell line B95.8, mRNA Partial, 1131 nt]
#> ATGAATGTCAAAGGAAAAGTAATTCTGTCGATGCTGGTTGTCTCAACTGTGATTGTTGTGTTTTGGGAAT
#> ATATCAACAGCCCAGAAGGCTCTTTCTTGTGGATATATCACTCAAAGAACCCAGAAGTTGATGACAGCAG
#> TGCTCAGAAGGACTGGTGGTTTCCTGGCTGGTTTAACAATGGGATCCACAATTATCAACAAGAGGAAGAA
#> GACACAGACAAAGAAAAAGGAAGAGAGGAGGAACAAAAAAAGGAAGATGACACAACAGAGCTTCGGCTAT
#> GGGACTGGTTTAATCCAAAGAAACGCCCAGAGGTTATGACAGTGACCCAATGGAAGGCGCCGGTTGTGTG
#> GGAAGGCACTTACAACAAAGCCATCCTAGAAAATTATTATGCCAAACAGAAAATTACCGTGGGGTTGACG
#> GTTTTTGCTATTGGAAGATATATTGAGCATTACTTGGAGGAGTTCGTAACATCTGCTAATAGGTACTTCA
#> TGGTCGGCCACAAAGTCATATTTTATGTCATGGTGGATGATGTCTCCAAGGCGCCGTTTATAGAGCTGGG
#> TCCTCTGCGTTCCTTCAAAGTGTTTGAGGTCAAGCCAGAGAAGAGGTGGCAAGACATCAGCATGATGCGT
#> ATGAAGACCATCGGGGAGCACATCTTGGCCCACATCCAACACGAGGTTGACTTCCTCTTCTGCATGGATG
#> TGGACCAGGTCTTCCAAGACCATTTTGGGGTAGAGACCCTGGGCCAGTCGGTGGCTCAGCTACAGGCCTG
#> GTGGTACAAGGCAGATCCTGATGACTTTACCTATGAGAGGCGGAAAGAGTCGGCAGCATATATTCCATTT
#> GGCCAGGGGGATTTTTATTACCATGCAGCCATTTTTGGAGGAACACCGATTCAGGTTCTCAACATCACCC
#> AGGAGTGCTTTAAGGGAATCCTCCTGGACAAGAAAAATGACATAGAAGCCGAGTGGCATGATGAAAGCCA
#> CCTAAACAAGTATTTCCTTCTCAACAAACCCTCTAAAATCTTATCTCCAGAATACTGCTGGGATTATCAT
#> ATAGGCCTGCCTTCAGATATTAAAACTGTCAAGCTATCATGGCAAACAAAAGAGTATAATTTGGTTAGAA
#> AGAATGTCTGA
restez_disconnect()
Want to contribute? Check the contributing page.
Release version 1.
MIT
Benson, D. A., Karsch-Mizrachi, I., Clark, K., Lipman, D. J., Ostell, J., & Sayers, E. W. (2012). GenBank. Nucleic Acids Research, 40(Database issue), D48–D53. http://doi.org/10.1093/nar/gkr1202
Winter DJ. (2017) rentrez: An R package for the NCBI eUtils API. PeerJ Preprints 5:e3179v2 https://doi.org/10.7287/peerj.preprints.3179v2
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