bold
bold accesses BOLD barcode data.
The Barcode of Life Data Systems (BOLD) is designed to support the generation and application of DNA barcode data. The platform consists of four main modules: a data portal, a database of barcode clusters, an educational portal, and a data collection workbench.
This package retrieves data from the BOLD database of barcode clusters, and allows for searching of over 1.7M public records using multiple search criteria including sequence data, specimen data, specimen plus sequence data, as well as trace files.
Documentation for the BOLD API.
See also the taxize book for more options for taxonomic workflows with BOLD: https://ropensci.github.io/taxize-book/
Package status and installation
Installation instructions
Stable Version
install.packages("bold")Development Version
Install sangerseqR first
source("http://bioconductor.org/biocLite.R")
biocLite("sangerseqR")Then bold
devtools::install_github("ropensci/bold")Usage
library("bold")Search for sequence data only
Default is to get a list back
bold_seq(taxon='Coelioxys')[[1]]
#> $id
#> [1] "ABEE117-17"
#>
#> $name
#> [1] "Coelioxys elongata"
#>
#> $gene
#> [1] "ABEE117-17"
#>
#> $sequence
#> [1] "------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TTATCATTATATACATATCATCCTTCCCCATCAGTTGATTTAGCAATTTTTTYTTTACATTTATCAGGAATTTYTTYTATTATCGGATCAATAAATTTTATTGTAACAATTTTAATAATAAAAAATTATTCAATAAATTATAATCAAATACCTTTATTTCCATGATCAATTTTAATTACTACAATTTTATTATTATTATCATTACCTGTATTAGCAGGAGCTATTACAATATTATTATTTGATCGTAATTTAAATTCATCATTTTTTGACCCAATAGGAGGAGGAGATCCTATTTTATATCAACATTTATTTTG------------------------------------\r"You can optionally get back the httr response object
res <- bold_seq(taxon='Coelioxys', response=TRUE)
res$response_headers
#> $status
#> [1] "HTTP/1.1 200 OK"
#>
#> $date
#> [1] "Fri, 26 Oct 2018 17:24:49 GMT"
#>
#> $server
#> [1] "Apache/2.2.15 (Red Hat)"
#>
#> $`x-powered-by`
#> [1] "PHP/5.3.15"
#>
#> $`content-disposition`
#> [1] "attachment; filename=fasta.fas"
#>
#> $connection
#> [1] "close"
#>
#> $`transfer-encoding`
#> [1] "chunked"
#>
#> $`content-type`
#> [1] "application/x-download"Search for specimen data only
By default you download tsv format data, which is given back to you as a data.frame
res <- bold_specimens(taxon='Osmia')
head(res[,1:8])
#> processid sampleid recordID catalognum fieldnum
#> 1 ABEE158-17 NHMW-HYM 877 8362257
#> 2 BBHEC461-09 09BBEHY-0492 1301732 09BBEHY-0492 L#09KJ-102
#> 3 BBHYL362-10 10BBCHY-3316 1769805 10BBCHY-3316 L#PC2010EI-002
#> 4 BCHYM412-13 BC ZSM HYM 18272 3896353 BC ZSM HYM 18272 BC ZSM HYM 18272
#> 5 BCHYM414-13 BC ZSM HYM 18274 3896355 BC ZSM HYM 18274 BC ZSM HYM 18274
#> 6 BCT020-06 06-BCT-020 240796 06-BCT-020
#> institution_storing collection_code bin_uri
#> 1 Naturhistorisches Museum Wien NA
#> 2 Centre for Biodiversity Genomics NA BOLD:AAB8874
#> 3 Centre for Biodiversity Genomics NA BOLD:AAB8874
#> 4 SNSB, Zoologische Staatssammlung Muenchen NA BOLD:AAP2416
#> 5 SNSB, Zoologische Staatssammlung Muenchen NA
#> 6 Centre for Biodiversity Genomics NA BOLD:AAC0884Search for specimen plus sequence data
By default you download tsv format data, which is given back to you as a data.frame
res <- bold_seqspec(taxon='Osmia', sepfasta=TRUE)
res$fasta[1:2]
#> $`ABEE158-17`
#> [1] "--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TTCTTCTAATTTATTTCATTCTTCCCCYTCTGTAGATTTAGCTATTTTCTCTCTTCATATTTCTGGTTTATCTTCTATTATAGGTTCATTAAATTTTATTGTTACAATTATTATAATAAAAAATATTTCATTAAAACATATTCAACTTCCTTTATTTCCTTGATCTGTTTTTATTACTACTATTTTATTATTATTTTCTTTACCAGTTCTAGCTGGAGCAATTACTATATTATTATTTGATCGAAATTTTAATACTTCATTTTTTGATCCTACTGGAGGAGGAGATCCAATTCTTTATCAACATTTATTTTG------------------------------------"
#>
#> $`BBHEC461-09`
#> [1] "AATTTTATATATAATTTTTGCTATATGATCAGGAATAATTGGTTCAGCAATAAGAATTATTATTCGAATAGAATTAAGAATTCCTGGTTCATGAATTTCAAATGATCAAACTTATAATTCTTTAGTTACTGCTCATGCTTTTTTAATAATTTTTTTCTTAGTTATACCATTCTTAATTGGGGGATTTGGAAATTGATTAATTCCTTTAATATTAGGAATTCCAGATATAGCATTTCCACGAATAAATAATATTAGATTTTGACTTTTACCTCCTTCTTTAATACTTTTATTATTAAGAAATTTTATAAATCCTAGTCCAGGAACTGGATGAACTGTTTATCCACCTTTATCTTCTCATTTATTTCATTCTTCTCCTTCAGTTGATATAGCTATTTTTTCTTTACATATTTCTGGTTTATCTTCTATTATAGGTTCATTAAATTTTATTGTTACAATTATTATAATAAAAAATATTTCTTTAAAACATATTCAATTACCTTTATTTCCTTGATCTGTCTTTATTACTACTATTTTATTACTTTTTTCTTTACCTGTTTTAGCAGGTGCAATTACTATATTATTATTTGATCGAAATTTTAATACTTCATTTTTTGATCCTACAGGAGGAGGAGATCCTATTCTTTATCAACATTTATTT"Or you can index to a specific sequence like
res$fasta['GBAH0293-06']
#> $`GBAH0293-06`
#> [1] "------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TTAATGTTAGGGATTCCAGATATAGCTTTTCCACGAATAAATAATATTAGATTTTGACTGTTACCTCCATCTTTAATATTATTACTTTTAAGAAATTTTTTAAATCCAAGTCCTGGAACAGGATGAACAGTTTATCCTCCTTTATCATCAAATTTATTTCATTCTTCTCCTTCAGTTGATTTAGCAATTTTTTCTTTACATATTTCAGGTTTATCTTCTATTATAGGTTCATTAAATTTTATTGTTACAATTATTATAATAAAAAATATTTCTTTAAAATATATTCAATTACCTTTATTTTCTTGATCTGTATTTATTACTACTATTCTTTTATTATTTTCTTTACCTGTATTAGCTGGAGCTATTACTATATTATTATTTGATCGAAATTTTAATACATCTTTTTTTGATCCAACAGGAGGGGGAGATCCAATTCTTTATCAACATTTATTTTGATTTTTTGGTCATCCTGAAGTTTATATTTTAATTTTACCTGGATTTGGATTAATTTCTCAAATTATTTCTAATGAAAGAGGAAAAAAAGAAACTTTTGGAAATATTGGTATAATTTATGCTATATTAAGAATTGGACTTTTAGGTTTTATTGTT---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------"Get trace files
This function downloads files to your machine - it does not load them into your R session - but prints out where the files are for your information.
x <- bold_trace(ids = 'ACRJP618-11', progress = FALSE)
read_trace(x$ab1)
#> Number of datapoints: 8877
#> Number of basecalls: 685
#>
#> Primary Basecalls: NNNNNNNNNNNNNNNNNNGNNNTTGAGCAGGNATAGTAGGANCTTCTCTTAGTCTTATTATTCGAACAGAATTAGGAAATCCAGGATTTTTAATTGGAGATGATCAAATCTACAATACTATTGTTACGGCTCATGCTTTTATTATAATTTTTTTTATAGTTATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTTCCCCTTATACTAGGAGCCCCAGATATAGCTTTCCCTCGAATAAACAATATAAGTTTTTGGCTTCTTCCCCCTTCACTATTACTTTTAATTTCCAGAAGAATTGTTGAAAATGGAGCTGGAACTGGATGAACAGTTTATCCCCCACTGTCATCTAATATTGCCCATAGAGGTACATCAGTAGATTTAGCTATTTTTTCTTTACATTTAGCAGGTATTTCCTCTATTTTAGGAGCGATTAATTTTATTACTACAATTATTAATATACGAATTAACAGTATAAATTATGATCAAATACCACTATTTGTGTGATCAGTAGGAATTACTGCTTTACTCTTATTACTTTCTCTTCCAGTATTAGCAGGTGCTATCACTATATTATTAACGGATCGAAATTTAAATACATCATTTTTTGATCCTGCAGGAGGAGGAGATCCAATTTTATATCAACATTTATTTTGATTTTTTGGACNTCNNNNAAGTTTAAN
#>
#> Secondary Basecalls:Citation
Get citation information for bold in R by running: citation(package = 'bold')
Meta
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- License: MIT
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boldin R doingcitation(package = 'bold') - Please note that this project is released with a Contributor Code of Conduct. By participating in this project you agree to abide by its terms.