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View Code? Open in Web Editor NEWInterface to the Bold Systems barcode webservice
Home Page: https://docs.ropensci.org/bold
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fmichonneau alexxnica katieroserice graceli8 heibl jorisdhondt jdeck88 ghostsofhiroshima lung1984 salix-d cjfieldsbold's Issues
dual set of parents with genus Ormosia
When i bold_identify() and bold_identify_parents() the following sequence, i get two sets of parents, in two sets of columns. The reason is that the genus name for this sequence (Ormosia) is used in both plants and insects. This makes the identification ambiguous (although I know in this case that the sequence is from an insect). Not sure how to fix this except that the plant and insect Ormosia id numbers are different. thus, i'm not sure how bold_identify_parents could get this wrong?
GMGLM411_13
ACTTTATATTTTATTTTTGGGGCATGAGCGGGTATAGTAGGAACTTCCCTAAGAATTTTAATTCGAGCAGAGCTTGGACACCCAGGAGCATTAATTGGTAATGATCAAATTTATAATGTAATTGTTACCGCTCATGCTTTTGTTATAATTTTTTTTATAGTAATACCAATTATAATTGGAGGATTTGGAAATTGATTAGTACCCCTAATATTAGGGGCTCCTGATATAGCTTTTCCTCGAATAAATAATATAAGTTTTTGATTATTGCCCCCTTCTCTTACTCTTCTTTTAGCAAGTAGTTTAATTGAAAACGGGGCTGGAACAGGTTGAACAGTATATCCCCCGCTATCAGCAGGGATTGCTCATGCCGGAGCTTCAGTTGATTTAGCTATTTTTTCTCTTCATTTAGCAGGAGTTTCTTCAATTTTAGGAGCTGTAAATTTTATTACTACAGTAATTAATATACGATCAACAGGAATTACTTTTGATCGTATACCTTTATTTGTTTGAGCTGTAATTATTACTGCTGTTTTATTATTATTATCTCTCCCAGTTTTAGCAGGAGCTATTACTATACTATTAACAGATCGAAATTTTAATACATCATTTTTTGATCCTGCAGGAGGAGGAGACCCTATTTTATATCAACACTTA
long vectors not supported yet?
I'm very excited to use the bold R-package but have been running into trouble when trying to pull a large dataset together using the bold_seqspec script. Specifically, I'm trying to grab all COI-5P sequences from BOLD's database. That's a lot of data.
I started by installing the package and ran the following script successfully:
install.packages("bold")
library(bold)
df_tiny <- bold_seqspec(taxon="Echiura", marker="COI-5P")
write.table(df_tiny, file = "/home/R/euthria_bold_seqspec.txt", sep = "\t")This creates a 53-column, 58-line text file. I've performed this task in both R-studio and from the command line (running Linux 3.13.0-85-generic, R version 3.3.0) successfully for the above script.
However, I wanted to be able to modify the script above to include the biggest group in one chunk - Arthropods - by running these commands:
df_large <- bold_seqspec(taxon="Arthropoda", marker="COI-5P")
write.table(df_large, file = "/home/R/arthropoda_bold_seqspec.txt", sep = "\t").Unfortunately I get an error message:
Error in rawToChar(content(out, encoding = "UTF-8")) :
long vectors not supported yet: raw.c:68I was under the impression that the relatively recent releases of R have enabled long vectors to be supported. Perhaps more to the point, I wasn't thinking that this was a particularly long vector in terms of columns, but perhaps it does exceed that 900,000 limit in terms of rows (there certainly are more than 900,000 rows in this dataset).
To that end, perhaps you can speak to the maximum number of entries that may be downloaded at once by these scripts (should one exist).
Thanks very much
Submit new version to CRAN once httr v0.4 is on CRAN
bug in bold_identify_parents?
Hello,
bold_identify_parents works fine for me for now, but one sequence does produce an error.
When running:
hittable <- bold_identify("AACGTTATATTTTATTTTTGGAGCATGATCAGGAATAGTAGGAACTTCTTTAAGAATTTTAATTCGAGCTGAATTAGGTCACCCTGGAACATTAATTGGAGATGACCAAATTTATAATGTTATTGTTACAGCACATGCTTTTGTTATAATTTTTTTTATAGTTATACCAATTTTAATT", db="COX1")`
hittable <- bold_identify_parents(hittable, wide=T)I get the following error:
Error in apply(h, 1, function(x) { : dim(X) must have a positive length
in the bold_identify_parents command. This happens every time I try to run it with this sequence. Could you please look into this? Thanks = )
here also my R session info:
sessionInfo()
R version 3.3.2 (2016-10-31)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X El Capitan 10.11.6
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] JAMP_0.1 bold_0.4.0 seqinr_3.3-3
loaded via a namespace (and not attached):
[1] Rcpp_0.12.8 reshape_0.8.6 assertthat_0.1 R6_2.2.0
[5] plyr_1.8.4 jsonlite_1.2 magrittr_1.5 httr_1.2.1
[9] stringi_1.1.2 curl_2.3 data.table_1.10.0 xml2_1.1.0
[13] tools_3.3.2 stringr_1.1.0 ade4_1.7-5bold_seqspec function gives a mixed set of markers when using marker argument
Session Info
Session info -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
setting value
version R version 3.4.1 (2017-06-30)
system x86_64, darwin15.6.0
ui AQUA
language (EN)
collate en_US.UTF-8
tz America/New_York
date 2017-10-16
Packages -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
package * version date source
ade4 1.7-6 2017-03-23 CRAN (R 3.4.0)
ape * 4.1 2017-02-14 CRAN (R 3.4.0)
base * 3.4.1 2017-07-07 local
BiocGenerics * 0.22.1 2017-10-07 Bioconductor
BiocInstaller * 1.26.1 2017-09-01 Bioconductor
bold * 0.5.0 2017-07-21 CRAN (R 3.4.1)
colorspace 1.3-2 2016-12-14 CRAN (R 3.4.0)
compiler 3.4.1 2017-07-07 local
crayon 1.3.2 2016-06-28 CRAN (R 3.4.0)
crul 0.3.8 2017-06-15 CRAN (R 3.4.0)
curl 2.8.1 2017-07-21 CRAN (R 3.4.1)
datasets * 3.4.1 2017-07-07 local
datelife * 0.2.13 2017-10-13 Github (phylotastic/datelife@ae43b8f)
devtools 1.13.3 2017-08-02 CRAN (R 3.4.1)
digest 0.6.12 2017-01-27 CRAN (R 3.4.0)
fastmatch 1.1-0 2017-01-28 CRAN (R 3.4.0)
git2r 0.19.0 2017-07-19 CRAN (R 3.4.1)
graphics * 3.4.1 2017-07-07 local
grDevices * 3.4.1 2017-07-07 local
grid 3.4.1 2017-07-07 local
httr 1.3.1 2017-08-20 cran (@1.3.1)
igraph 1.1.2 2017-07-21 CRAN (R 3.4.1)
ips 0.0-7 2014-11-10 CRAN (R 3.4.0)
IRanges * 2.10.5 2017-10-08 Bioconductor
jsonlite 1.5 2017-06-01 CRAN (R 3.4.0)
lattice 0.20-35 2017-03-25 CRAN (R 3.4.1)
magrittr 1.5 2014-11-22 CRAN (R 3.4.0)
Matrix 1.2-10 2017-05-03 CRAN (R 3.4.1)
memoise 1.1.0 2017-04-21 CRAN (R 3.4.0)
methods * 3.4.1 2017-07-07 local
nlme 3.1-131 2017-02-06 CRAN (R 3.4.1)
parallel * 3.4.1 2017-07-07 local
phangorn 2.2.0 2017-04-03 CRAN (R 3.4.0)
pkgconfig 2.0.1 2017-03-21 CRAN (R 3.4.0)
plyr 1.8.4 2016-06-08 CRAN (R 3.4.0)
quadprog 1.5-5 2013-04-17 CRAN (R 3.4.0)
R6 2.2.2 2017-06-17 CRAN (R 3.4.0)
Rcpp 0.12.12 2017-07-15 CRAN (R 3.4.1)
reshape 0.8.6 2016-10-21 CRAN (R 3.4.0)
S4Vectors * 0.14.7 2017-10-08 Bioconductor
seqinr * 3.4-5 2017-08-01 CRAN (R 3.4.1)
stats * 3.4.1 2017-07-07 local
stats4 * 3.4.1 2017-07-07 local
stringi 1.1.5 2017-04-07 CRAN (R 3.4.0)
stringr 1.2.0 2017-02-18 CRAN (R 3.4.0)
testthat * 1.0.2 2016-04-23 CRAN (R 3.4.0)
tools 3.4.1 2017-07-07 local
triebeard 0.3.0 2016-08-04 CRAN (R 3.4.0)
urltools 1.6.0 2016-10-17 CRAN (R 3.4.0)
utils * 3.4.1 2017-07-07 local
withr 2.0.0 2017-07-28 CRAN (R 3.4.1)
XML * 3.98-1.9 2017-06-19 CRAN (R 3.4.1)
xml2 1.1.1 2017-01-24 CRAN (R 3.4.0) Hi! I've been using bold::bold_seqspec() to search for plant and fungi markers. There appears to be an error with the marker argument, since it will output different types of markers for a single marker query:
library(bold)
res <- bold_seqspec(taxon="Arabidopsis", marker="rbcL")
res$markercode
[1] "rbcL" "rbcL" "rbcL" "rbcL" "rbcL" "rbcL" "rbcL" "rbcL" "rbcL" "rbcL" "rbcL" "rbcL" "rbcL" "rbcL" "rbcL" "rbcL" "rbcL" "rbcL" "rbcL" "rbcL" "rbcL" "rbcL" "rbcL" "rbcL" "rbcL" "rbcL" [27] "rbcL" "rbcL" "matK" "rbcL" "matK" "rbcL" "rbcL" "rbcL" "matK" "rbcL" "rbcL" "matK" "rbcL" "matK" "matK" "rbcL"
And searching for these markers with blast shows that they correspond to the gene specified in $markercode:
which(res$markercode=="rbcL") is rbcL in blast
which(res$markercode=="matK") is matK in blast
res2 <- bold_seqspec(taxon="Arabidopsis", marker=c("ITS2"))
res2$markercode we get a wide mixture of different markers
[1] "ITS2" "rbcLa" "rbcLa" "ITS2" "ITS2" "rbcLa" "rbcLa" "COI-5P" "ITS2" "rbcLa" "ITS2" "rbcLa" "ITS2" "ITS2" "ITS2" "ITS2" "ITS2" "ITS2" "ITS2" "ITS2" [21] "ITS2" "ITS2" "ITS2" "ITS2" "ITS2" "ITS2" "ITS2" "ITS2" "ITS2" "ITS2" "ITS2" "ITS2" "ITS2" "ITS2" "rbcLa" "matK" "ITS2" "rbcLa" "ITS2" "matK" [41] "rbcLa" "ITS2" "matK" "ITS2" "rbcLa" "ITS2" "matK" "rbcLa" "rbcLa" "ITS2"
res3 <- bold_seqspec(taxon="Arabidopsis", marker=c("matK")) # the same problem res3$markercode
[1] "rbcLa" "matK" "matK" "rbcLa" "rbcLa" "matK" "matK" "rbcLa" "matK" "rbcLa" "matK" "matK" "matK" "matK" "matK" "matK" "matK" "matK" "matK" "matK" "matK" "matK" "matK" [24] "matK" "matK" "matK" "matK" "matK" "matK" "rbcL" "matK" "matK" "matK" "rbcL" "rbcLa" "ITS2" "matK" "ITS2" "rbcLa" "matK" "matK" "rbcLa" "ITS2" "matK" "rbcLa" "ITS2" [47] "matK" "rbcL" "rbcL" "matK" "matK" "rbcL" "rbcL" "matK" "rbcLa" "matK"
via email, user reports bug in bold_identify
he says apparently due to xml2
UPdate pkg
Looks like api is working again, update code, etc.
bold_specimens returning poorly formatted data.frame with option format="tsv"
I am using bold::bold_specimens within a custom function to return specimen records for a given taxon in "tsv" format. I am pretty sure this worked fine in the past for me, however now the resulting data.frame is not well formatted. The header line partly wraps into the first row of the data.frame, resulting in a dodgy row 1 and extra 'NA' entries in other rows that shouldn't be there.
Example:
specimen_table <- bold::bold_specimens(taxon="Anaspididae", format="tsv")
specimen_table
processid sampleid recordID catalognum fieldnum
1 image_ids image_urls copyright_licenses trace_ids trace_links
2 GBCM0002-06 AF048821 468923
3
4 GBCM0381-06 DQ310660 501348 HBLB 047 (BIO)
5
6 RBGC001-03 MaAna000 4901 MaAna000
7
institution_storing bin_uri phylum_taxID phylum_name class_taxID
1 run_dates sequencing_centers directions seq_primers marker_codes
2 Mined from GenBank, NCBI BOLD:AAF3961 20 Arthropoda 69
3
4 Mined from GenBank, NCBI BOLD:AAF3962 20 Arthropoda 69
5
6 Biodiversity Institute of Ontario BOLD:AAF3961 20 Arthropoda 69
7
class_name order_taxID order_name family_taxID family_name subfamily_taxID subfamily_name
1 NA NA NA NA
2 Malacostraca 352 Anaspidacea 1697 Anaspididae NA NA
3 NA NA NA NA
4 Malacostraca 352 Anaspidacea 1697 Anaspididae NA NA
5 NA NA NA NA
6 Malacostraca 352 Anaspidacea 1697 Anaspididae NA NA
7 NA NA NA NA
genus_taxID genus_name species_taxID species_name subspecies_taxID subspecies_name
1 NA NA NA NA
2 5694 Anaspides 8241 Anaspides tasmaniae NA NA
3 NA NA NA NA
4 5694 Anaspides 8241 Anaspides tasmaniae NA NA
5 NA NA NA NA
6 5694 Anaspides 8241 Anaspides tasmaniae NA NA
7 NA NA NA NA
identification_provided_by voucher_type tissue_type collectors collectiondate lifestage sex
1 NA NA NA NA NA NA NA
2 NA NA NA NA NA NA NA
3 NA NA NA NA NA NA NA
4 NA NA NA NA NA NA NA
5 NA NA NA NA NA NA NA
6 NA NA NA NA NA NA NA
7 NA NA NA NA NA NA NA
reproduction extrainfo notes lat lon coord_source coord_accuracy country province
1 NA NA NA NA NA NA NA NA
2 NA NA NA NA NA NA NA NA
3 NA NA NA NA NA NA NA NA
4 NA NA NA NA NA NA NA NA
5 NA NA NA NA NA NA NA NA
6 NA Anaspides tasmaniae NA NA NA NA NA NA NA
7 NA NA NA NA NA NA NA NA
region exactsite X
1 NA NA NA
2 NA NA NA
3 NA NA NA
4 NA NA NA
5 NA NA NA
6 NA NA NA
7 NA NA NA
> str(specimen_table)
'data.frame': 7 obs. of 42 variables:
$ processid : chr "image_ids" "GBCM0002-06" "" "GBCM0381-06" ...
$ sampleid : chr "image_urls" "AF048821" "" "DQ310660" ...
$ recordID : chr "copyright_licenses" "468923" "" "501348" ...
$ catalognum : chr "trace_ids" " " "" "HBLB 047 (BIO)" ...
$ fieldnum : chr "trace_links" " " "" " " ...
$ institution_storing : chr "run_dates" "Mined from GenBank, NCBI" "" "Mined from GenBank, NCBI" ...
$ bin_uri : chr "sequencing_centers" "BOLD:AAF3961" "" "BOLD:AAF3962" ...
$ phylum_taxID : chr "directions" "20" "" "20" ...
$ phylum_name : chr "seq_primers" "Arthropoda" "" "Arthropoda" ...
$ class_taxID : chr "marker_codes" "69" "" "69" ...
$ class_name : chr "" "Malacostraca" "" "Malacostraca" ...
$ order_taxID : int NA 352 NA 352 NA 352 NA
$ order_name : chr "" "Anaspidacea" "" "Anaspidacea" ...
$ family_taxID : int NA 1697 NA 1697 NA 1697 NA
$ family_name : chr "" "Anaspididae" "" "Anaspididae" ...
$ subfamily_taxID : logi NA NA NA NA NA NA ...
$ subfamily_name : logi NA NA NA NA NA NA ...
$ genus_taxID : int NA 5694 NA 5694 NA 5694 NA
$ genus_name : chr "" "Anaspides" "" "Anaspides" ...
$ species_taxID : int NA 8241 NA 8241 NA 8241 NA
$ species_name : chr "" "Anaspides tasmaniae" "" "Anaspides tasmaniae" ...
$ subspecies_taxID : logi NA NA NA NA NA NA ...
$ subspecies_name : logi NA NA NA NA NA NA ...
$ identification_provided_by: logi NA NA NA NA NA NA ...
$ voucher_type : logi NA NA NA NA NA NA ...
$ tissue_type : logi NA NA NA NA NA NA ...
$ collectors : logi NA NA NA NA NA NA ...
$ collectiondate : logi NA NA NA NA NA NA ...
$ lifestage : logi NA NA NA NA NA NA ...
$ sex : logi NA NA NA NA NA NA ...
$ reproduction : logi NA NA NA NA NA NA ...
$ extrainfo : chr "" " " "" " " ...
$ notes : logi NA NA NA NA NA NA ...
$ lat : logi NA NA NA NA NA NA ...
$ lon : logi NA NA NA NA NA NA ...
$ coord_source : logi NA NA NA NA NA NA ...
$ coord_accuracy : logi NA NA NA NA NA NA ...
$ country : logi NA NA NA NA NA NA ...
$ province : logi NA NA NA NA NA NA ...
$ region : logi NA NA NA NA NA NA ...
$ exactsite : logi NA NA NA NA NA NA ...
$ X : logi NA NA NA NA NA NA ...
Any help would be very welcome! Thanks in advance.
Session info here:
> devtools::session_info()
Session info --------------------------------------------------------------------------------------
setting value
version R version 3.4.0 (2017-04-21)
system x86_64, darwin15.6.0
ui RStudio (1.0.143)
language (EN)
collate en_AU.UTF-8
tz Australia/Melbourne
date 2017-07-19
Packages ------------------------------------------------------------------------------------------
package * version date source
ape 4.1 2017-02-14 CRAN (R 3.4.0)
assertthat 0.2.0 2017-04-11 CRAN (R 3.4.0)
backports 1.0.5 2017-01-18 CRAN (R 3.4.0)
base * 3.4.0 2017-04-21 local
bindr 0.1 2016-11-13 cran (@0.1)
bindrcpp 0.2 2017-06-17 cran (@0.2)
bold 0.4.0 2017-01-06 CRAN (R 3.4.0)
codetools 0.2-15 2016-10-05 CRAN (R 3.4.0)
commonmark 1.2 2017-03-01 CRAN (R 3.4.0)
compiler 3.4.0 2017-04-21 local
crayon 1.3.2 2016-06-28 CRAN (R 3.4.0)
curl 2.7 2017-06-26 cran (@2.7)
data.table 1.10.4 2017-02-01 CRAN (R 3.4.0)
datasets * 3.4.0 2017-04-21 local
desc 1.1.0 2017-01-27 CRAN (R 3.4.0)
devtools * 1.13.2 2017-06-02 CRAN (R 3.4.0)
digest 0.6.12 2017-01-27 CRAN (R 3.4.0)
dplyr 0.7.1 2017-06-22 cran (@0.7.1)
foreach 1.4.3 2015-10-13 CRAN (R 3.4.0)
git2r 0.18.0 2017-01-01 CRAN (R 3.4.0)
glue 1.1.1 2017-06-21 cran (@1.1.1)
graphics * 3.4.0 2017-04-21 local
grDevices * 3.4.0 2017-04-21 local
grid 3.4.0 2017-04-21 local
httr 1.2.1 2016-07-03 CRAN (R 3.4.0)
iterators 1.0.8 2015-10-13 CRAN (R 3.4.0)
jsonlite 1.5 2017-06-01 cran (@1.5)
lattice 0.20-35 2017-03-25 CRAN (R 3.4.0)
magrittr 1.5 2014-11-22 CRAN (R 3.4.0)
memoise 1.1.0 2017-04-21 CRAN (R 3.4.0)
metabarcodedb * 0.0.0.9000 2017-07-19 local (griffinp/metabarcodedb@b70ec4c)
methods * 3.4.0 2017-04-21 local
nlme 3.1-131 2017-02-06 CRAN (R 3.4.0)
parallel 3.4.0 2017-04-21 local
pbapply 1.3-3 2017-07-04 CRAN (R 3.4.1)
pkgconfig 2.0.1 2017-03-21 cran (@2.0.1)
plyr 1.8.4 2016-06-08 CRAN (R 3.4.0)
R6 2.2.2 2017-06-17 cran (@2.2.2)
Rcpp 0.12.11 2017-05-22 cran (@0.12.11)
rentrez 1.1.0 2017-06-01 cran (@1.1.0)
reshape 0.8.6 2016-10-21 CRAN (R 3.4.0)
reshape2 1.4.2 2016-10-22 CRAN (R 3.4.0)
rlang 0.1.1 2017-05-18 cran (@0.1.1)
roxygen2 * 6.0.1 2017-02-06 CRAN (R 3.4.0)
rprojroot 1.2 2017-01-16 CRAN (R 3.4.0)
stats * 3.4.0 2017-04-21 local
stringi 1.1.5 2017-04-07 CRAN (R 3.4.0)
stringr 1.2.0 2017-02-18 CRAN (R 3.4.0)
taxize 0.8.8 2017-07-01 cran (@0.8.8)
testthat 1.0.2 2016-04-23 CRAN (R 3.4.0)
tibble 1.3.3 2017-05-28 cran (@1.3.3)
tools 3.4.0 2017-04-21 local
utils * 3.4.0 2017-04-21 local
withr 1.0.2 2016-06-20 CRAN (R 3.4.0)
XML 3.98-1.9 2017-06-19 cran (@3.98-1.)
xml2 1.1.1 2017-01-24 CRAN (R 3.4.0)
dependencies not available
I'm not being able to install the package in Ubuntu RStudio. I get the following error:
ERROR: dependencies ‘xml2’, ‘reshape’, ‘plyr’ are not available for package ‘bold’
Whenever I try to install these packages individually, I get that they are not available for R version 3.0.2.
Any suggestion?
link to taxize book in readme/vignette for taxonomic cenetered use cases
Some parsing not working correctly
bold_seq: trim off returns
e.g., bold_seq(taxon='Coelioxys')[[1]]
$id
[1] "ABEE117-17"
$name
[1] "Coelioxys elongata"
$gene
[1] "ABEE117-17"
$sequence
[1] "------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TTATCATTATATACATATCATCCTTCCCCATCAGTTGATTTAGCAATTTTTTYTTTACATTTATCAGGAATTTYTTYTATTATCGGATCAATAAATTTTATTGTAACAATTTTAATAATAAAAAATTATTCAATAAATTATAATCAAATACCTTTATTTCCATGATCAATTTTAATTACTACAATTTTATTATTATTATCATTACCTGTATTAGCAGGAGCTATTACAATATTATTATTTGATCGTAATTTAAATTCATCATTTTTTGACCCAATAGGAGGAGGAGATCCTATTTTATATCAACATTTATTTTG------------------------------------\r"add more tests
replace xml2::xml_find_one with xml2::xml_find_first
bold_specimens returns no records with format="tsv" for taxa with large numbers of records
Hi @sckott, thanks for fixing issue #46 so promptly, the table format seems fine now.
I have run into another issue when using bold_specimens to retrieve info in tsv format for some taxa. I suspect this is a problem for taxa with large numbers of records only. The command returns a (kind of) NA value and no records and does not generate an error message. xml format seems to return okay.
For example:
> bold_specimen_records <- bold::bold_specimens(taxon="Carabidae", format="tsv")
> bold_specimen_records
[1] NA.
<0 rows> (or 0-length row.names)
Whereas it works fine for a taxon with not many sequence records:
> bold_specimen_records <- bold::bold_specimens(taxon="Athericidae", format="tsv")
> bold_specimen_records[1:5,1:5]
processid sampleid recordID catalognum fieldnum
1 BYRN013-12 Byrn12E1 2895459 ByrnE1
2 GBDP14660-13 KC592679 3662005 PLIM180
3 GBDP14675-13 KC592664 3662020 PEET1005
4 GBDP15865-15 KM243490 5649052 NCSU08021521 KM243490
5 MHTAB099-09 ACTDpON10A 1085756 DpONT10A
Session Info
Session info ---------------------------------------------------------------------
setting value
version R version 3.4.0 (2017-04-21)
system x86_64, darwin15.6.0
ui RStudio (1.0.143)
language (EN)
collate en_AU.UTF-8
tz Australia/Melbourne
date 2017-07-21
Packages -------------------------------------------------------------------------
package * version date source
ape 4.1 2017-02-14 CRAN (R 3.4.0)
assertthat 0.2.0 2017-04-11 CRAN (R 3.4.0)
backports 1.1.0 2017-05-22 CRAN (R 3.4.0)
base * 3.4.0 2017-04-21 local
bindr 0.1 2016-11-13 cran (@0.1)
bindrcpp 0.2 2017-06-17 cran (@0.2)
bold 0.5.0 2017-07-21 Github (ropensci/bold@48a9fe9)
codetools 0.2-15 2016-10-05 CRAN (R 3.4.0)
commonmark 1.2 2017-03-01 CRAN (R 3.4.0)
compiler 3.4.0 2017-04-21 local
crayon 1.3.2 2016-06-28 CRAN (R 3.4.0)
crul 0.3.8 2017-06-15 cran (@0.3.8)
curl 2.7 2017-06-26 cran (@2.7)
data.table 1.10.4 2017-02-01 CRAN (R 3.4.0)
datasets * 3.4.0 2017-04-21 local
desc 1.1.0 2017-01-27 CRAN (R 3.4.0)
devtools * 1.13.2 2017-06-02 CRAN (R 3.4.0)
digest 0.6.12 2017-01-27 CRAN (R 3.4.0)
dplyr 0.7.1 2017-06-22 CRAN (R 3.4.1)
foreach 1.4.3 2015-10-13 CRAN (R 3.4.0)
git2r 0.18.0 2017-01-01 CRAN (R 3.4.0)
glue 1.1.1 2017-06-21 cran (@1.1.1)
graphics * 3.4.0 2017-04-21 local
grDevices * 3.4.0 2017-04-21 local
grid 3.4.0 2017-04-21 local
httr 1.2.1 2016-07-03 CRAN (R 3.4.0)
iterators 1.0.8 2015-10-13 CRAN (R 3.4.0)
jsonlite 1.5 2017-06-01 cran (@1.5)
lattice 0.20-35 2017-03-25 CRAN (R 3.4.0)
magrittr 1.5 2014-11-22 CRAN (R 3.4.0)
memoise 1.1.0 2017-04-21 CRAN (R 3.4.0)
metabarcodedb * 0.0.0.9000 <NA> local
methods * 3.4.0 2017-04-21 local
nlme 3.1-131 2017-02-06 CRAN (R 3.4.0)
parallel 3.4.0 2017-04-21 local
pbapply * 1.3-3 2017-07-04 CRAN (R 3.4.1)
pkgconfig 2.0.1 2017-03-21 cran (@2.0.1)
plyr 1.8.4 2016-06-08 CRAN (R 3.4.0)
R6 2.2.2 2017-06-17 cran (@2.2.2)
Rcpp 0.12.12 2017-07-15 CRAN (R 3.4.1)
rentrez 1.1.0 2017-06-01 cran (@1.1.0)
reshape 0.8.6 2016-10-21 CRAN (R 3.4.0)
reshape2 1.4.2 2016-10-22 CRAN (R 3.4.0)
rlang 0.1.1 2017-05-18 cran (@0.1.1)
roxygen2 * 6.0.1 2017-02-06 CRAN (R 3.4.0)
rprojroot 1.2 2017-01-16 CRAN (R 3.4.0)
stats * 3.4.0 2017-04-21 local
stringi 1.1.5 2017-04-07 CRAN (R 3.4.0)
stringr * 1.2.0 2017-02-18 CRAN (R 3.4.0)
taxize 0.8.9 2017-07-11 CRAN (R 3.4.1)
testthat * 1.0.2 2016-04-23 CRAN (R 3.4.0)
tibble 1.3.3 2017-05-28 cran (@1.3.3)
tools 3.4.0 2017-04-21 local
triebeard 0.3.0 2016-08-04 CRAN (R 3.4.0)
urltools 1.6.0 2016-10-17 CRAN (R 3.4.0)
utils * 3.4.0 2017-04-21 local
withr 1.0.2 2016-06-20 CRAN (R 3.4.0)
XML 3.98-1.9 2017-06-19 cran (@3.98-1.)
xml2 1.1.1 2017-01-24 CRAN (R 3.4.0) bioc package isn't installing right, appveyor failing
readme xhtml
From kurt hornik
These have README.md files which when converted to (X)HTML using a
current version of pandoc show problems when validated using W3C Markup
Validator, see below.Most of these problems are caused by using images without giving a name
(so the required alt attribute for<img>is not provided), or using<br>
instead of<br/>.Pls fix these problems in your README.md files for your next release: in
all cases I inspected, the fixes were obvious and confirmation using
pandoc and W3C markup validator seemed unnecessary.Please also visit your package check web page at http://cran.r-project.org/web/checks/check_results_PACKAGENAME.html to see if other problems need to be addressed as well.
switch XML to xml2
Add function for the seq matching API
Add bold taxonomy API functions
related in taxize: ropensci/taxize#301
Add more tests
Change callopts param to ... throughout all fxns
Add parentnames to output of bold_identify()
Hi there,
When I use bold_identify, I get the lowest level taxonomic identification for that sequence (taxonomicidentification field), but it would be very useful if we could get the parentnames for that identification. The bold APIs do provide this information if i use 3 different bold package commands (see below), but i now would have to do some programming in R (not my strength) to insert the parentnames into the bold_identify output table. It seems to me that this would be better done within the bold package, if you fancy it.
also, maybe i have missed something, but i think it would be nicer to get parentnames from a taxid, not a taxonomicidentification field, given the (small) possibility for ambiguity.
thanks,
doug
library(bold)
library(plyr)
testseq <- list(eb4909 = "GAATAAATAATATAAGATTTTGATTACTCCCTCCTTCTTTATTtttATTAATTTTAAGAAATTTTATTGGAACGGGTGTAGGAACCGGATGAACTTTATATCCTCCTTTATCATCTATTGTTGGACATGATTCACCTTCTGTAGATTTAGGAATTttttCTATCCATATTGCTGGAATTTCCTCAATTATAGGATCAATTAATTTTATTGTTACTATTTTAAATATACacacaAaaaCTCATTCACTAAATTTTCTTCCTTTATTCACATGATCAATTTTAATTACAGCAATTCTTCTTCTGTTATCATTACCAGTTCTTGCAGGAGCAATTACTATACTTCTTACAGATCGAAATCTTAATACATCTTtttttGATCCCGCAGGTGGgggggATCCAATTTTATACCAACACTTATTTT")
boldoutput_public <- bold_identify(testseq, db="COX1_SPECIES_PUBLIC")
boldoutput_public.df <- ldply(boldoutput_public, data.frame)
boldoutput_public_tax_name <- bold_tax_name(name=boldoutput_public.df[3,6]) # for a particular identification (third row)
boldoutput_public_tax_name.parents <- bold_tax_id(id=boldoutput_public_tax_name$taxid, includeTree = TRUE)
bug in internal parser
private data API
will be coming next year probably, keep eye out on the api docs
Package does not load with install_github
Fix this...
Make vignette better
It's super basic right now, give more examples
Don't run tests on CRAN
...
Remove methods/stats/utils imports and namespace those calls
network error
bold_identify() is returning a network error (I think this has arisen only in the last few days). the BOLD website is accepting sequences for identification. I'm guessing this is really a BOLD website problem, but i thought i would flag it up.
testseq <- list(eb4909 = "GAATAAATAATATAAGATTTTGATTACTCCCTCCTTCTTTATTtttATTAATTTTAAGAAATTTTATTGGAACGGGTGTAGGAACCGGATGAACTTTATATCCTCCTTTATCATCTATTGTTGGACATGATTCACCTTCTGTAGATTTAGGAATTttttCTATCCATATTGCTGGAATTTCCTCAATTATAGGATCAATTAATTTTATTGTTACTATTTTAAATATACacacaAaaaCTCATTCACTAAATTTTCTTCCTTTATTCACATGATCAATTTTAATTACAGCAATTCTTCTTCTGTTATCATTACCAGTTCTTGCAGGAGCAATTACTATACTTCTTACAGATCGAAATCTTAATACATCTTtttttGATCCCGCAGGTGGgggggATCCAATTTTATACCAACACTTATTTT")
boldoutput <- bold_identify(testseq, db="COX1_SPECIES")
Error in FUN(X[[i]], ...) : Internal Server Error (HTTP 500).bold_tax_name Error in CRAN version
Dear Scott!
Do you plan push the dev version to CRAN some time soon? Just wondering as bold_tax_name() in CRAN (bold v.0.2.0) has this behavior on some queries not found on boldsystems (see below). The CRAN and github code was restructured so I couldn't spot the bug fast enough (hence this post without a solution):
> bold_tax_name('Heteroptera')
Error in `[.data.frame`(data, , vars, drop = FALSE) :
undefined columns selected
Compared with (expected):
> bold_tax_name('Heteropter')
input
1 Heteropter
> bold_tax_name('xHeteroptera')
input
1 xHeteroptera
> bold_tax_name('HeteropteraX')
input
1 HeteropteraX
Cheers
Johan
`bold_tax_name()` throws an error in some cases
e.g.,
bold_tax_name("Cordulegaster erronea") # Throws an error
Error in data.frame(input = y, df, stringsAsFactors = FALSE) :
arguments imply differing number of rows: 1, 0Reported by Bill Buaas
Error in bold_seq (str_split: subscript out of bounds)
Session Info
R version 3.3.2 (2016-10-31)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)
locale:
[1] LC_COLLATE=English_United Kingdom.1252 LC_CTYPE=English_United Kingdom.1252 LC_MONETARY=English_United Kingdom.1252
[4] LC_NUMERIC=C LC_TIME=English_United Kingdom.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] bold_0.8.0
loaded via a namespace (and not attached):
[1] Rcpp_0.12.19 rstudioapi_0.8 xml2_1.2.0 magrittr_1.5 usethis_1.4.0 devtools_2.0.1 pkgload_1.0.1
[8] R6_2.3.0 rlang_0.1.6 stringr_1.2.0 plyr_1.8.4 tools_3.3.2 pkgbuild_1.0.2 sessioninfo_1.1.0
[15] cli_1.0.1 withr_2.1.2 remotes_2.0.1 assertthat_0.2.0 digest_0.6.18 rprojroot_1.3-2 httpcode_0.2.0
[22] crayon_1.3.4 processx_3.2.0 callr_3.0.0 base64enc_0.1-3 fs_1.2.6 ps_1.2.0 triebeard_0.3.0
[29] crul_0.6.0 curl_3.2 testthat_2.0.1 memoise_1.1.0 glue_1.3.0 stringi_1.1.6 urltools_1.7.1
[36] desc_1.2.0 backports_1.1.2 prettyunits_1.0.2 reshape_0.8.8 jsonlite_1.5Hi, I am enjoying playing with this package. Thanks for developing it. When trying this command
bold_arth<-bold_seq(taxon = "Arthropoda")
I get the error
Error in str_split(str_replace(temp[[1]], "\n", "<<<"), "<<<")[[1]][[2]] :
subscript out of bounds
This seems to be a different issue to this resolved issue regarding long vectors with bold_seqspec. I see Arthropoda contains a lot of sequences, but it would still be great to be able to download everything in one go.
Any help would be appreciated.
Add travis file
Add vignette
bold_seq: error well when BOLD server times out
via #52
Markers option not working
A minor bug ... selecting markers has no effect in bold_seqspec.
Not such a high priority, as markers other than COI can be discarded manually after the dataframe is downloaded, but took me a while to work out why my sequences would not align!
unique(bold_seqspec(taxon="Melanogrammus aeglefinus", marker="COI-5P")$markercode)`bold_tax_id()` throws an error in some cases
Add user seqID to bold_identify results
I am trying to batch process sequences with bold_identify and then write results to xlsx. I have completed this task but I lose the original sequence IDs when only the sequences are passed to bold_identify. Would it be possible to add an option to include those when bold_identify returns data from the BOLD API?
> output <- bold_identify (mydata$seqs, db = "COX1", response=FALSE)
> out20 <- lapply(output, head, n=20)
> outframe <- do.call("rbind", lapply(out20, data.frame))
> write.xlsx (outframe, "outframe.xlsx")This bold package is great as I prefer denovo clustering with post hoc taxonomy assignment over clustering with a reference database.
Thank you for any help with this, Tim
Import all non-base R fxns
help files aren't available (0.4.0)
I get this message when trying to read the help files.
Error in fetch(key) : lazy-load database '/Library/Frameworks/R.framework/Versions/3.3/Resources/library/bold/help/bold.rdb' is corrupt
Fungi/plant identification APIs
BOLD responded on 2015-01-31:
We don’t yet have web services for plant and fungi identification but will be making them available within the next 6 months.
keep an eye out for this...ping peggy from email once in the pkg
replace httr with crul
Database description switcheroo in bold_identify documentation
The descriptions of these two databases in the documentation for bold_identify() seem to have been switched around, compared to the boldsystems website.
-
COX1 Every COI barcode record with a species level identification and a minimum sequence length of 500bp. This includes many species represented by only one or two specimens as well as all species with interim taxonomy.
-
COX1_SPECIES Every COI barcode record on BOLD with a minimum sequence length of 500bp (warning: unvalidated library and includes records without species level identification). This includes many species represented by only one or two specimens as well as all species with interim taxonomy. This search only returns a list of the nearest matches and does not provide a probability of placement to a taxon.
See if can fix can't install sangserseq pkg from bioconductor
add slack integration
Graceful failure for lists of taxa
Hi Scott, for some reason a small number of taxa are returning NA dataframes, but more annoyingly, when combined with taxa that are working as expected, also return a NA dataframe. Taxa that are not in BOLD return nothing, and do not interfere with those that are. Hope this example makes sense.
Cheers!
cod <- "Gadus morhua"
haddock <- "Melanogrammus aeglefinus"
pipefish <- "Nerophis lumbriciformis"
str(bold_seqspec(taxon=cod))# taxon in BOLD, but doesn't work (returns a dataframe of NA)
str(bold_seqspec(taxon=haddock))# taxon in BOLD, works (returns nice dataframe)
str(bold_seqspec(taxon=pipefish))# taxon not in BOLD, returns nothing (i.e. works)
str(bold_seqspec(taxon=c(cod,haddock)))# when combined, both fail and a NA dataframe is returned
str(bold_seqspec(taxon=c(haddock,pipefish)))# when combined, returns just haddock data as expectedUpdate vignette with new taxonomy fxns
New v4 beta APIs
http://v4.boldsystems.org/index.php/api_home
See what needs changing, and when to change
Add test suite
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