A programmatic interface to the Web Service methods provided by Bold Systems (< http://www.boldsystems.org/>) 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
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"#>#> $`content-type`#> [1] "application/x-download"
By default you download tsv
format data, which is given back to you as a data.frame
res <- bold_specimens(taxon='Osmia')head(res[,1:8])#> processid sampleid recordID catalognum fieldnum#> 1 ASGCB255-13 BIOUG07489-F04 3955532 BIOUG07489-F04#> 2 ASGCB258-13 BIOUG07489-F07 3955535 BIOUG07489-F07#> 3 BBHYA3298-12 BIOUG02688-A06 2711807 BIOUG02688-A06 L#11BIOBUS-2558#> 4 BBHYL310-10 10BBCHY-3264 1769753 10BBCHY-3264 L#PC2010KT-025#> 5 BCHYM1496-13 BC ZSM HYM 19356 4005345 BC ZSM HYM 19356 BC ZSM HYM 19356#> 6 BCHYM412-13 BC ZSM HYM 18272 3896353 BC ZSM HYM 18272 BC ZSM HYM 18272#> institution_storing collection_code#> 1 Biodiversity Institute of Ontario NA#> 2 Biodiversity Institute of Ontario NA#> 3 University of Guelph, Centre for Biodiversity Genomics NA#> 4 University of Guelph, Centre for Biodiversity Genomics NA#> 5 SNSB, Zoologische Staatssammlung Muenchen NA#> 6 SNSB, Zoologische Staatssammlung Muenchen NA#> bin_uri#> 1 BOLD:ABZ2181#> 2 BOLD:AAC0884#> 3 BOLD:ACF5858#> 4 BOLD:AAC3295#> 5 BOLD:AAI2010#> 6 BOLD:AAP2416
By default you download tsv
format data, which is given back to you as a data.frame
res <- bold_seqspec(taxon='Osmia', sepfasta=TRUE)res$fasta[1:2]#> $`ASGCB255-13`#> [1] "-------------------------------GGAATAATTGGTTCTGCTATAAGTATTATTATTCGAATAGAATTAAGAATTCCTGGATCATTCATTTCTAATGATCAAACTTATAATTCTTTAGTAACAGCTCATGCTTTTTTAATAATTTTTTTTCTTGTAATACCATTTTTAATTGGTGGATTTGGAAATTGATTAATTCCATTAATATTAGGAATCCCAGATATAGCATTTCCTCGAATAAATAATATTAGATTTTGACTTTTACCCCCATCCTTAATAATTTTACTTTTAAGAAATTTCTTAAATCCAAGTCCAGGAACAGGTTGAACTGTATATCCCCCCCTTTCTTCTTATTTATTTCATTCTTCCCCTTCTGTTGATTTAGCTATTTTTTCTCTTCATATTTCTGGTTTATCTTCCATCATAGGTTCTTTAAATTTTATTGTTACAATTATTATAATAAAAAATATTTCATTAAAACATATTCAATTACCTTTATTTCCTTGATCCGTTTTTATTACAACTATTTTACTATTATTTTCTTTACCTGTTCTAGCAGGAGCTATTACTATATTATTATTTGATCGAAACTTTAATACTTCATTTTTTGATCCAACTGGAGGAGGAGATCCAATTTTATATCAACATTTATTC"#>#> $`ASGCB258-13`#> [1] "GATTTTATATATAATTTTTGCTATGTGATCAGGAATAATTGGTTCAGCAATAAGAATTATTATTCGAATAGAATTAAGAATTCCAGGTTCATGAATCTCTAATGATCAAATTTATAATTCTTTAGTTACTGCTCACGCTTTTTTAATAATTTTTTTTTTAGTAATACCATTTTTAATTGGAGGATTTGGTAATTGATTAGTTCCATTAATATTAGGAATTCCAGATATAGCATTTCCACGAATAAATAATATTAGATTTTGACTTTTACCTCCTTCTTTAATGTTATTACTTTTAAGAAATTTTTTAAATCCAAGTCCAGGAACTGGATGAACTGTATATCCTCCTCTTTCTTCTCATTTATTTCATTCTTCTCCTTCAGTTGATATAGCTATTTTTTCTTTACATATTTCTGGTTTATCTTCTATTATAGGTTCATTAAATTTTATTGTTACAATTATTATAATAAAAAATATTTCATTAAAACATATTCAATTGCCTTTATTTCCTTGATCTGTTTTTATTACTACTATTTTATTACTTTTTTCTTTACCTGTTTTAGCTGGAGCAATTACTATATTATTATTTGATCGAAATTTTAATACTTCATTTTTTGATCCGACAGGAGGTGGAGATCCAATTCTTTATCAACATTTATTT"
Or you can index to a specific sequence like
res$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.
crul
for HTTP requests. Only really affects users in that
specifying curl options works slightly differenlty (#42)marker
parameter in bold_seqspec
was and maybe still is not working,
in the sense that using the parameter doesn't always limit results to the
marker you specify. Not really fixed - watch out for it, and filter after you
get results back to get markers you want. (#25)bold_identify_parents
- was failing when no match for a
parent name. (#41) thx @VascoElbrechttsv
results were erroring in bold_specimens
and other fxns (#46) - fixed
by switching to new BOLD v4 API (#30)stats
and utils
- replaced
is
with inherits
(#39)bold_identify_parents()
to add taxonomic information
to the output of bold_identif()
. We take the taxon names from bold_identify
output, and use bold_tax_name
to get the taxonomic ID, passing it to
bold_tax_id
to get the parent names, then attaches those to the input data.
There are two options given what you put for the wide
parameter. If TRUE
you get data.frames of the same dimensions with parent rank name and ID
as new columns (for each name going up the hierarchy) - while if FALSE
you get a long data.frame. thanks @dougwyu for inspiring this (#36)xml2::xml_find_one
with xml2::xml_find_first
(#33)db
options in bold_identify
man file -
COX1 and COX1_SPECIES were switched (#37) thanks for pointing that out
@dougwyubold_tax_id
for when some elements returned from the BOLD
API were empty/NULL
(#32) thanks @fmichonneau !!xml2
from XML
as the XML parser for this package (#26)bold_trace()
to create dir and tar file when it doesn't
already existcontent(x, "text")
, so now using rawToChar(content(x))
,
which works (#24)sangerseqR
package now in Suggests for reading trace files, and is only used in bold_trace()
function.bold_trace()
gains two new parameters: overwrite
to choose whether to overwrite an existing
file of the same name or not, progress
to show a progress bar for downloading or not.bold_trace()
gains a print method to show a tidy summary of the trace file downloaded.bold_tax_name()
(#17) and bold_tax_id()
(#18) in which species that were missing from the BOLD database returned empty arrays but 200 status codes. Parsing those as failed attempts now. Also fixes problem in taxize in bold_search()
that use these two functions.bold_tax_name()
and bold_tax_id()
, which search for taxonomic data from BOLD using either names or BOLD identifiers, respectively. (#11)jsonlite
and reshape
.callopts
parameter changed to ...
throughout the package, so that passing on options to httr::GET
is done via named parameters, e.g., config=verbose()
. (#13)httr
(v0.4) (#9), and added a few more tests (#7)