Interface to Bold Systems 'API'

A programmatic interface to the Web Service methods provided by Bold Systems for genetic 'barcode' data. Functions include methods for searching by sequences by taxonomic names, ids, collectors, and institutions; as well as a function for searching for specimens, and downloading trace files.

bold

bold accesses BOLD barcode data.

Documentation for the BOLD API.

Stable CRAN version

install.packages("bold")

Development version from Github

Install sangerseqR first

source("http://bioconductor.org/biocLite.R")
biocLite("sangerseqR")

Then bold

devtools::install_github("ropensci/bold")

library("bold")

Search for sequence data only

Default is to get a list back

bold_seq(taxon='Coelioxys')[[1]]
#> $id
#> [1] "FBAPB481-09"
#> 
#> $name
#> [1] "Coelioxys afra"
#> 
#> $gene
#> [1] "FBAPB481-09"
#> 
#> $sequence
#> [1] "----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TTTCCACGAATAAATAATGTAAGATTTTGACTATTACCTCCCTCAATTTTCTTATTATTATCAAGAACCCTAATTAACCCAAGTGCTGGTACTGGATGAACTGTATATCCTCCTTTATCCTTATATACATTTCATGCCTCACCTTCCGTTGATTTAGCAATTTTTTCACTTCATTTATCAGGAATTTCATCAATTATTGGATCAATAAATTTTATTGTTACAATCTTAATAATAAAAAATTTTTCTTTAAATTATAGACAAATACCATTATTTTCATGATCAGTTTTAATTACTACAATTTTACTTTTATTATCATTACCAATTTTAGCTGGAGCAATTACTATACTCCTATTTGATCGAAATTTAAATACCTCATTCTTTGACCCAATAGGAGGAGGAGATCCAATTTTATATCAACATTTATTT"

You can optionally get back the httr response object

res <- bold_seq(taxon='Coelioxys', response=TRUE)
res$headers
#> $date
#> [1] "Mon, 28 Mar 2016 20:35:02 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"
#> 
#> attr(,"class")
#> [1] "insensitive" "list"

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  ASGCB255-13   BIOUG07489-F04  3955532                    BIOUG07489-F04
#> 2 BCHYM1493-13 BC ZSM HYM 19353  4005342 BC ZSM HYM 19353 BC ZSM HYM 19353
#> 3  CHUBE002-06    CHU05-BEE-002   516711    CHU05-BEE-002    CHU05-BEE-002
#> 4  FBAPB679-09 BC ZSM HYM 02154  1289040 BC ZSM HYM 02154 BC ZSM HYM 02154
#> 5  FBAPB730-09 BC ZSM HYM 02205  1289091 BC ZSM HYM 02205 BC ZSM HYM 02205
#> 6  FBAPB743-09 BC ZSM HYM 02218  1289104 BC ZSM HYM 02218 BC ZSM HYM 02218
#>                                            institution_storing
#> 1                            Biodiversity Institute of Ontario
#> 2                    SNSB, Zoologische Staatssammlung Muenchen
#> 3 University of Manitoba, Wallis Roughley Museum of Entomology
#> 4                    SNSB, Zoologische Staatssammlung Muenchen
#> 5                    SNSB, Zoologische Staatssammlung Muenchen
#> 6                    SNSB, Zoologische Staatssammlung Muenchen
#>        bin_uri phylum_taxID
#> 1 BOLD:ABZ2181           20
#> 2 BOLD:AAK6070           20
#> 3 BOLD:AAD4181           20
#> 4 BOLD:AAI1788           20
#> 5 BOLD:AAK5820           20
#> 6                        20

Search 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]
#> $`ASGCB255-13`
#> [1] "-------------------------------GGAATAATTGGTTCTGCTATAAGTATTATTATTCGAATAGAATTAAGAATTCCTGGATCATTCATTTCTAATGATCAAACTTATAATTCTTTAGTAACAGCTCATGCTTTTTTAATAATTTTTTTTCTTGTAATACCATTTTTAATTGGTGGATTTGGAAATTGATTAATTCCATTAATATTAGGAATCCCAGATATAGCATTTCCTCGAATAAATAATATTAGATTTTGACTTTTACCCCCATCCTTAATAATTTTACTTTTAAGAAATTTCTTAAATCCAAGTCCAGGAACAGGTTGAACTGTATATCCCCCCCTTTCTTCTTATTTATTTCATTCTTCCCCTTCTGTTGATTTAGCTATTTTTTCTCTTCATATTTCTGGTTTATCTTCCATCATAGGTTCTTTAAATTTTATTGTTACAATTATTATAATAAAAAATATTTCATTAAAACATATTCAATTACCTTTATTTCCTTGATCCGTTTTTATTACAACTATTTTACTATTATTTTCTTTACCTGTTCTAGCAGGAGCTATTACTATATTATTATTTGATCGAAACTTTAATACTTCATTTTTTGATCCAACTGGAGGAGGAGATCCAATTTTATATCAACATTTATTC"
#> 
#> $`BCHYM1493-13`
#> [1] "AATTTTATATATAATTTTTGCTTTATGATCTGGAATAATTGGTTCATCAATAAGAATTTTAATTCGAATAGAATTAAGAATTCCTGGATCATGAATTTCTAATGATCAAGTTTATAATTCTTTAGTAACTGCTCATGCTTTTTTAATAATTTTTTTTCTTGTAATACCATTTTTAATTGGGGGATTTGGAAATTGATTAATTCCTTTAATATTAGGAATTCCTGATATAGCTTTTCCTCGAATAAATAATATTAGATTTTGACTTTTACCTCCATCTTTAATATTATTATTGTTAAGAAATTTTTTAAATCCAAGTCCAGGAACAGGATGAACTGTTTATCCTCCTCTTTCTTCAAATTTATTTCACTCTTCTCCTTCAGTAGATTTAGCAATTTTTTCATTACATATTTCAGGATTATCATCTATTATAGGATCATTAAATTTTATTGTTACAATTATTTTAATAAAAAATATTTCTTTAAAACATATTCAATTACCTTTATTTCCATGATCTGTTTTTATTACTACAATTCTTTTATTATTATCATTACCAGTTTTAGCAGGAGCTATTACTATACTTTTATTTGATCGAAATTTTAATACTTCTTTTTTTGACCCTATAGGAGGAGGAGATCCAATTCTTTATCAACATTTATTT"

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:

Meta

• Please report any issues or bugs.
• License: MIT
• Get citation information for bold in R doing 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.