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.
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")library("bold")Default is to get a list back
bold_seq(taxon='Coelioxys')[[1]]
#> $id
#> [1] "BBHYL404-10"
#>
#> $name
#> [1] "Coelioxys rufitarsis"
#>
#> $gene
#> [1] "BBHYL404-10"
#>
#> $sequence
#> [1] "TATAATATATATAATTTTTGCAATATGATCAGGTATAATTGGATCATCTTTAAGAATAATTATTCGAATAGAATTAAGAATCCCAGGTTCATGAATTAGAAATGATCAAATTTATAATTCTTTTATTACAGCACATGCATTTTTAATAATTTTTTTTTTAGTTATGCCTTTTCTAATTGGGGGATTTGGTAATTGATTAACACCATTAATACTTGGAGCTCCTGATATAGCTTTCCCCCGAATAAACAATATTAGATTTTGACTACTCCCACCTTCTTTATTACTTTTATTATCAAGAAATTTAATTAATCCAAGACCAGGAACAGGATGAACTGTTTATCCACCATTATCCTCTTATACATATCATCCATCTCCTTCTGTAGATTTAGCAATTTTTTCTTTACATTTATCAGGAATTTCCTCAATTATTGGATCAATAAATTTTATTGTTACAATTTTAATAATAAAAAATTATTCAATAAATTATAATCAAATACCATTATTCCCATGATCAGTTTTAATTACTACAATTTTATTATTACTATCACTTCCAGTATTAGCAGGAGCAATTACAATATTATTATTTGATCGAAATTTAAATTCTTCTTTTTTTGACCCAATAGGAGGAGGAGACCCAATTTTATATCAACATTTATTT\r"You can optionally get back the httr response object
res <- bold_seq(taxon='Coelioxys', response=TRUE)
res$response_headers
#> $status
#> [1] "HTTP/1.1 200 OK"
#>
#> $date
#> [1] "Thu, 20 Jul 2017 21:51:40 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"
#>
#> $`content-type`
#> [1] "application/x-download"By default you download tsv format data, which is given back to you as a data.frame
res <- bold_specimens(taxon='Osmia')
head(res[,1:8])
#> processid sampleid recordID catalognum fieldnum
#> 1 ASGCB255-13 BIOUG07489-F04 3955532 BIOUG07489-F04
#> 2 ASGCB258-13 BIOUG07489-F07 3955535 BIOUG07489-F07
#> 3 BBHYA3298-12 BIOUG02688-A06 2711807 BIOUG02688-A06 L#11BIOBUS-2558
#> 4 BBHYL310-10 10BBCHY-3264 1769753 10BBCHY-3264 L#PC2010KT-025
#> 5 BCHYM1496-13 BC ZSM HYM 19356 4005345 BC ZSM HYM 19356 BC ZSM HYM 19356
#> 6 BCHYM412-13 BC ZSM HYM 18272 3896353 BC ZSM HYM 18272 BC ZSM HYM 18272
#> institution_storing collection_code
#> 1 Biodiversity Institute of Ontario NA
#> 2 Biodiversity Institute of Ontario NA
#> 3 University of Guelph, Centre for Biodiversity Genomics NA
#> 4 University of Guelph, Centre for Biodiversity Genomics NA
#> 5 SNSB, Zoologische Staatssammlung Muenchen NA
#> 6 SNSB, Zoologische Staatssammlung Muenchen NA
#> bin_uri
#> 1 BOLD:ABZ2181
#> 2 BOLD:AAC0884
#> 3 BOLD:ACF5858
#> 4 BOLD:AAC3295
#> 5 BOLD:AAI2010
#> 6 BOLD:AAP2416By default you download tsv format data, which is given back to you as a data.frame
res <- bold_seqspec(taxon='Osmia', sepfasta=TRUE)
res$fasta[1:2]
#> $`ASGCB255-13`
#> [1] "-------------------------------GGAATAATTGGTTCTGCTATAAGTATTATTATTCGAATAGAATTAAGAATTCCTGGATCATTCATTTCTAATGATCAAACTTATAATTCTTTAGTAACAGCTCATGCTTTTTTAATAATTTTTTTTCTTGTAATACCATTTTTAATTGGTGGATTTGGAAATTGATTAATTCCATTAATATTAGGAATCCCAGATATAGCATTTCCTCGAATAAATAATATTAGATTTTGACTTTTACCCCCATCCTTAATAATTTTACTTTTAAGAAATTTCTTAAATCCAAGTCCAGGAACAGGTTGAACTGTATATCCCCCCCTTTCTTCTTATTTATTTCATTCTTCCCCTTCTGTTGATTTAGCTATTTTTTCTCTTCATATTTCTGGTTTATCTTCCATCATAGGTTCTTTAAATTTTATTGTTACAATTATTATAATAAAAAATATTTCATTAAAACATATTCAATTACCTTTATTTCCTTGATCCGTTTTTATTACAACTATTTTACTATTATTTTCTTTACCTGTTCTAGCAGGAGCTATTACTATATTATTATTTGATCGAAACTTTAATACTTCATTTTTTGATCCAACTGGAGGAGGAGATCCAATTTTATATCAACATTTATTC"
#>
#> $`ASGCB258-13`
#> [1] "GATTTTATATATAATTTTTGCTATGTGATCAGGAATAATTGGTTCAGCAATAAGAATTATTATTCGAATAGAATTAAGAATTCCAGGTTCATGAATCTCTAATGATCAAATTTATAATTCTTTAGTTACTGCTCACGCTTTTTTAATAATTTTTTTTTTAGTAATACCATTTTTAATTGGAGGATTTGGTAATTGATTAGTTCCATTAATATTAGGAATTCCAGATATAGCATTTCCACGAATAAATAATATTAGATTTTGACTTTTACCTCCTTCTTTAATGTTATTACTTTTAAGAAATTTTTTAAATCCAAGTCCAGGAACTGGATGAACTGTATATCCTCCTCTTTCTTCTCATTTATTTCATTCTTCTCCTTCAGTTGATATAGCTATTTTTTCTTTACATATTTCTGGTTTATCTTCTATTATAGGTTCATTAAATTTTATTGTTACAATTATTATAATAAAAAATATTTCATTAAAACATATTCAATTGCCTTTATTTCCTTGATCTGTTTTTATTACTACTATTTTATTACTTTTTTCTTTACCTGTTTTAGCTGGAGCAATTACTATATTATTATTTGATCGAAATTTTAATACTTCATTTTTTGATCCGACAGGAGGTGGAGATCCAATTCTTTATCAACATTTATTT"Or you can index to a specific sequence like
res$fasta['GBAH0293-06']
#> $`GBAH0293-06`
#> [1] "------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TTAATGTTAGGGATTCCAGATATAGCTTTTCCACGAATAAATAATATTAGATTTTGACTGTTACCTCCATCTTTAATATTATTACTTTTAAGAAATTTTTTAAATCCAAGTCCTGGAACAGGATGAACAGTTTATCCTCCTTTATCATCAAATTTATTTCATTCTTCTCCTTCAGTTGATTTAGCAATTTTTTCTTTACATATTTCAGGTTTATCTTCTATTATAGGTTCATTAAATTTTATTGTTACAATTATTATAATAAAAAATATTTCTTTAAAATATATTCAATTACCTTTATTTTCTTGATCTGTATTTATTACTACTATTCTTTTATTATTTTCTTTACCTGTATTAGCTGGAGCTATTACTATATTATTATTTGATCGAAATTTTAATACATCTTTTTTTGATCCAACAGGAGGGGGAGATCCAATTCTTTATCAACATTTATTTTGATTTTTTGGTCATCCTGAAGTTTATATTTTAATTTTACCTGGATTTGGATTAATTTCTCAAATTATTTCTAATGAAAGAGGAAAAAAAGAAACTTTTGGAAATATTGGTATAATTTATGCTATATTAAGAATTGGACTTTTAGGTTTTATTGTT---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------"This function downloads files to your machine - it does not load them into your R session - but prints out where the files are for your information.
x <- bold_trace(ids = 'ACRJP618-11', progress = FALSE)
read_trace(x$ab1)
#> Number of datapoints: 8877
#> Number of basecalls: 685
#>
#> Primary Basecalls: NNNNNNNNNNNNNNNNNNGNNNTTGAGCAGGNATAGTAGGANCTTCTCTTAGTCTTATTATTCGAACAGAATTAGGAAATCCAGGATTTTTAATTGGAGATGATCAAATCTACAATACTATTGTTACGGCTCATGCTTTTATTATAATTTTTTTTATAGTTATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTTCCCCTTATACTAGGAGCCCCAGATATAGCTTTCCCTCGAATAAACAATATAAGTTTTTGGCTTCTTCCCCCTTCACTATTACTTTTAATTTCCAGAAGAATTGTTGAAAATGGAGCTGGAACTGGATGAACAGTTTATCCCCCACTGTCATCTAATATTGCCCATAGAGGTACATCAGTAGATTTAGCTATTTTTTCTTTACATTTAGCAGGTATTTCCTCTATTTTAGGAGCGATTAATTTTATTACTACAATTATTAATATACGAATTAACAGTATAAATTATGATCAAATACCACTATTTGTGTGATCAGTAGGAATTACTGCTTTACTCTTATTACTTTCTCTTCCAGTATTAGCAGGTGCTATCACTATATTATTAACGGATCGAAATTTAAATACATCATTTTTTGATCCTGCAGGAGGAGGAGATCCAATTTTATATCAACATTTATTTTGATTTTTTGGACNTCNNNNAAGTTTAAN
#>
#> Secondary Basecalls:Get citation information for bold in R by running: citation(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.
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