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commit 768c4aa204fba0a4e22d32f7415821dccd70480e Author: Graham Inggs <[email protected]> Date: Tue Dec 19 20:49:02 2017 +0200 New upstream version 1.0.0 --- DESCRIPTION | 4 ++-- inst/scripts/updateGenomeInfoDbData.R | 8 ++++---- man/GenomeInfoDbData-package.Rd | 14 +++++++------- 3 files changed, 13 insertions(+), 13 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 4735e28..19f4baa 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -2,11 +2,11 @@ Package: GenomeInfoDbData Title: Species and taxonomy ID look up tables used by GenomeInfoDb Description: Files for mapping between NCBI taxonomy ID and species. Used by functions in the GenomeInfoDb package. -Version: 0.99.1 +Version: 1.0.0 Author: Bioconductor Core Team Maintainer: Bioconductor Maintainer <[email protected]> Depends: R (>= 3.3) biocViews: AnnotationData, Organism License: Artistic-2.0 NeedsCompilation: no -Packaged: 2017-10-26 14:18:36 UTC; da42327_ca +Packaged: 2017-12-14 12:34:59 UTC; lori diff --git a/inst/scripts/updateGenomeInfoDbData.R b/inst/scripts/updateGenomeInfoDbData.R index d688958..5e7cedc 100644 --- a/inst/scripts/updateGenomeInfoDbData.R +++ b/inst/scripts/updateGenomeInfoDbData.R @@ -1,6 +1,6 @@ ## Scripts for updating specData, speciesMap and validTaxId -## Download and unpack mapping file: +## Download and unpack mapping file: ## ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz ## Generates specData @@ -21,7 +21,7 @@ keep <- grepl('scientific name', species[[3]]) keep2 <- grepl('synonym', species[[3]]) species <- species[(keep | keep2), 1:2] - + ## split second column by first space: rawSpec <- species[[2]] spltSpec <- strsplit(rawSpec, split=" ") @@ -54,9 +54,9 @@ splt <- splt[idx] ## and keep only 1st two elements taxon <- as.integer(unlist(lapply(splt, function(x){x[1]}))) - species <- unlist(lapply(splt, function(x){x[2]})) + species <- unlist(lapply(splt, function(x){x[2]})) speciesMap <- data.frame(taxon, ## integer - species, ## character + species, ## character stringsAsFactors=FALSE) save(speciesMap, file='speciesMap.rda', compress="xz") diff --git a/man/GenomeInfoDbData-package.Rd b/man/GenomeInfoDbData-package.Rd index c80a8a5..a810a17 100644 --- a/man/GenomeInfoDbData-package.Rd +++ b/man/GenomeInfoDbData-package.Rd @@ -9,14 +9,14 @@ \description{ This package contains three mapping objects: - \itemize{ + \itemize{ \item speciesMap: A data frame with columns \sQuote{tax_id}, - \sQuote{genus}, and \sQuote{species}. Used to retrieve taxonomy - ID by species and returns list of available species. + \sQuote{genus}, and \sQuote{species}. Used to retrieve taxonomy + ID by species and returns list of available species. \item validTaxIds: An integer vector of valid taxonomy IDs created from - \code{speciesMap}. Used internally for quick taxonomy ID look ups. + \code{speciesMap}. Used internally for quick taxonomy ID look ups. \item specData: A data frame with columns \sQuote{taxon} and - \sQuote{species}. Used internally to retrieve species by taxonomy ID. + \sQuote{species}. Used internally to retrieve species by taxonomy ID. } } @@ -34,8 +34,8 @@ data(specData) \examples{ data(speciesMap) -sapply(speciesMap, class) # taxon species - # "integer" "character" +sapply(speciesMap, class) # taxon species + # "integer" "character" subset(speciesMap, species=="Homo sapiens")$taxon # [1] 9606 } -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/r-bioc-genomeinfodbdata.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
