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bold is an R package to connect to BOLD Systems \url{http://www.boldsystems.org/} via their API. Functions in bold let you search for sequence data, specimen data, sequence + specimen data, and download raw trace files.
bold info
Using bold
Install
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Install bold | devtools::install_github("ropensci/bold")
library("bold")
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Search for sequence data only
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Default is to get a list back | bold_seq(taxon='Coelioxys')[1:2]
## [[1]]
## [[1]]$id
## [1] "CNPPJ1450-12"
##
## [[1]]$name
## [1] "Coelioxys sayi"
##
## [[1]]$gene
## [1] "CNPPJ1450-12"
##
## [[1]]$sequence
## [1] "TATTATATATATAATTTTTGCAATATGATCAGGAATAATTGGATCTTCCTTAAGAATAATTATTCGAATAGAATTAAGAATT---CCAGGATCATGAATTAGTAATGACCAAATTTATAATTCCTTTATTACAGCGCACGCATTTTTAATAATTTTCTTTTTAGTTATACCGTTTTTAATTGGTGGATTTGGAAATTGACTCACACCTTTAATATTAGGAGCCCCTGATATAGCTTTCCCCCGTATAAATAATATTAGATTTTGATTATTACCCCCCTCATTATTAATATTATTATCAAGAAATTTAATTAACCCAAGACCTGGAACAGGATGAACAGTTTATCCACCACTATCTTCTTATACTTATCATCCTTCTCCTTCTGTAGATCTAGCAATTTTTTCTTTACACTTATCAGGTATTTCTTCTATTATTGGATCAATAAATTTTATTGTAACAATTTTATTAATAAAAAATTATTCAATAAATTATAATCAAATACCTTTATTTCCCTGATCTGTTTTAATTACAACAATTTTATTACTATTATCACTACCTGTATTAGCAGGAGCAATTACAATATTATTATTT---------GATCGAAATTTAAATTCATCATTTTTCGACCCTATAGGAGGAGGAG-----------------------------"
##
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## [[2]]
## [[2]]$id
## [1] "GBMIN26386-13"
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## [[2]]$name
## [1] "Coelioxys sp. HMG-2011"
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## [[2]]$gene
## [1] "GBMIN26386-13"
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## [[2]]$sequence
## [1] "CGAATAAATAATATTAGATTTTGATTATTACCCCCATCACTATTATTACTTCTATTAAGTAATTTGATTAAACCAAGACCAGGTACAGGATGAACCGTATACCCTCCCTTATCTTTATATCTTTATCACCCTTCACCATCAGTTGATTTTGCAATTTTTTCTTTACATTTATCAGGAATTTCATCTATTATTGGTTCATTAAATTTTATTGTAACAATTTTAATAATAAAAAATTGATCTTTAAATTATAGACAAATATCATTATTTCCTTGATCAATTTTTATTACTACAATTTTATTATTA"
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You can optionally get back the httr response object | res <- bold_seq(taxon='Coelioxys', response=TRUE)
res$headers
## $date
## [1] "Wed, 28 May 2014 20:11:59 GMT"
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## $server
## [1] "Apache/2.2.15 (Red Hat)"
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## $`x-powered-by`
## [1] "PHP/5.3.15"
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## $`content-disposition`
## [1] "attachment; filename=fasta.fas"
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## $connection
## [1] "close"
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## $`transfer-encoding`
## [1] "chunked"
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## $`content-type`
## [1] "application/x-download"
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## $status
## [1] "200"
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## $statusmessage
## [1] "OK"
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## attr(,"class")
## [1] "insensitive" "list"
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Search for specimen data only
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By default you download tsv format data, which is given back to you as a data.frame | res <- bold_specimens(taxon='Osmia')
head(res[,1:8])
## processid sampleid recordID catalognum fieldnum
## 1 GBAH0293-06 AF250940 470890
## 2 GBAH3879-08 EU726628 856410 EU726628
## 3 GBAH3880-08 EU726627 856411 EU726627
## 4 GBAH3888-08 EU726619 856419 EU726619
## 5 GBAH3904-08 EU726603 856435 EU726603
## 6 GBAH3909-08 EU726598 856440 EU726598
## institution_storing bin_uri phylum_taxID
## 1 Mined from GenBank, NCBI BOLD:AAD6282 20
## 2 Mined from GenBank, NCBI BOLD:AAA4494 20
## 3 Mined from GenBank, NCBI BOLD:AAA4494 20
## 4 Mined from GenBank, NCBI BOLD:AAA4494 20
## 5 Mined from GenBank, NCBI BOLD:AAA4494 20
## 6 Mined from GenBank, NCBI BOLD:AAA4494 20
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Search for specimen plus sequence data
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By default you download tsv format data, which is given back to you as a data.frame | res <- bold_seqspec(taxon='Osmia', sepfasta=TRUE)
res$fasta[1:2]
## $`GBAH0293-06`
## [1] "------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TTAATGTTAGGGATTCCAGATATAGCTTTTCCACGAATAAATAATATTAGATTTTGACTGTTACCTCCATCTTTAATATTATTACTTTTAAGAAATTTTTTAAATCCAAGTCCTGGAACAGGATGAACAGTTTATCCTCCTTTATCATCAAATTTATTTCATTCTTCTCCTTCAGTTGATTTAGCAATTTTTTCTTTACATATTTCAGGTTTATCTTCTATTATAGGTTCATTAAATTTTATTGTTACAATTATTATAATAAAAAATATTTCTTTAAAATATATTCAATTACCTTTATTTTCTTGATCTGTATTTATTACTACTATTCTTTTATTATTTTCTTTACCTGTATTAGCTGGAGCTATTACTATATTATTATTTGATCGAAATTTTAATACATCTTTTTTTGATCCAACAGGAGGGGGAGATCCAATTCTTTATCAACATTTATTTTGATTTTTTGGTCATCCTGAAGTTTATATTTTAATTTTACCTGGATTTGGATTAATTTCTCAAATTATTTCTAATGAAAGAGGAAAAAAAGAAACTTTTGGAAATATTGGTATAATTTATGCTATATTAAGAATTGGACTTTTAGGTTTTATTGTT---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------"
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## $`GBAH3879-08`
## [1] "---------------------------------------ATTCTATATATAATTTTTGCTTTATGATCTGGAATAATTGGATCAGCAATA---AGAATTATTATTCGAATAGAATTAAGTATCCCAGGATCATGAATTTCTAAT---GATCAAATTTATAATTCTTTAGTAACTGGTCATGCCTTTTTAATAATTTTTTTTCTTGTCATACCATTTTTAATTGGAGGATTTGGAAATTGATTAATTCCATTAATA---TTAGGAATTCCAGATATAGCTTTTCCTCGAATAAATAATATTAGATTTTGACTTTTACCACCATCCTTAATATTATTACTTTTAAGAAATTTTTTAAATCCAAGACCTGGAACAGGATGAACAATTTATCCACCTTTATCATCAAATTTATTTCATTCTTCTCCTTCAGTTGATTTA---GCAATTTTTTCTTTACATATTTCAGGTTTATCTTCTATTATAGGTTCATTAAATTTTATTGTTACAATTATTATAATAAAAAACATTTCCTTAAAATATATTCAATTATCCTTATTTCCTTGATCTGTATTTATTACTACTATTCTTTTACTTTTTTCTTTACCTGTATTAGCTGGA---GCAATTACTATATTATTATTTGATCGAAATTTTAATACATCTTTTTTTGATCCAACAGGAGGTGGAGATCCAATTCTTTATCAACATTTA------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------"
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Or you can index to a specific sequence like | res$fasta['GBAH0293-06']
## $`GBAH0293-06`
## [1] "------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TTAATGTTAGGGATTCCAGATATAGCTTTTCCACGAATAAATAATATTAGATTTTGACTGTTACCTCCATCTTTAATATTATTACTTTTAAGAAATTTTTTAAATCCAAGTCCTGGAACAGGATGAACAGTTTATCCTCCTTTATCATCAAATTTATTTCATTCTTCTCCTTCAGTTGATTTAGCAATTTTTTCTTTACATATTTCAGGTTTATCTTCTATTATAGGTTCATTAAATTTTATTGTTACAATTATTATAATAAAAAATATTTCTTTAAAATATATTCAATTACCTTTATTTTCTTGATCTGTATTTATTACTACTATTCTTTTATTATTTTCTTTACCTGTATTAGCTGGAGCTATTACTATATTATTATTTGATCGAAATTTTAATACATCTTTTTTTGATCCAACAGGAGGGGGAGATCCAATTCTTTATCAACATTTATTTTGATTTTTTGGTCATCCTGAAGTTTATATTTTAATTTTACCTGGATTTGGATTAATTTCTCAAATTATTTCTAATGAAAGAGGAAAAAAAGAAACTTTTGGAAATATTGGTATAATTTATGCTATATTAAGAATTGGACTTTTAGGTTTTATTGTT---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------"
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Get trace files
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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. | bold_trace(taxon='Osmia', quiet=TRUE)
## Trace file extracted with files:
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## /Users/sacmac/github/ropensci/bold/inst/vign/bold_trace_files/HMBCH056-07_F.ab1
## /Users/sacmac/github/ropensci/bold/inst/vign/bold_trace_files/HMBCH056-07_R.ab1
## /Users/sacmac/github/ropensci/bold/inst/vign/bold_trace_files/HMBCH063-07_F.ab1
## /Users/sacmac/github/ropensci/bold/inst/vign/bold_trace_files/HMBCH063-07_R.ab1
## /Users/sacmac/github/ropensci/bold/inst/vign/bold_trace_files/Osm_aur_T505_LCOHym_D04_008_copy.ab1
## /Users/sacmac/github/ropensci/bold/inst/vign/bold_trace_files/Osm_aur_T505_NancyFull_D10_008_copy.ab1
## /Users/sacmac/github/ropensci/bold/inst/vign/bold_trace_files/Osm_ruf_T309_LCOHym_C06_006_copy.ab1
## /Users/sacmac/github/ropensci/bold/inst/vign/bold_trace_files/Osm_ruf_T309_Nancy_C06_006_copy.ab1
## /Users/sacmac/github/ropensci/bold/inst/vign/bold_trace_files/TRACE_FILE_INFO.txt
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