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/man/
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Package: ROBIBarcodes
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Type: Package
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Title: Metabarcoding barcode database
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Version: 0.1
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Date: 2013-10-24
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Author: LECA - Laboratoire d'ecologie alpine
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Maintainer: LECA OBITools team <obitools@metabarcoding.org>
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Description: More about what it does (maybe more than one line)
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License: CeCILL v2.0
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LazyLoad: yes
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RoxygenNote: 5.0.1
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Collate:
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'ROBIBarcodes.R'
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'xmlMods.R'
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'bibliography.R'
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'ecopcr.R'
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'emptydb.R'
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'logo.R'
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'mismatchplot.R'
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'piexy.R'
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'primer_table.R'
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'primers.R'
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'resolution.R'
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'taxonomy.R'
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'taxonomy_table.R'
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'xmlspare.R'
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# Generated by roxygen2: do not edit by hand
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export(add.reference.barcodedb)
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export(add.taxon.barcodedb)
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export(addmodsnamespace)
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export(bezier3)
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export(bib2mods)
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export(dna.shanon)
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export(dnalogo)
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export(dnalogoplot)
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export(ecopcr.forward.frequencies)
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export(ecopcr.forward.shanon)
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export(ecopcr.reverse.frequencies)
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export(ecopcr.reverse.shanon)
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export(has.bibliography)
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export(metabarcodedb)
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export(metabarcodedb.taxonomy)
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export(mismatchplot)
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export(pie.xy)
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export(plotDNAletter)
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export(primers.data.frame)
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export(read.ecopcr.result)
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export(resolution)
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export(taxonomy.data.frame)
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export(whitepaper)
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import(ROBITaxonomy)
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import(XML)
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useDynLib(ROBIBarcodes)
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#' A package to manipulate DNA metabarcoding data.
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#'
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#' This package was written as a following of the OBITools.
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#'
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#' \tabular{ll}{
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#' Package: \tab ROBIBarcodes\cr
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#' Type: \tab Package\cr
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#' Version: \tab 0.1\cr
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#' Date: \tab 2013-06-27\cr
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#' License: \tab CeCILL 2.0\cr
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#' LazyLoad: \tab yes\cr
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#'}
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#'
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#' @name ROBIBarcodes-package
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#' @aliases ROBIBarcodes
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#' @docType package
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#' @title A package to manipulate DNA metabarcoding marker database.
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#' @author Frederic Boyer
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#' @author Aurelie Bonin
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#' @author Lucie Zinger
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#' @author Eric Coissac
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#'
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#' @references http://metabarcoding.org/obitools
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#'
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NULL
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#'@include xmlMods.R
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#'@import XML
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#'
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NULL
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#' Tests if the metabarcode database has at least one bibliography reference
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#'
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#' @export
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has.bibliography = function(barcodedb) {
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length(getNodeSet(barcodedb,
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path='/obi:obimetabarcodedb/obi:bibliography',
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c(obi="http://metabarcoding.org/OBIMetabarcodes")))>0
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}
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#' @export
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add.reference.barcodedb = function(barcodedb,bibfile,bibutils='bib2xml') {
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if (! has.bibliography(barcodedb)) {
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# We create the bibliography node
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metabarcode = getNodeSet(barcodedb,
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path='/obi:obimetabarcodedb',
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c(obi="http://metabarcoding.org/OBIMetabarcodes"))[[1]]
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spare = sparexmltree()
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bibliography = getNodeSet(spare,
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path='/obi:obimetabarcodedb/obi:bibliography',
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c(obi="http://metabarcoding.org/OBIMetabarcodes"))[[1]]
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bibliography = xmlClone(bibliography)
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addChildren(metadata,bibliography,
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at = NA)
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}
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bibliography=getNodeSet(barcodedb,
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path='/obi:obimetabarcodedb/obi:bibliography',
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c(obi="http://metabarcoding.org/OBIMetabarcodes"))
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ref = bib2mods(bibfile,bibutils)
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hidden=addChildren(bibliography[[1]],kids=ref)
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}
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#'@include ROBIBarcodes.R
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NULL
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# column 1 : accession number
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# column 2 : sequence length
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# column 3 : taxonomic id
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# column 4 : rank
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# column 5 : species taxonomic id
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# column 6 : scientific name
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# column 7 : genus taxonomic id
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# column 8 : genus name
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# column 9 : family taxonomic id
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# column 10 : family name
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# column 11 : super kingdom taxonomic id
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# column 12 : super kingdom name
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# column 13 : strand (direct or reverse)
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# column 14 : first oligonucleotide
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# column 15 : number of errors for the first strand
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# column 16 : Tm for hybridization of primer 1 at this site
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# column 17 : second oligonucleotide
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# column 18 : number of errors for the second strand
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# column 19 : Tm for hybridization of primer 1 at this site
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# column 20 : amplification length
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# column 21 : sequence
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# column 22 : definition
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#' Read the result file produced by the ecoPCR program.
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#'
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#' @export
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read.ecopcr.result = function(file)
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{
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split.line = function(line) {
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l = strsplit(line,split=" +\\| +")[[1]]
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l = c(l[1:21],paste(l[-c(1:21)],sep="|"))
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return(l)
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}
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if (missing(file) && !missing(text)) {
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file <- textConnection(text)
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on.exit(close(file))
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}
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if (is.character(file)) {
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file <- file(file, "rt")
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on.exit(close(file))
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}
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if (!inherits(file, "connection"))
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stop("'file' must be a character string or connection")
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if (!isOpen(file, "rt")) {
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open(file, "rt")
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on.exit(close(file))
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}
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line = readLines(file,1)
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while (length(grep('^#',line))==1) {
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line = readLines(file,1)
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}
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pushBack(line,file)
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lines = lapply(readLines(file),split.line)
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nlines = length(lines)
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AC = sapply(1:nlines,function(x) lines[[x]][1])
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seq_length = as.integer(sapply(1:nlines,function(x) lines[[x]][2]))
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taxid = as.integer(sapply(1:nlines,function(x) lines[[x]][3]))
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rank = as.factor(sapply(1:nlines,function(x) lines[[x]][4]))
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species = type.convert(sapply(1:nlines,function(x) lines[[x]][5]),na.string="###")
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species_name = sapply(1:nlines,function(x) lines[[x]][6])
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genus = type.convert(sapply(1:nlines,function(x) lines[[x]][7]),na.string="###")
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genus_name = sapply(1:nlines,function(x) lines[[x]][8])
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family = type.convert(sapply(1:nlines,function(x) lines[[x]][9]),na.string="###")
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family_name = sapply(1:nlines,function(x) lines[[x]][10])
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superkingdom = type.convert(sapply(1:nlines,function(x) lines[[x]][11]),na.string="###")
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superkingdom_name = sapply(1:nlines,function(x) lines[[x]][12])
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strand = as.factor(sapply(1:nlines,function(x) lines[[x]][13]))
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forward_match = sapply(1:nlines,function(x) lines[[x]][14])
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forward_mismatch = as.integer(sapply(1:nlines,function(x) lines[[x]][15]))
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forward_tm = as.double(sapply(1:nlines,function(x) lines[[x]][16]))
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reverse_match = sapply(1:nlines,function(x) lines[[x]][17])
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reverse_mismatch = as.integer(sapply(1:nlines,function(x) lines[[x]][18]))
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reverse_tm = as.double(sapply(1:nlines,function(x) lines[[x]][19]))
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amplicon_length = as.integer(sapply(1:nlines,function(x) lines[[x]][20]))
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sequence = sapply(1:nlines,function(x) lines[[x]][21])
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definition = sapply(1:nlines,function(x) lines[[x]][22])
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eco = data.frame(AC,seq_length,taxid,rank,
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species,species_name,
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genus,genus_name,
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family,family_name,
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superkingdom,superkingdom_name,
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strand,
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forward_match,forward_mismatch,forward_tm,
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reverse_match,reverse_mismatch,reverse_tm,
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amplicon_length,sequence,definition
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)
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return(eco)
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}
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ecopcr.frequencies = function(matches,group=NULL) {
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compute = function(matches) {
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w = as.matrix(do.call(rbind,strsplit(as.character(matches),'')))
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d = dim(w)
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w=factor(w,levels=c('A','C','G','T'))
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dim(w)=d
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w=t(w)
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freq = mapply(function(x) table(w[x,]),1:d[2])
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freq = freq[c('A','C','G','T'),]
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csum = colSums(freq)
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freq = sweep(freq,2,csum,'/')
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attr(freq,'count')=length(w)
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return(freq)
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}
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if (is.null(group))
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return(compute(matches))
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else {
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lmatches = aggregate(matches,by=list(group=as.factor(group)),as.character)
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w = lmatches$x
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names(w)=lmatches$group
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lf = lapply(w,compute)
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return(lf)
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}
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}
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#' @export
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ecopcr.forward.frequencies = function(ecopcr,group=NULL) {
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return(ecopcr.frequencies(ecopcr$forward_match,group))
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}
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#' @export
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ecopcr.reverse.frequencies = function(ecopcr,group=NULL) {
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return(ecopcr.frequencies(ecopcr$reverse_match,group))
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}
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#' @export
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dna.shanon = function(freq,base=2) {
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shanon = log(4)/log(base) - colSums(-freq *log(freq) / log(base),na.rm=TRUE)
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return(sweep(freq,2,shanon,'*'))
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}
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ecopcr.shanon = function(matches,group=NULL,base=2) {
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if (is.null(group)) {
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freq = ecopcr.frequencies(matches)
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return(dna.shanon(freq))
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}
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else {
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lf = lapply(ecopcr.frequencies(matches,group),dna.shanon)
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return(lf)
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}
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}
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#' @export
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ecopcr.forward.shanon = function(ecopcr,group=NULL,base=2) {
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return(ecopcr.shanon(ecopcr$forward_match,group,base))
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}
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#' @export
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ecopcr.reverse.shanon = function(ecopcr,group=NULL,base=2) {
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return(ecopcr.shanon(ecopcr$reverse_match,group,base))
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}
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#'@include ROBIBarcodes.R
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#'@import XML
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#'
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NULL
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#' Creates a new empty metabarcode database.
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#'
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#' @export
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metabarcodedb = function() {
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emptyfile = paste(system.file("extdata",
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package="ROBIBarcodes"),
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'empty.xml',
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sep='/')
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empty = xmlParseDoc(emptyfile)
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return(empty)
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}
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#'@include ROBIBarcodes.R
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NULL
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|
||||
svg.S.path="m 59.912109,-70.605469 0,15.429688 c -4.003962,-1.790308 -7.910208,-3.141218 -11.71875,-4.052735 -3.808638,-0.911398 -7.405639,-1.367127 -10.791015,-1.367187 -4.492221,6e-5 -7.81253,0.618549 -9.960938,1.855469 -2.148463,1.237036 -3.22268,3.157607 -3.222656,5.761718 -2.4e-5,1.953176 0.716121,3.483123 2.148437,4.589844 1.464816,1.074266 4.101533,2.002 7.910157,2.783203 l 8.007812,1.611328 c 8.105419,1.627647 13.867132,4.101603 17.285156,7.421875 3.417906,3.320346 5.126889,8.040393 5.126954,14.160157 -6.5e-5,8.040379 -2.392641,14.0299559 -7.177735,17.9687496 -4.752657,3.90625056 -12.02804,5.8593736 -21.826172,5.859375 C 31.070932,1.4160142 26.432265,0.97656152 21.777344,0.09765625 17.122379,-0.78124922 12.467435,-2.0833313 7.8125,-3.8085938 l 0,-15.8691402 c 4.654935,2.473975 9.147118,4.345718 13.476562,5.615234 4.361954,1.236992 8.561169,1.855481 12.597657,1.855469 4.101524,1.2e-5 7.242797,-0.683581 9.423828,-2.050782 2.180944,-1.367171 3.271438,-3.320294 3.271484,-5.859374 -4.6e-5,-2.278624 -0.748744,-4.036435 -2.246094,-5.273438 -1.464886,-1.236953 -4.410847,-2.343722 -8.83789,-3.320312 l -7.275391,-1.611329 c -7.291687,-1.562468 -12.630224,-4.0527 -16.015625,-7.470703 -3.3528732,-3.417927 -5.0293038,-8.024042 -5.0292966,-13.818359 -7.2e-6,-7.259056 2.3437405,-12.841733 7.0312496,-16.748047 4.687481,-3.906178 11.425756,-5.859301 20.214844,-5.859375 4.003868,7.4e-5 8.121702,0.309319 12.353516,0.927734 4.23172,0.586011 8.60997,1.481192 13.134765,2.685547"
|
||||
svg.B.path="m 38.378906,-44.677734 c 2.962198,4.4e-5 5.20829,-0.650997 6.738281,-1.953125 1.529902,-1.302036 2.294875,-3.222607 2.294922,-5.761719 -4.7e-5,-2.506456 -0.76502,-4.410751 -2.294922,-5.712891 -1.529991,-1.334576 -3.776083,-2.001893 -6.738281,-2.001953 l -10.40039,0 0,15.429688 10.40039,0 m 0.634766,31.884765 c 3.775999,1.3e-5 6.608027,-0.797512 8.496094,-2.392578 1.920523,-1.595035 2.880809,-4.003887 2.880859,-7.226562 -5e-5,-3.157527 -0.94406,-5.517551 -2.832031,-7.080078 -1.888067,-1.595021 -4.736371,-2.392547 -8.544922,-2.392579 l -11.035156,0 0,19.091797 11.035156,0 m 17.480469,-26.220703 c 4.036397,1.171913 7.161394,3.336624 9.375,6.494141 2.213473,3.157581 3.320243,7.031275 3.320312,11.621094 -6.9e-5,7.031263 -2.376369,12.2721435 -7.128906,15.7226558 C 57.307885,-1.7252587 50.08133,0 40.380859,0 l -31.2011715,0 0,-72.900391 28.2226565,0 c 10.12365,7.3e-5 17.447862,1.53002 21.972656,4.589844 4.557228,3.059961 6.835871,7.959045 6.835937,14.697266 -6.6e-5,3.548227 -0.830143,6.575568 -2.490234,9.082031 -1.660218,2.474 -4.06907,4.313191 -7.226562,5.517578"
|
||||
svg.D.path="m 27.978516,-58.691406 0,44.482422 6.738281,0 c 7.682249,1.4e-5 13.541618,-1.904281 17.578125,-5.712891 4.068954,-3.80857 6.103457,-9.342419 6.103515,-16.601562 -5.8e-5,-7.226519 -2.018285,-12.727816 -6.054687,-16.503907 -4.036507,-3.775985 -9.912152,-5.664004 -17.626953,-5.664062 l -6.738281,0 m -18.7988285,-14.208985 19.8242185,0 c 11.067669,7.3e-5 19.303337,0.797599 24.707031,2.392579 5.436139,1.562568 10.091083,4.231837 13.964844,8.007812 3.417898,3.28782 5.956958,7.080134 7.617188,11.376953 1.660079,4.296922 2.490156,9.163454 2.490234,14.59961 -7.8e-5,5.501333 -0.830155,10.416692 -2.490234,14.746093 -1.66023,4.296893 -4.19929,8.089207 -7.617188,11.376953 -3.906314,3.7760487 -8.593809,6.4615929 -14.0625,8.056641 C 48.144483,-0.78124922 39.941366,0 29.003906,0 l -19.8242185,0 0,-72.900391"
|
||||
svg.H.path="m 9.1796875,-72.900391 18.7988285,0 0,27.783204 27.734375,0 0,-27.783204 18.798828,0 0,72.900391 -18.798828,0 0,-30.908203 -27.734375,0 0,30.908203 -18.7988285,0 0,-72.900391"
|
||||
svg.V.path="m 0.48828125,-72.900391 18.89648475,0 19.335937,53.808594 19.287109,-53.808594 18.896485,0 L 49.902344,0 27.490234,0 0.48828125,-72.900391"
|
||||
svg.N.path="m 9.1796875,-72.900391 20.9960935,0 26.513672,50 0,-50 17.822266,0 0,72.900391 -20.996094,0 -26.513672,-50 0,50 -17.8222655,0 0,-72.900391"
|
||||
|
||||
svg.dash.path="m 5.4199219,-35.888672 l 30.6640621,0 0,14.208985 -30.6640621,0 0,-14.208985"
|
||||
|
||||
#' Compute the cubic bezier function
|
||||
#'
|
||||
#' The \code{bezier3} function computes the point of the cubic bezier
|
||||
#' curve linking the point P0 to P3 and using P1 and P2 as control points
|
||||
#'
|
||||
#' @param t the position on the curve estimated as a float between 0 the
|
||||
#' starting point and 1 the ending point
|
||||
#'
|
||||
#' @param p0 a vector of numeric describing the coordinates of the p0 point,
|
||||
#' the starting point of the curve.
|
||||
#'
|
||||
#' @param p1 a vector of numeric describing the coordinates of the p1 point,
|
||||
#' the first control point.
|
||||
#'
|
||||
#' @param p2 a vector of numeric describing the coordinates of the p2 point,
|
||||
#' the second control point.
|
||||
#'
|
||||
#' @param p3 a vector of numeric describing the coordinates of the p3 point,
|
||||
#' the final point of the curve.
|
||||
#'
|
||||
#' @return a numric matrix containing the coordinates of the bezier curve/
|
||||
#'
|
||||
#' @examples
|
||||
#'
|
||||
#' bezier3((1:10)/10,c(1,1),c(1,2),c(2,2),c(2,1))
|
||||
#'
|
||||
#' @author Eric Coissac
|
||||
#' @export
|
||||
bezier3 = function(t,p0,p1,p2,p3) {
|
||||
outer((1-t)^3,p0) + outer(t*(1-t)^2,3*p1) + outer(t^2*(1-t),3*p2) + outer(t^3,p3)
|
||||
}
|
||||
|
||||
lmin = function(l) min(sapply(l,min))
|
||||
lmax = function(l) max(sapply(l,max))
|
||||
|
||||
path.to.polygon = function(path,scalex=TRUE,scaley=TRUE) {
|
||||
|
||||
x = strsplit(path," ")[[1]]
|
||||
y = c()
|
||||
for (c in x) {
|
||||
if (length(grep(',',c))==0)
|
||||
current=c
|
||||
else {
|
||||
y = c(y,current,c)
|
||||
if (current=='m')
|
||||
current='l'
|
||||
if (current=='M')
|
||||
current='L'
|
||||
|
||||
}
|
||||
}
|
||||
|
||||
dim(y)=c(2,length(y)/2)
|
||||
y=t(y)
|
||||
operations = y[,1]
|
||||
positions = do.call(rbind,strsplit(y[,2],","))
|
||||
positions = apply(positions,2,as.numeric)
|
||||
|
||||
positions = data.frame(operations,x=positions[,1],y=positions[,2])
|
||||
|
||||
|
||||
relatives = positions$operations == tolower(positions$operations)
|
||||
operations=toupper(operations)
|
||||
|
||||
current.x=0
|
||||
current.y=0
|
||||
|
||||
n = dim(positions)[1]
|
||||
|
||||
absolute.x=c()
|
||||
absolute.y=c()
|
||||
|
||||
remains=0
|
||||
|
||||
for (i in 1:n) {
|
||||
|
||||
if (remains==0) {
|
||||
if (operations[i]=='C')
|
||||
remains=3
|
||||
else
|
||||
remains=1
|
||||
}
|
||||
if (relatives[i]) {
|
||||
new.x = current.x + positions$x[i]
|
||||
new.y = current.y + positions$y[i]
|
||||
}
|
||||
else {
|
||||
new.x = positions$x[i]
|
||||
new.y = positions$y[i]
|
||||
}
|
||||
|
||||
absolute.x = c(absolute.x,new.x)
|
||||
absolute.y = c(absolute.y,new.y)
|
||||
|
||||
remains=remains-1
|
||||
|
||||
if (remains==0) {
|
||||
current.x=new.x
|
||||
current.y=new.y
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
c = (1:length(operations))[operations=='C']
|
||||
|
||||
if (length(c)>0){
|
||||
p0=c[0:(length(c)/3-1)*3+1]
|
||||
operations[p0+1]="X"
|
||||
operations[p0+2]="X"
|
||||
}
|
||||
|
||||
allpath.x=list()
|
||||
allpath.y=list()
|
||||
path.x = c()
|
||||
path.y = c()
|
||||
for (i in 1:length(operations)) {
|
||||
if (operations[i]=='M' & length(path.x)>0) {
|
||||
allpath.x[[length(allpath.x)+1]]=path.x
|
||||
allpath.y[[length(allpath.y)+1]]=path.y
|
||||
path.x = c()
|
||||
path.y = c()
|
||||
}
|
||||
|
||||
|
||||
if (operations[i]=='M' | operations[i]=='L') {
|
||||
path.x = append(path.x,absolute.x[i])
|
||||
path.y = append(path.y,absolute.y[i])
|
||||
}
|
||||
if (operations[i]=='C') {
|
||||
b = bezier3((0:10)/10,c(absolute.x[i-1],absolute.y[i-1]),
|
||||
c(absolute.x[i],absolute.y[i]),
|
||||
c(absolute.x[i+1],absolute.y[i+1]),
|
||||
c(absolute.x[i+2],absolute.y[i+2]))
|
||||
path.x = c(path.x,b[-1,1])
|
||||
path.y = c(path.y,b[-1,2])
|
||||
}
|
||||
}
|
||||
|
||||
allpath.x[[length(allpath.x)+1]]=path.x
|
||||
allpath.y[[length(allpath.y)+1]]=path.y
|
||||
|
||||
allpath.y=lapply(allpath.y,"-")
|
||||
|
||||
|
||||
if (scalex) {
|
||||
xmin = lmin(allpath.x)
|
||||
sx=lmax(allpath.x)-xmin
|
||||
allpath.x=lapply(allpath.x,function(x) (x-xmin)/sx)
|
||||
}
|
||||
else
|
||||
allpath.x=lapply(allpath.x,function(x) x/100)
|
||||
|
||||
if (scaley) {
|
||||
ymin = lmin(allpath.y)
|
||||
sy=lmax(allpath.y)-ymin
|
||||
allpath.y=lapply(allpath.y,function(x) (x-ymin)/sy)
|
||||
}
|
||||
else
|
||||
allpath.y=lapply(allpath.y,function(x) x/100)
|
||||
|
||||
o = order(-sapply(allpath.x,length))
|
||||
|
||||
return(list(x=allpath.x[o],y=allpath.y[o]))
|
||||
}
|
||||
|
||||
#' Draw an empy plot without axis
|
||||
#'
|
||||
#' The \code{whitepaper} function open a new plot of the given size where
|
||||
#' you can add graphical elements. Coordinates on this plot range from
|
||||
#' 0 to \code{width} and 0 to \code{height}.
|
||||
#'
|
||||
#' @param width a numeric value indicating the plot width
|
||||
#'
|
||||
#' @param height a numeric value indicating the plot height
|
||||
#'
|
||||
#' @examples
|
||||
#'
|
||||
#' # open a new empty plot
|
||||
#' whitepaper(20,10)
|
||||
#'
|
||||
#' # add two point on this plot
|
||||
#' points(c(10,15),c(3,8))
|
||||
#'
|
||||
#' @author Eric Coissac
|
||||
#'
|
||||
#' @export
|
||||
whitepaper= function(width,height,xmin=0,ymin=0,asp=NA) {
|
||||
plot(c(xmin,xmin+width),c(ymin,ymin+height),
|
||||
xlab="",
|
||||
ylab="",xaxt="n",yaxt="n",type="n",asp=asp)
|
||||
}
|
||||
|
||||
|
||||
#
|
||||
# We just prepare the polygon coordinates for all the 16 DNA letters
|
||||
#
|
||||
|
||||
letter.polygons = list(A=path.to.polygon(svg.A.path),
|
||||
C=path.to.polygon(svg.C.path),
|
||||
G=path.to.polygon(svg.G.path),
|
||||
T=path.to.polygon(svg.T.path),
|
||||
R=path.to.polygon(svg.R.path),
|
||||
Y=path.to.polygon(svg.Y.path),
|
||||
M=path.to.polygon(svg.M.path),
|
||||
K=path.to.polygon(svg.K.path),
|
||||
W=path.to.polygon(svg.W.path),
|
||||
S=path.to.polygon(svg.S.path),
|
||||
B=path.to.polygon(svg.B.path),
|
||||
D=path.to.polygon(svg.D.path),
|
||||
H=path.to.polygon(svg.H.path),
|
||||
V=path.to.polygon(svg.V.path),
|
||||
N=path.to.polygon(svg.N.path),
|
||||
dash=path.to.polygon(svg.dash.path,scaley=FALSE)
|
||||
)
|
||||
|
||||
|
||||
#' Draw a single DNA letter on a plot
|
||||
#'
|
||||
#' The function \code{plotDNAletter} draws a single DNA letter on an existing
|
||||
#' plot. The alphabet is restricted to the IUPAC DNA characters plus the dash
|
||||
#' '-' allowing to indicate gaps.
|
||||
#'
|
||||
#' @param x an value indicating the x coordinate for locating the letter
|
||||
#' on the plot.
|
||||
#'
|
||||
#' @param y an value indicating the y coordinate for locating the letter
|
||||
#' on the plot.
|
||||
#'
|
||||
#' @param cex the X character expension factor. By default a letter width is of
|
||||
#' one unit in the user coordinate system.
|
||||
#'
|
||||
#' @param cey the Y character expension factor. By default a letter height is of
|
||||
#' one unit in the user coordinate system.
|
||||
#'
|
||||
#' @param col the color used to fill the letter.
|
||||
#'
|
||||
#' @param background the background color of the letter.
|
||||
#'
|
||||
#' @param border the color of the border of the letter.
|
||||
#'
|
||||
#' @examples
|
||||
#'
|
||||
#' # open an empty plot
|
||||
#' whitepaper(10,10)
|
||||
#'
|
||||
#' # plot some DNA letters
|
||||
#' plotDNAletter(5,5,'A',col='green')
|
||||
#' plotDNAletter(7,6,'C',cex=2,cey=1.5,col='blue')
|
||||
#' plotDNAletter(2,3,'-')
|
||||
#' plotDNAletter(2,7,'A',col='green',background="yellow",border="black")
|
||||
#'
|
||||
#' @seealso \code{\link{whitepaper}}
|
||||
#' @author Eric Coissac
|
||||
#' @export
|
||||
plotDNAletter = function(x,y,c,cex=1,cey=1,col="black",background="white",border=col) {
|
||||
if (cex > 0 & cey > 0){
|
||||
if (c=="-")
|
||||
p=letter.polygons[['dash']]
|
||||
else
|
||||
p=letter.polygons[[c]]
|
||||
|
||||
px = lapply(p$x,function(a) a*cex+x)
|
||||
py = lapply(p$y,function(a) a*cey+y)
|
||||
color=c(col,rep(background,length(px)-1))
|
||||
border=c(border,rep(background,length(px)-1))
|
||||
polygon(c(x,x,x+cex,x+cex),c(y,y+cey,y+cey,y),col=background,border=background)
|
||||
mapply(polygon,px,py,col=color,border=border)
|
||||
}
|
||||
}
|
||||
|
||||
#' Draw a DNA logo on a graph
|
||||
#'
|
||||
#' The function \code{dnalogo} draws a DNA logo on an already existing plot.
|
||||
#'
|
||||
#' @param data a matrix where each line represents a symbol and each column
|
||||
#' represents a position. The values stored in the matrice indicate
|
||||
#' the relative weight of a symbol at the considered position.
|
||||
#'
|
||||
#' @param x an value indicating the x coordinate for locating the logo
|
||||
#' on the plot.
|
||||
#'
|
||||
#' @param y an value indicating the y coordinate for locating the logo
|
||||
#' on the plot.
|
||||
#'
|
||||
#' @param width a value indicating the total width of the logo
|
||||
#'
|
||||
#' @param height a value indicating the total height of the logo
|
||||
#'
|
||||
#' @param col a named character vector (e.g \code{(A="purple",T="yellow")})
|
||||
#' or a matrix of the same size than data indicating the color
|
||||
#' for each letter.
|
||||
#'
|
||||
#' @param cex a float between 0 and 1 indicating the relative width
|
||||
#' of a letter column.
|
||||
#'
|
||||
#'
|
||||
#' @examples
|
||||
#' # Load the sample ecoPCR data file
|
||||
#' data(GH.ecopcr)
|
||||
#'
|
||||
#' # create a blank plot
|
||||
#' whitepaper(25,10)
|
||||
#'
|
||||
#' # computes the logo shape with the shanon formula
|
||||
#' G.shanon = ecopcr.forward.shanon(GH.ecopcr)
|
||||
#'
|
||||
#' # plot the logo
|
||||
#' dnalogo(G.shanon,2,6,width=20,height=2)
|
||||
#'
|
||||
#' # computes the logo shape with the shanon formula
|
||||
#' # by grouping matches according to their mismatches
|
||||
#' G.shanon.error = ecopcr.forward.shanon(GH.ecopcr,
|
||||
#' group=GH.ecopcr$forward_mismatch>=1)
|
||||
#'
|
||||
#' # Display the structure
|
||||
#' G.shanon.error
|
||||
#'
|
||||
#' # Plot the logo corresponding only to matches with errors
|
||||
#' dnalogo(G.shanon.error$'TRUE',2,3,width=20,height=2)
|
||||
#'
|
||||
#' @seealso \code{\link{dnalogoplot}}
|
||||
#' @author Eric Coissac
|
||||
#' @keywords metabarcodes
|
||||
#'
|
||||
#' @export
|
||||
dnalogo = function(data,x=0,y=0,width=NULL,height=NULL,col=NULL,cex=0.8)
|
||||
{
|
||||
computey = function(p) {
|
||||
o = draworder[,p]
|
||||
x = c(0,cumsum(data[o,p])[2:length(o) - 1])
|
||||
names(x)=letters[o]
|
||||
return(x[letters])
|
||||
}
|
||||
|
||||
ddata = dim(data)
|
||||
ncol = ddata[2]
|
||||
nrow = ddata[1]
|
||||
letters = row.names(data)
|
||||
|
||||
|
||||
if (is.character(col) | is.null(col)) {
|
||||
dnacol = c(A='green',C='blue',G='orange',T='red')
|
||||
name.color = names(col)
|
||||
dnacol[name.color]=col
|
||||
dnacol=dnacol[letters]
|
||||
dnacol=sapply(dnacol,function(x) do.call(rgb,as.list(col2rgb(x)/255)))
|
||||
dnacol=matrix(rep(dnacol,ncol),nrow=nrow)
|
||||
}
|
||||
|
||||
draworder = apply(data,2,order)
|
||||
ypos = sapply(1:ncol,computey)
|
||||
xpos = matrix(rep(1:ncol,rep(nrow,ncol)),nrow=4) - 0.5
|
||||
|
||||
|
||||
if (! is.null(width)) {
|
||||
actualwidth = ncol + 1
|
||||
xpos = xpos / actualwidth * width
|
||||
cex = cex / actualwidth * width
|
||||
}
|
||||
|
||||
if (! is.null(height)) {
|
||||
actualheight= max(colSums(data))
|
||||
ypos = ypos / actualheight * height
|
||||
data = data / actualheight * height
|
||||
}
|
||||
|
||||
if (! is.null(x))
|
||||
xpos = xpos + x
|
||||
|
||||
if (! is.null(y))
|
||||
ypos = ypos + y
|
||||
|
||||
hide = mapply(plotDNAletter,
|
||||
as.vector(xpos),as.vector(ypos),
|
||||
rep(letters,ncol),
|
||||
cex,as.vector(data),
|
||||
as.vector(dnacol))
|
||||
}
|
||||
|
||||
#' Plot a DNA logo
|
||||
#'
|
||||
#' The function \code{dnalogoplot} draws a DNA logo.
|
||||
#'
|
||||
#' @param data a matrix where each line represents a symbol and each column
|
||||
#' represents a position. The values stored in the matrice indicate
|
||||
#' the relative weight of a symbol at the considered position.
|
||||
#'
|
||||
#' @param col a named character vector (e.g \code{(A="purple",T="yellow")})
|
||||
#' or a matrix of the same size than data indicating the color
|
||||
#' for each letter.
|
||||
#'
|
||||
#' @param primer the primer sequence. THe letters will be used to label the
|
||||
#' X axis.
|
||||
#'
|
||||
#' @param xlab X axis label using font and character expansion
|
||||
#' par("font.lab") and color par("col.lab")
|
||||
#'
|
||||
#' @param ylab Y axis label, same font attributes as xlab.
|
||||
#'
|
||||
#' @param main The main title (on top) using font and size (character expansion)
|
||||
#' \code{par("font.main")} and color \code{par("col.main")}.
|
||||
#'
|
||||
#' @param sub Sub-title (at bottom) using font and size \code{par("font.sub")}
|
||||
#' and color \code{par("col.sub")}.
|
||||
#'
|
||||
#' @param line specifying a value for line overrides the default placement of
|
||||
#' labels, and places them this many lines outwards
|
||||
#' from the plot edge.
|
||||
#'
|
||||
#' @param outer a logical value. If \code{TRUE}, the titles are placed in the outer
|
||||
#' margins of the plot.
|
||||
#'
|
||||
#' @param cex a float between 0 and 1 indicating the relative width
|
||||
#' of a letter column.
|
||||
#'
|
||||
#' @param cex.primer a float between 0 and 1 indicating the size
|
||||
#' of the primer axis.
|
||||
#'
|
||||
#' @examples
|
||||
#' # Load the sample ecoPCR data file
|
||||
#' data(GH.ecopcr)
|
||||
#'
|
||||
#' # computes the logo shape with the shanon formula
|
||||
#' G.shanon = ecopcr.forward.shanon(GH.ecopcr)
|
||||
#'
|
||||
#' par(mfrow=c(2,1))
|
||||
#'
|
||||
#' # plot the logo
|
||||
#' dnalogoplot(G.shanon,primer="GGGCAATCCTGAGCCAA",
|
||||
#' xlab="Primer H",ylab='bits',
|
||||
#' main="Primer conservation")
|
||||
#'
|
||||
#' # computes the logo shape with the shanon formula
|
||||
#' # by grouping matches according to their mismatches
|
||||
#' G.shanon.error = ecopcr.forward.shanon(GH.ecopcr,
|
||||
#' group=GH.ecopcr$forward_mismatch>=1)
|
||||
#'
|
||||
#' # Display the structure
|
||||
#' G.shanon.error
|
||||
#'
|
||||
#' # Plot the logo corresponding only to matches with errors
|
||||
#' dnalogoplot(G.shanon.error$'TRUE',ylab='bits')
|
||||
#'
|
||||
#' @seealso \code{\link{dnalogo}}
|
||||
#' @author Eric Coissac
|
||||
#' @keywords metabarcodes
|
||||
#'
|
||||
#' @export
|
||||
dnalogoplot = function(data,col=NULL,primer=NULL,cex=0.8,cex.lab=1.0,xlab=NULL,ylab=NULL,main=NULL,sub=NULL,line=NA,outer=FALSE) {
|
||||
ddata = dim(data)
|
||||
ncol = ddata[2]
|
||||
nrow = ddata[1]
|
||||
actualwidth = ncol + 1
|
||||
actualheight= max(colSums(data))
|
||||
|
||||
whitepaper(actualwidth,actualheight)
|
||||
if (is.null(primer))
|
||||
labels= TRUE
|
||||
else
|
||||
labels = strsplit(primer,"")[[1]]
|
||||
axis(1,at=1:ncol,labels=labels,cex.axis=cex.lab)
|
||||
axis(2)
|
||||
title(main=main,sub=sub,xlab=xlab,ylab=ylab,line=line,outer=outer)
|
||||
dnalogo(data,col=col,cex=cex)
|
||||
}
|
||||
|
||||
|
||||
@@ -0,0 +1,106 @@
|
||||
#'@include ROBIBarcodes.R
|
||||
#'@include logo.R
|
||||
NULL
|
||||
|
||||
#' Draw a scatter plot of the reverse mismatches as a function of forward mismatches.
|
||||
#'
|
||||
#' The \code{mismatchplot} function draws a scatter plot of the number of mismatches
|
||||
#' observed in an ecoPCR result for the reverse primer as a function of the mismatches
|
||||
#' for the reverse primer. Each point for a pair (forward_mismatch,reverse_mismatch) is
|
||||
#' drawn as a circle having a surface proportional to the aboundance of this pair in the
|
||||
#' results. If a grouping factor is specified, then the circle is replaced by a pie chart.
|
||||
#'
|
||||
#' @param ecopcr an ecoPCR result data.frame as returned by the \code{\link{read.ecopcr.result}}
|
||||
#' function.
|
||||
#'
|
||||
#' @param group a factor decribing classes amongst the amplicon described in the ecoPCR
|
||||
#' result
|
||||
#'
|
||||
#' @param col a vector describing the colored used for the bubble or the pie charts
|
||||
#'
|
||||
#' @param legend a character vector describing the legend for each modality of the
|
||||
#' grouping factor. By default the factor levels are used for the legend
|
||||
#'
|
||||
#' @param legend.cex the expension factor for the legend text
|
||||
#'
|
||||
#' @param inset the distance to the margin of the legend box (see the \code{\link{legend}}
|
||||
#' documentation)
|
||||
#'
|
||||
#' @examples
|
||||
#'
|
||||
#' # Load the ROBITools library
|
||||
#' library(ROBITools)
|
||||
#'
|
||||
#' # Load the default taxonomy
|
||||
#' taxo = default.taxonomy()
|
||||
#'
|
||||
#' # Load the sample ecoPCR data file
|
||||
#' data(GH.ecopcr)
|
||||
#'
|
||||
#' # Computes classes associated to each taxid
|
||||
#' orders = as.factor(taxonatrank(taxo,GH.ecopcr$taxid,'order',name=T))
|
||||
#'
|
||||
#' # Plot the graph
|
||||
#' mismatchplot(GH.ecopcr,group=orders)
|
||||
#'
|
||||
#' @seealso \code{\link{read.ecopcr.result}}
|
||||
#' @author Eric Coissac
|
||||
#' @export
|
||||
mismatchplot = function(ecopcr,group=NULL,
|
||||
col=NULL,legend=NULL,
|
||||
legend.cex=0.7,inset=c(0.02,0.02)) {
|
||||
|
||||
maxforward_error = max(ecopcr$forward_mismatch)
|
||||
maxreverse_error = max(ecopcr$reverse_mismatch)
|
||||
maxerror=max(maxforward_error,maxreverse_error)
|
||||
|
||||
if (is.null(group))
|
||||
group=factor(rep("all",dim(ecopcr)[1]))
|
||||
else
|
||||
group=as.factor(group)
|
||||
|
||||
if (is.null(legend))
|
||||
legend = levels(group)
|
||||
|
||||
actualheight= maxerror + 1
|
||||
actualwidth = maxerror + 1
|
||||
|
||||
if (length(levels(group)) > 1)
|
||||
actualwidth = actualwidth + 2
|
||||
|
||||
whitepaper(actualwidth,actualheight,xmin=-0.5,ymin=-0.5,asp=1)
|
||||
|
||||
axis(1,at=0:maxerror,
|
||||
labels=0:maxerror)
|
||||
|
||||
axis(2,at=0:maxerror,
|
||||
labels=0:maxerror)
|
||||
|
||||
|
||||
data = aggregate(group,by=list(forward=ecopcr$forward_mismatch,
|
||||
reverse=ecopcr$reverse_mismatch),
|
||||
table)
|
||||
|
||||
data <- data[rowSums(data[,c(-1,-2),drop=FALSE])>0, , drop=FALSE]
|
||||
|
||||
if (is.null(col))
|
||||
col <- c("white", "lightblue", "mistyrose", "lightcyan",
|
||||
"lavender", "cornsilk")
|
||||
|
||||
|
||||
value=data[,c(-1,-2),drop=FALSE]
|
||||
x = as.integer(data[,1])
|
||||
y = as.integer(data[,2])
|
||||
diam = sqrt(rowSums(value))
|
||||
radius = diam / max(diam) / 2
|
||||
|
||||
hide = mapply(pie.xy,x,y,
|
||||
data=lapply(1:(dim(value)[1]),function(y) value[y,]),
|
||||
radius=radius,
|
||||
label="",MoreArgs=list(col=col))
|
||||
|
||||
|
||||
if (length(levels(group)) > 1)
|
||||
legend('topright',legend=legend,fill=col, cex=legend.cex, inset=inset)
|
||||
|
||||
}
|
||||
@@ -0,0 +1,68 @@
|
||||
#'@include ROBIBarcodes.R
|
||||
NULL
|
||||
|
||||
#' @export
|
||||
pie.xy = function (x,y,data, labels = names(x), edges = 200, radius = 0.8, clockwise = FALSE,
|
||||
init.angle = if (clockwise) 90 else 0, density = NULL, angle = 45,
|
||||
col = NULL, border = NULL, lty = NULL, ...)
|
||||
{
|
||||
if (!is.numeric(data) || any(is.na(data) | data < 0))
|
||||
stop("'data' values must be positive.")
|
||||
if (is.null(labels))
|
||||
labels <- as.character(seq_along(data))
|
||||
else labels <- as.graphicsAnnot(labels)
|
||||
data <- c(0, cumsum(data)/sum(data))
|
||||
dx <- diff(data)
|
||||
nx <- length(dx)
|
||||
# plot.new()
|
||||
# pin <- par("pin")
|
||||
xlim <- ylim <- c(-1, 1)
|
||||
# if (pin[1L] > pin[2L])
|
||||
# xlim <- (pin[1L]/pin[2L]) * xlim
|
||||
# else ylim <- (pin[2L]/pin[1L]) * ylim
|
||||
# dev.hold()
|
||||
# on.exit(dev.flush())
|
||||
# plot.window(xlim, ylim, "", asp = 1)
|
||||
if (is.null(col))
|
||||
col <- if (is.null(density))
|
||||
c("white", "lightblue", "mistyrose", "lightcyan",
|
||||
"lavender", "cornsilk")
|
||||
else par("fg")
|
||||
if (!is.null(col))
|
||||
col <- rep_len(col, nx)
|
||||
if (!is.null(border))
|
||||
border <- rep_len(border, nx)
|
||||
if (!is.null(lty))
|
||||
lty <- rep_len(lty, nx)
|
||||
angle <- rep(angle, nx)
|
||||
if (!is.null(density))
|
||||
density <- rep_len(density, nx)
|
||||
twopi <- if (clockwise)
|
||||
-2 * pi
|
||||
else 2 * pi
|
||||
t2xy <- function(t) {
|
||||
t2p <- twopi * t + init.angle * pi/180
|
||||
list(x = radius * cos(t2p) , y = radius * sin(t2p))
|
||||
}
|
||||
for (i in 1L:nx) {
|
||||
n <- max(2, floor(edges * dx[i]))
|
||||
P <- t2xy(seq.int(data[i], data[i + 1], length.out = n))
|
||||
if (nx>1)
|
||||
polygon(c(P$x + x, x), c(P$y + y , y),
|
||||
density = density[i], angle = angle[i],
|
||||
border = border[i], col = col[i], lty = lty[i])
|
||||
else
|
||||
polygon(P$x + x, P$y + y,
|
||||
density = density[i], angle = angle[i],
|
||||
border = border[i], col = col[i], lty = lty[i])
|
||||
P <- t2xy(mean(data[i + 0:1]))
|
||||
lab <- as.character(labels[i])
|
||||
if (!is.na(lab) && nzchar(lab)) {
|
||||
lines(c(1 , 1.05) * P$x + x, c(1, 1.05) * P$y + y)
|
||||
text(1.1 * P$x + x , 1.1 * P$y + y, labels[i], xpd = TRUE,
|
||||
adj = ifelse(P$x < 0, 1, 0), ...)
|
||||
}
|
||||
}
|
||||
# title(main = main, ...)
|
||||
invisible(NULL)
|
||||
}
|
||||
@@ -0,0 +1,57 @@
|
||||
#Commentaires lus par roxygen
|
||||
#'@include ROBIBarcodes.R
|
||||
#'@import XML
|
||||
#'
|
||||
NULL
|
||||
|
||||
#NULL termine le commentaire pour roxygen
|
||||
|
||||
extractPrimers <-function(primer){
|
||||
|
||||
id=xmlAttrs(primer)["ID"]
|
||||
name=xmlValue(xmlChildren(xmlChildren(primer)$name)$text)
|
||||
sequence=xmlValue(xmlChildren(xmlChildren(primer)$sequence)$text)
|
||||
coding=as.logical(xmlValue(xmlChildren(xmlChildren(primer)$coding)$text))
|
||||
|
||||
p=list(id=id, name=name, sequence=sequence, coding=coding)
|
||||
|
||||
return(p)
|
||||
}
|
||||
|
||||
#Export pour rendre publique la fonction
|
||||
|
||||
#' Builds primer data frame from metabarcodedb
|
||||
#'
|
||||
#' The \code{primers.data.frame} function extracts all the primer information
|
||||
#' from the \code{metabarcodedb} database.
|
||||
#'
|
||||
#' @param barcodedb a xml document containing a metabarcodedb.
|
||||
#'
|
||||
#' @return a \code{data.frame} describing primers.
|
||||
#'
|
||||
#' @examples
|
||||
#' # load the XML library
|
||||
#' library(XML)
|
||||
#'
|
||||
#' # load the example metabarcodedb database
|
||||
#' db = xmlParseDoc(system.file("extdata/barcodedb.xml", package="ROBIBarcodes"))
|
||||
#'
|
||||
#' # extracts the primer table
|
||||
#' primers.data.frame(db)
|
||||
#'
|
||||
#' @author Aurelie Bonin
|
||||
#' @keywords metabarcodes
|
||||
#'
|
||||
#' @export
|
||||
primers.data.frame <-function(barcodedb){
|
||||
p=getNodeSet(db,
|
||||
path="/obi:obimetabarcodedb/obi:primers/obi:primer" ,
|
||||
namespaces=c(obi="http://metabarcoding.org/OBIMetabarcodes"))
|
||||
|
||||
primerTable=as.data.frame(do.call(rbind,lapply(p,extractPrimers)))
|
||||
|
||||
rownames(primerTable)=primerTable$id
|
||||
primerTable=primerTable[,-1]
|
||||
|
||||
return(primerTable)
|
||||
}
|
||||
+18
@@ -0,0 +1,18 @@
|
||||
#'@include xmlMods.R
|
||||
#'@import XML
|
||||
#'
|
||||
NULL
|
||||
|
||||
|
||||
add.primer.barcodedb = function(barcodedb,
|
||||
name,
|
||||
sequence,
|
||||
coding,
|
||||
documentation) {
|
||||
' <primer ID="PR.XXX">
|
||||
<name>Xxx</name>
|
||||
<sequence>CGATCGATGCTAGCTAGCTGAT</sequence>
|
||||
<coding>false</coding>
|
||||
</primer>'
|
||||
|
||||
}
|
||||
@@ -0,0 +1,15 @@
|
||||
#'@import ROBITaxonomy
|
||||
#'@include ROBIBarcodes.R
|
||||
NULL
|
||||
|
||||
|
||||
#'@export
|
||||
resolution = function(taxonomy,ecopcr) {
|
||||
l = aggregate(ecopcr$taxid,
|
||||
by=list(barcode=ecopcr$sequence),
|
||||
function(x) lowest.common.ancestor(taxo,x))
|
||||
r = taxonomicrank(taxo,l$x)
|
||||
names(r)=as.character(l$barcode)
|
||||
|
||||
return(r[as.character(ecopcr$sequence)])
|
||||
}
|
||||
@@ -0,0 +1,81 @@
|
||||
#'@include xmlMods.R
|
||||
#'@import XML
|
||||
#'@import ROBITaxonomy
|
||||
#'@include ROBIBarcodes.R
|
||||
NULL
|
||||
|
||||
|
||||
taxon.data.frame = function(taxonomy,taxids,strict=TRUE,known.taxid=c()) {
|
||||
taxids = as.integer(sub("TX.","",as.character(taxids)))
|
||||
good.taxid = validate(taxonomy,taxids)
|
||||
|
||||
if (strict & any(is.na(good.taxid)))
|
||||
stop(sprintf("The following taxids are absent from the taxonomy : %s",
|
||||
toString(taxids[is.na(good.taxid)])))
|
||||
|
||||
good.taxid = good.taxid[! is.na(good.taxid)]
|
||||
all.path = path(taxonomy,good.taxid)
|
||||
all.taxid = Reduce(union,all.path)
|
||||
all.taxid = sort(union(all.taxid,known.taxid))[-1]
|
||||
all.parent = sprintf("TX.%d",parent(taxonomy,all.taxid))
|
||||
all.rank = taxonomicrank(taxonomy,all.taxid)
|
||||
all.scientificname = scientificname(taxonomy,all.taxid)
|
||||
|
||||
all.id = sprintf("TX.%d",all.taxid)
|
||||
|
||||
rep = data.frame(taxid=all.id,
|
||||
name=all.scientificname,
|
||||
rank=all.rank,
|
||||
partof=all.parent,
|
||||
stringsAsFactors=FALSE)
|
||||
|
||||
return(rep)
|
||||
}
|
||||
|
||||
build.taxon.node = function(taxid,name,rank,partof) {
|
||||
nodes = lapply(sprintf('\n<taxon ID="%s"><name>%s</name><rank>%s</rank><partof>%s</partof></taxon>',
|
||||
taxid,
|
||||
name,
|
||||
rank,
|
||||
partof),
|
||||
xmlParseString)
|
||||
|
||||
|
||||
return(nodes)
|
||||
|
||||
}
|
||||
|
||||
#'@export
|
||||
add.taxon.barcodedb = function(barcodedb,
|
||||
taxonomy,
|
||||
taxids) {
|
||||
|
||||
taxonomy.node = getNodeSet(barcodedb,
|
||||
path='/obi:obimetabarcodedb/obi:taxonomy',
|
||||
c(obi="http://metabarcoding.org/OBIMetabarcodes"))[[1]]
|
||||
|
||||
known.taxid = as.character(
|
||||
getNodeSet(
|
||||
taxonomy.node,
|
||||
path="./obi:taxon/@ID",
|
||||
c(obi="http://metabarcoding.org/OBIMetabarcodes")))
|
||||
|
||||
known.taxid = as.integer(sub("TX.","",known.taxid))
|
||||
|
||||
taxon = taxon.data.frame(taxonomy,taxids,strict=TRUE,known.taxid)
|
||||
|
||||
taxon.nodes = c(xmlChildren(taxonomy.node)$root,
|
||||
build.taxon.node(taxon$taxid,
|
||||
taxon$name,
|
||||
taxon$rank,
|
||||
taxon$partof))
|
||||
spare = sparexmltree()
|
||||
new.taxonomy.node = getNodeSet(spare,
|
||||
path='/obi:obimetabarcodedb/obi:taxonomy',
|
||||
c(obi="http://metabarcoding.org/OBIMetabarcodes"))[[1]]
|
||||
|
||||
replaceNodes(taxonomy.node,new.taxonomy.node)
|
||||
|
||||
hidden = addChildren(new.taxonomy.node,kids=taxon.nodes,append=FALSE)
|
||||
}
|
||||
|
||||
@@ -0,0 +1,97 @@
|
||||
#' @include ROBIBarcodes.R
|
||||
#' @import ROBITaxonomy
|
||||
#' @import XML
|
||||
#' @useDynLib ROBIBarcodes
|
||||
#'
|
||||
NULL
|
||||
|
||||
|
||||
extractTaxa <-function(taxon){
|
||||
|
||||
id=xmlAttrs(taxon)["ID"]
|
||||
name=xmlValue(xmlChildren(xmlChildren(taxon)$name)$text)
|
||||
rank=xmlValue(xmlChildren(xmlChildren(taxon)$rank)$text)
|
||||
partof=xmlValue(xmlChildren(xmlChildren(taxon)$partof)$text)
|
||||
|
||||
p=list(id=id, name=name, rank=rank, partof=partof)
|
||||
|
||||
return(p)
|
||||
}
|
||||
|
||||
#' Builds taxa data frame from metabarcodedb
|
||||
#'
|
||||
#' The \code{taxonomy.data.frame} function extracts all the taxon information
|
||||
#' from the \code{metabarcodedb} database.
|
||||
#'
|
||||
#' @param barcodedb a xml document containing a metabarcodedb.
|
||||
#'
|
||||
#' @return a \code{data.frame} describing taxa.
|
||||
#'
|
||||
#' @examples
|
||||
#' # load the XML library
|
||||
#' library(XML)
|
||||
#'
|
||||
#' # load the example metabarcodedb database
|
||||
#' db = xmlParseDoc(system.file("extdata/barcodedb.xml", package="ROBIBarcodes"))
|
||||
#'
|
||||
#' # extracts the taxonomy table
|
||||
#' taxonomy.data.frame(db)
|
||||
#'
|
||||
#' @author Eric Coissac
|
||||
#' @keywords metabarcodes
|
||||
#'
|
||||
#' @export
|
||||
taxonomy.data.frame = function(barcodedb) {
|
||||
p=getNodeSet(db,
|
||||
path="/obi:obimetabarcodedb/obi:taxonomy/obi:taxon" ,
|
||||
namespaces=c(obi="http://metabarcoding.org/OBIMetabarcodes"))
|
||||
|
||||
taxonomyTable=as.data.frame(do.call(rbind,lapply(p,extractTaxa)))
|
||||
|
||||
|
||||
rownames(taxonomyTable)=unlist(taxonomyTable$id)
|
||||
taxonomyTable=taxonomyTable[,-1]
|
||||
|
||||
taxonomyTable$name=unlist(taxonomyTable$name)
|
||||
taxonomyTable$rank=unlist(taxonomyTable$rank)
|
||||
taxonomyTable$partof=unlist(taxonomyTable$partof)
|
||||
|
||||
return(taxonomyTable)
|
||||
|
||||
}
|
||||
|
||||
#' Builds a \code{taxonomy.obitools} from a metabarcodedb
|
||||
#'
|
||||
#' The \code{metabarcodedb.taxonomy} function extracts all the taxon information
|
||||
#' from the \code{metabarcodedb} database and create a \code{taxonomy.obitools}
|
||||
#' instance with them.
|
||||
#'
|
||||
#' @param barcodedb a xml document containing a metabarcodedb.
|
||||
#'
|
||||
#' @return a \code{taxonomy.obitools} instance.
|
||||
#'
|
||||
#' @examples
|
||||
#' # load the XML library
|
||||
#' library(XML)
|
||||
#'
|
||||
#' # load the example metabarcodedb database
|
||||
#' db = xmlParseDoc(system.file("extdata/barcodedb.xml", package="ROBIBarcodes"))
|
||||
#'
|
||||
#' # extracts the taxonomy table
|
||||
#' barcodetaxo = metabarcodedb.taxonomy(db)
|
||||
#'
|
||||
#' # Look for the Verbrata taxid
|
||||
#' ecofind(barcodetaxo,"vertebrata")
|
||||
#'
|
||||
#' @author Eric Coissac
|
||||
#' @keywords metabarcodes
|
||||
#'
|
||||
#' @export
|
||||
metabarcodedb.taxonomy = function(barcodedb) {
|
||||
|
||||
table = taxonomy.data.frame(barcodedb)
|
||||
|
||||
t <- .Call('R_buildbarcodetaxo',table,TRUE,PACKAGE="ROBIBarcodes")
|
||||
|
||||
return(ROBITools:::build.taxonomy.obitools(t,"barcodedb",getwd(),FALSE))
|
||||
}
|
||||
+88
@@ -0,0 +1,88 @@
|
||||
#'@include ROBIBarcodes.R
|
||||
#'@import XML
|
||||
#'
|
||||
NULL
|
||||
|
||||
|
||||
#
|
||||
# Checks that bibutils is installed on the system
|
||||
#
|
||||
hasBibUtils = !system("bib2xml -h",
|
||||
intern=FALSE,
|
||||
ignore.stdout = TRUE,
|
||||
ignore.stderr = TRUE)
|
||||
|
||||
if (!hasBibUtils) {
|
||||
message("\n============================================================\n",
|
||||
"Bibutils are not installed on your system\n",
|
||||
"or is not correctly setup\n",
|
||||
"Consider to visit: http://sourceforge.net/projects/bibutils/\n",
|
||||
"============================================================\n")
|
||||
}
|
||||
|
||||
|
||||
#'Qualify the elements of the `mods` elements with the \code{mods:} namespace.
|
||||
#'
|
||||
#' The \code{bibutils} programs generate XML file not qualified by a schema.
|
||||
#' To respect the OBIBarcodes schema the mods elements must be qualified.
|
||||
#' This function take a XML document produce by a \code{bibutils} program and
|
||||
#' add the \code{mods:} namespace.
|
||||
#'
|
||||
#' @note This function modifies the document past in argument and returns
|
||||
#' nothing
|
||||
#'
|
||||
#' @note This is an internal function and consequently has not to be called by
|
||||
#' end users.
|
||||
#'
|
||||
#' @param modsdoc a XMLInternalDocument instance corresponding to a
|
||||
#' modsCollectionDefinition element.
|
||||
#'
|
||||
#' @export
|
||||
addmodsnamespace = function(modsdoc) {
|
||||
|
||||
root = xmlRoot(modsdoc)
|
||||
xmlNamespaces(root,set=TRUE)=c(mods="http://www.loc.gov/mods/v3")
|
||||
hiden=xpathApply(modsdoc,
|
||||
path='/.//*',
|
||||
fun= function(n) xmlNamespace(n,set=TRUE)="mods")
|
||||
|
||||
}
|
||||
|
||||
patchmodsID = function(modsdoc) {
|
||||
hiden= xpathApply(modsdoc,'/.//*[attribute::ID]',
|
||||
function(n) xmlAttrs(n)=list(ID=paste('BI.',
|
||||
toupper(gsub('[^A-Za-z0-9_]',
|
||||
'_',
|
||||
xmlAttrs(n)['ID']
|
||||
)
|
||||
),
|
||||
sep=""
|
||||
))
|
||||
)
|
||||
}
|
||||
|
||||
#'@export
|
||||
bib2mods = function(bibfile,bibutils='bib2xml') {
|
||||
|
||||
tmp=tempfile()
|
||||
xmlerr=system(paste(bibutils,bibfile,'>',tmp,sep=' '),
|
||||
intern=FALSE,
|
||||
ignore.stderr=TRUE)
|
||||
|
||||
if (xmlerr!=0)
|
||||
stop(paste("Cannot run ",bibutils))
|
||||
xml = paste(tmp,collapse='\n')
|
||||
xml = xmlParseDoc(tmp,asText=FALSE)
|
||||
file.remove(tmp)
|
||||
addmodsnamespace(xml)
|
||||
patchmodsID(xml)
|
||||
mods=getNodeSet(xml,'/.//mods:mods[attribute::ID]')
|
||||
|
||||
return(mods)
|
||||
}
|
||||
|
||||
if (!hasBibUtils) {
|
||||
bib2mods = function(bibfile,bibutils) {
|
||||
stop("Bibutils not install visit: http://sourceforge.net/projects/bibutils/")
|
||||
}
|
||||
}
|
||||
@@ -0,0 +1,23 @@
|
||||
#'@include ROBIBarcodes.R
|
||||
#'@import XML
|
||||
#'
|
||||
NULL
|
||||
|
||||
.__spare_tree__ = NULL
|
||||
|
||||
sparexmltree = function() {
|
||||
|
||||
if (is.null(get(".__spare_tree__",envir = environment()))) {
|
||||
|
||||
sparefile = paste(system.file("extdata",
|
||||
package="ROBIBarcodes"),
|
||||
'spare.xml',
|
||||
sep='/')
|
||||
|
||||
spare = xmlParseDoc(sparefile)
|
||||
|
||||
assign(".__spare_tree__",spare, envir=globalenv())
|
||||
}
|
||||
|
||||
return(get(".__spare_tree__",envir = globalenv()))
|
||||
}
|
||||
@@ -0,0 +1,17 @@
|
||||
Version: 1.0
|
||||
|
||||
RestoreWorkspace: Default
|
||||
SaveWorkspace: Default
|
||||
AlwaysSaveHistory: Default
|
||||
|
||||
EnableCodeIndexing: Yes
|
||||
UseSpacesForTab: Yes
|
||||
NumSpacesForTab: 2
|
||||
Encoding: LATIN1
|
||||
|
||||
RnwWeave: Sweave
|
||||
LaTeX: pdfLaTeX
|
||||
|
||||
BuildType: Package
|
||||
PackageInstallArgs: --no-multiarch
|
||||
PackageRoxygenize: rd,collate,namespace
|
||||
Binary file not shown.
Vendored
+565
@@ -0,0 +1,565 @@
|
||||
<?xml version="1.0" encoding="UTF-8"?>
|
||||
<?xml-stylesheet type="text/xsl" href="xs3p.xsl"?>
|
||||
|
||||
<!--
|
||||
|
||||
The OBIMetabarcode schema
|
||||
|
||||
|
||||
-->
|
||||
|
||||
<xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema"
|
||||
targetNamespace="http://metabarcoding.org/OBIMetabarcodes" xmlns:tns="http://metabarcoding.org/OBIMetabarcodes"
|
||||
elementFormDefault="qualified" xmlns:mods="http://www.loc.gov/mods/v3">
|
||||
|
||||
|
||||
<!-- *************************************************************
|
||||
|
||||
We import the MODS schema which define the model
|
||||
for bibliographic references produced by the library
|
||||
of congress
|
||||
|
||||
http://www.loc.gov/standards/mods/
|
||||
|
||||
You can also check the CSL schema which can be use
|
||||
for declaring way to present bibliography references
|
||||
|
||||
http://citationstyles.org
|
||||
|
||||
************************************************************* -->
|
||||
|
||||
<xs:import namespace="http://www.loc.gov/mods/v3"
|
||||
schemaLocation="mods-3-5.xsd" />
|
||||
|
||||
<!-- *************************************************************
|
||||
|
||||
Declaration of the simple types
|
||||
|
||||
************************************************************* -->
|
||||
|
||||
<!-- documentation_t : subclass of xs:string for documentation elememts -->
|
||||
|
||||
<xs:simpleType name="documentation_t">
|
||||
<xs:annotation>
|
||||
<xs:documentation>The documentation_t type is a string of characters allowing to document an instance in the database.</xs:documentation>
|
||||
</xs:annotation>
|
||||
<xs:restriction base="xs:string"></xs:restriction>
|
||||
</xs:simpleType>
|
||||
|
||||
<!-- organelle_t : subclass of xs:string for documentation elememts -->
|
||||
|
||||
<xs:simpleType name="organelle_t">
|
||||
<xs:annotation>
|
||||
<xs:documentation>
|
||||
The organelle_t type allows to specify a value
|
||||
indicating on which organelle is located another element
|
||||
</xs:documentation>
|
||||
</xs:annotation>
|
||||
<xs:restriction base="xs:string">
|
||||
<xs:enumeration value="nucleus">
|
||||
<xs:annotation>
|
||||
<xs:documentation>
|
||||
Indicates that the marker corresponds to a locus
|
||||
belonging the nuclear genome
|
||||
</xs:documentation>
|
||||
</xs:annotation>
|
||||
</xs:enumeration>
|
||||
<xs:enumeration value="chloroplast">
|
||||
<xs:annotation>
|
||||
<xs:documentation>
|
||||
Indicates that the marker corresponds to a locus
|
||||
belonging the chloroplastic genome
|
||||
</xs:documentation>
|
||||
</xs:annotation>
|
||||
</xs:enumeration>
|
||||
<xs:enumeration value="mitochondria">
|
||||
<xs:annotation>
|
||||
<xs:documentation>
|
||||
Indicates that the marker corresponds to a locus
|
||||
belonging the mitochondrial genome
|
||||
</xs:documentation>
|
||||
</xs:annotation>
|
||||
</xs:enumeration>
|
||||
</xs:restriction>
|
||||
</xs:simpleType>
|
||||
|
||||
<!-- identifier_t : subclass of xs:string for identifier -->
|
||||
<!-- and its subclasses for each type of identifiers -->
|
||||
|
||||
<xs:simpleType name="identifier_t">
|
||||
<xs:restriction base="xs:string">
|
||||
<xs:pattern value="[A-Z]{2}\.[A-Z0-9_]+"></xs:pattern>
|
||||
</xs:restriction>
|
||||
</xs:simpleType>
|
||||
|
||||
<xs:simpleType name="locusid_t">
|
||||
<xs:restriction base="tns:identifier_t">
|
||||
<xs:pattern value="LO\..+"></xs:pattern>
|
||||
</xs:restriction>
|
||||
</xs:simpleType>
|
||||
|
||||
<xs:simpleType name="primerid_t">
|
||||
<xs:restriction base="tns:identifier_t">
|
||||
<xs:pattern value="PR\..+"></xs:pattern>
|
||||
</xs:restriction>
|
||||
</xs:simpleType>
|
||||
|
||||
<xs:simpleType name="biblioid_t">
|
||||
<xs:restriction base="tns:identifier_t">
|
||||
<xs:pattern value="BI\..+"></xs:pattern>
|
||||
</xs:restriction>
|
||||
</xs:simpleType>
|
||||
|
||||
<xs:simpleType name="taxid_t">
|
||||
<xs:restriction base="tns:identifier_t">
|
||||
<xs:pattern value="TX\.[0-9]+"></xs:pattern>
|
||||
</xs:restriction>
|
||||
</xs:simpleType>
|
||||
|
||||
<xs:simpleType name="metabarcodeid_t">
|
||||
<xs:restriction base="tns:identifier_t">
|
||||
<xs:pattern value="MB\..+"></xs:pattern>
|
||||
</xs:restriction>
|
||||
</xs:simpleType>
|
||||
|
||||
<xs:simpleType name="roottaxid_t">
|
||||
<xs:restriction base="tns:taxid_t">
|
||||
<xs:pattern value="TX\.1"></xs:pattern>
|
||||
</xs:restriction>
|
||||
</xs:simpleType>
|
||||
|
||||
<xs:simpleType name="rank_t">
|
||||
<xs:restriction base="xs:string">
|
||||
<xs:enumeration value="class"></xs:enumeration>
|
||||
<xs:enumeration value="family"></xs:enumeration>
|
||||
<xs:enumeration value="forma"></xs:enumeration>
|
||||
<xs:enumeration value="genus"></xs:enumeration>
|
||||
<xs:enumeration value="infraclass"></xs:enumeration>
|
||||
<xs:enumeration value="infraorder"></xs:enumeration>
|
||||
<xs:enumeration value="kingdom"></xs:enumeration>
|
||||
<xs:enumeration value="no rank"></xs:enumeration>
|
||||
<xs:enumeration value="order"></xs:enumeration>
|
||||
<xs:enumeration value="parvorder"></xs:enumeration>
|
||||
<xs:enumeration value="phylum"></xs:enumeration>
|
||||
<xs:enumeration value="species"></xs:enumeration>
|
||||
<xs:enumeration value="[species group"></xs:enumeration>
|
||||
<xs:enumeration value="species subgroup"></xs:enumeration>
|
||||
<xs:enumeration value="subclass"></xs:enumeration>
|
||||
<xs:enumeration value="subfamily"></xs:enumeration>
|
||||
<xs:enumeration value="subgenus"></xs:enumeration>
|
||||
<xs:enumeration value="subkingdom"></xs:enumeration>
|
||||
<xs:enumeration value="suborder"></xs:enumeration>
|
||||
<xs:enumeration value="subphylum"></xs:enumeration>
|
||||
<xs:enumeration value="subspecies"></xs:enumeration>
|
||||
<xs:enumeration value="subtribe"></xs:enumeration>
|
||||
<xs:enumeration value="superclass"></xs:enumeration>
|
||||
<xs:enumeration value="superfamily"></xs:enumeration>
|
||||
<xs:enumeration value="superkingdom"></xs:enumeration>
|
||||
<xs:enumeration value="superorder"></xs:enumeration>
|
||||
<xs:enumeration value="superphylum"></xs:enumeration>
|
||||
<xs:enumeration value="tribe"></xs:enumeration>
|
||||
<xs:enumeration value="varietas"></xs:enumeration>
|
||||
</xs:restriction>
|
||||
</xs:simpleType>
|
||||
|
||||
<xs:simpleType name="rootrank_t">
|
||||
<xs:restriction base="tns:rank_t">
|
||||
<xs:enumeration value="no rank"></xs:enumeration>
|
||||
</xs:restriction>
|
||||
</xs:simpleType>
|
||||
|
||||
<xs:simpleType name="iupac_t">
|
||||
<xs:annotation>
|
||||
<xs:documentation>
|
||||
The iupc_t type is a string of characters symbolizing
|
||||
nucleotides in the iupac system, and thus belonging to
|
||||
the folowing list of letters:
|
||||
A,C,G,T,U,R,Y,M,K,W,S,B,D,H,V,N. The type also contrains
|
||||
the sequence to be written in upper cases.
|
||||
</xs:documentation>
|
||||
</xs:annotation>
|
||||
<xs:restriction base="xs:string">
|
||||
<xs:pattern value="[ACGTRYMKWSBDHVN]+"></xs:pattern>
|
||||
<xs:minLength value="15"></xs:minLength>
|
||||
<xs:whiteSpace value="collapse"></xs:whiteSpace>
|
||||
</xs:restriction>
|
||||
</xs:simpleType>
|
||||
|
||||
<!-- *************************************************************
|
||||
|
||||
Declaration of the complex types
|
||||
|
||||
************************************************************* -->
|
||||
|
||||
<!-- obimetabarcodedb_t : the main type of the schema -->
|
||||
|
||||
<xs:complexType name="obimetabarcodedb_t">
|
||||
<xs:sequence>
|
||||
<xs:element name="metadata" type="tns:metadata_t"
|
||||
maxOccurs="1" minOccurs="1">
|
||||
</xs:element>
|
||||
<xs:element name="taxonomy" type="tns:taxa_t" maxOccurs="1" minOccurs="1"></xs:element>
|
||||
<xs:element name="primers" type="tns:primers_t"
|
||||
maxOccurs="1" minOccurs="1">
|
||||
</xs:element>
|
||||
<xs:element name="metabarcodes" type="tns:metabarcodes_t"
|
||||
maxOccurs="1" minOccurs="1">
|
||||
</xs:element>
|
||||
<xs:element name="bibliography"
|
||||
type="mods:modsCollectionDefinition" maxOccurs="1" minOccurs="0">
|
||||
</xs:element>
|
||||
</xs:sequence>
|
||||
</xs:complexType>
|
||||
|
||||
<!-- metadata_t : contains the metadata related to the database -->
|
||||
|
||||
<xs:complexType name="metadata_t">
|
||||
<xs:sequence>
|
||||
<xs:element name="loci" type="tns:loci_t" maxOccurs="1"
|
||||
minOccurs="1"></xs:element>
|
||||
</xs:sequence>
|
||||
</xs:complexType>
|
||||
|
||||
<!-- The metabarcode descriptions by themselves -->
|
||||
|
||||
<xs:complexType name="metabarcodes_t">
|
||||
<xs:sequence>
|
||||
<xs:element name="metabarcode" type="tns:metabarcode_t"
|
||||
maxOccurs="unbounded" minOccurs="0">
|
||||
|
||||
<!-- insure that the same primer is not used twice -->
|
||||
|
||||
<xs:unique name="uniqbarcodeprimer">
|
||||
<xs:selector xpath="tns:forward|tns:reverse" />
|
||||
<xs:field xpath="." />
|
||||
</xs:unique>
|
||||
|
||||
</xs:element>
|
||||
</xs:sequence>
|
||||
</xs:complexType>
|
||||
|
||||
<xs:complexType name="metabarcode_t">
|
||||
<xs:sequence>
|
||||
|
||||
|
||||
<xs:element name="name" type="xs:string" maxOccurs="1"
|
||||
minOccurs="1">
|
||||
</xs:element>
|
||||
|
||||
<xs:element name="locus" type="tns:locusid_t" maxOccurs="1"
|
||||
minOccurs="1">
|
||||
</xs:element>
|
||||
|
||||
<xs:element name="forward" type="tns:primerid_t"
|
||||
maxOccurs="unbounded" minOccurs="1">
|
||||
</xs:element>
|
||||
|
||||
<xs:element name="reverse" type="tns:primerid_t"
|
||||
maxOccurs="unbounded" minOccurs="1">
|
||||
</xs:element>
|
||||
|
||||
<xs:element name="targettaxon" type="tns:taxid_t"
|
||||
maxOccurs="unbounded" minOccurs="1">
|
||||
</xs:element>
|
||||
|
||||
<xs:element name="excludedtaxon" type="tns:taxid_t"
|
||||
maxOccurs="unbounded" minOccurs="0">
|
||||
</xs:element>
|
||||
|
||||
<xs:element name="targetlength" type="tns:interval_t" maxOccurs="1" minOccurs="0"></xs:element>
|
||||
<xs:element name="documentation" type="tns:documentation_t"
|
||||
maxOccurs="1" minOccurs="0">
|
||||
</xs:element>
|
||||
|
||||
<xs:element name="references" type="tns:references_t"
|
||||
maxOccurs="1" minOccurs="0">
|
||||
|
||||
<!-- insure that the same bibliographic reference is not used twice -->
|
||||
|
||||
<xs:unique name="uniqbarcodereference">
|
||||
<xs:selector xpath="tns:describedin|tns:usedin" />
|
||||
<xs:field xpath="@biblioid" />
|
||||
</xs:unique>
|
||||
|
||||
</xs:element>
|
||||
|
||||
</xs:sequence>
|
||||
|
||||
<xs:attribute name="ID" type="tns:metabarcodeid_t" use="required"></xs:attribute>
|
||||
|
||||
</xs:complexType> <!-- end of metabarcode_t -->
|
||||
|
||||
|
||||
|
||||
<xs:complexType name="loci_t">
|
||||
<xs:sequence>
|
||||
<xs:element name="abstractlocus" type="tns:abstractlocus_t"
|
||||
maxOccurs="unbounded" minOccurs="0">
|
||||
</xs:element>
|
||||
<xs:element name="locus" type="tns:locus_t" maxOccurs="unbounded" minOccurs="0"></xs:element>
|
||||
</xs:sequence>
|
||||
</xs:complexType>
|
||||
|
||||
<xs:complexType name="locus_t">
|
||||
<xs:complexContent>
|
||||
<xs:extension base="tns:abstractlocus_t">
|
||||
<xs:sequence>
|
||||
<xs:element name="organelle" type="tns:organelle_t" maxOccurs="1" minOccurs="1"></xs:element>
|
||||
</xs:sequence>
|
||||
</xs:extension>
|
||||
</xs:complexContent>
|
||||
</xs:complexType>
|
||||
|
||||
|
||||
|
||||
<xs:complexType name="primers_t">
|
||||
<xs:annotation>
|
||||
<xs:documentation>The primers_t type gathers several (usually two) primer_t elements</xs:documentation>
|
||||
</xs:annotation>
|
||||
<xs:sequence>
|
||||
<xs:element name="primer" type="tns:primer_t" maxOccurs="unbounded"
|
||||
minOccurs="0">
|
||||
</xs:element>
|
||||
</xs:sequence>
|
||||
</xs:complexType>
|
||||
|
||||
<xs:complexType name="primer_t">
|
||||
<xs:annotation>
|
||||
<xs:documentation>
|
||||
This type describes a PCR primer.
|
||||
It has a mandatory attribut "name" containing a unique identifier.
|
||||
Primer is described by ...
|
||||
The primer_t type has an attribute name specifying its name,
|
||||
and includes a sequence element specifying its nucleotide sequence.
|
||||
</xs:documentation>
|
||||
</xs:annotation>
|
||||
<xs:sequence>
|
||||
<xs:element name="name" type="xs:string" maxOccurs="1"
|
||||
minOccurs="1">
|
||||
</xs:element>
|
||||
<xs:element name="sequence" type="tns:iupac_t" maxOccurs="1"
|
||||
minOccurs="1">
|
||||
<xs:annotation>
|
||||
<xs:documentation>
|
||||
The nucleic sequence of the primer. The primer
|
||||
length must be greater than 15bp
|
||||
</xs:documentation>
|
||||
</xs:annotation>
|
||||
</xs:element>
|
||||
<xs:element name="coding" type="xs:boolean" maxOccurs="1"
|
||||
minOccurs="1">
|
||||
</xs:element>
|
||||
<xs:element name="documentation" type="tns:documentation_t"
|
||||
maxOccurs="1" minOccurs="0">
|
||||
</xs:element>
|
||||
</xs:sequence>
|
||||
<xs:attribute name="ID" type="tns:primerid_t" use="required">
|
||||
<xs:annotation>
|
||||
<xs:documentation>The name of the primer</xs:documentation>
|
||||
</xs:annotation>
|
||||
</xs:attribute>
|
||||
</xs:complexType>
|
||||
|
||||
<xs:complexType name="references_t">
|
||||
<xs:sequence>
|
||||
<xs:element name="describedin" type="tns:reference_t"
|
||||
maxOccurs="1" minOccurs="0">
|
||||
</xs:element>
|
||||
<xs:element name="usedin" type="tns:reference_t"
|
||||
maxOccurs="unbounded" minOccurs="0"></xs:element>
|
||||
</xs:sequence>
|
||||
</xs:complexType>
|
||||
|
||||
|
||||
<xs:complexType name="reference_t">
|
||||
<xs:simpleContent>
|
||||
<xs:extension base="tns:documentation_t">
|
||||
<xs:attribute name="biblioid" type="tns:biblioid_t"></xs:attribute>
|
||||
</xs:extension>
|
||||
</xs:simpleContent>
|
||||
</xs:complexType>
|
||||
|
||||
<xs:complexType name="taxa_t">
|
||||
<xs:sequence>
|
||||
<xs:element name="root" type="tns:roottaxon_t" maxOccurs="1" minOccurs="1"></xs:element>
|
||||
<xs:element name="taxon" type="tns:taxon_t" maxOccurs="unbounded" minOccurs="0"></xs:element>
|
||||
</xs:sequence>
|
||||
</xs:complexType>
|
||||
|
||||
<xs:complexType name="abstracttaxon_t" abstract="true">
|
||||
<xs:sequence>
|
||||
<xs:element name="name" type="xs:string"></xs:element>
|
||||
<xs:element name="rank" type="tns:rank_t"></xs:element>
|
||||
</xs:sequence>
|
||||
<xs:attribute name="ID" type="tns:taxid_t"></xs:attribute>
|
||||
</xs:complexType>
|
||||
|
||||
<xs:complexType name="taxon_t">
|
||||
<xs:complexContent>
|
||||
<xs:extension base="tns:abstracttaxon_t">
|
||||
<xs:sequence>
|
||||
<xs:element name="partof" type="tns:taxid_t"></xs:element>
|
||||
</xs:sequence>
|
||||
</xs:extension>
|
||||
</xs:complexContent>
|
||||
</xs:complexType>
|
||||
|
||||
<xs:complexType name="roottaxon_t">
|
||||
<xs:complexContent>
|
||||
<xs:restriction base="tns:abstracttaxon_t">
|
||||
<xs:sequence>
|
||||
<xs:element name="name">
|
||||
<xs:simpleType>
|
||||
<xs:restriction base="xs:string">
|
||||
<xs:pattern value="Root"></xs:pattern>
|
||||
</xs:restriction>
|
||||
</xs:simpleType>
|
||||
</xs:element>
|
||||
<xs:element name="rank" type="tns:rootrank_t"></xs:element>
|
||||
</xs:sequence>
|
||||
<xs:attribute name="ID" type="tns:roottaxid_t"></xs:attribute>
|
||||
</xs:restriction>
|
||||
</xs:complexContent>
|
||||
</xs:complexType>
|
||||
|
||||
|
||||
|
||||
<!-- The root xs:element of the library -->
|
||||
|
||||
<xs:element name="obimetabarcodedb" type="tns:obimetabarcodedb_t">
|
||||
|
||||
<!-- Unicity constraints -->
|
||||
|
||||
<xs:unique name="uniqprimer">
|
||||
<xs:selector xpath="./tns:primers/tns:primer" />
|
||||
<xs:field xpath="tns:sequence" />
|
||||
</xs:unique>
|
||||
|
||||
|
||||
<!-- Primary key constraints -->
|
||||
|
||||
<xs:key name="barcodeid">
|
||||
<xs:selector xpath="./tns:metabarcodes/tns:metabarcode" />
|
||||
<xs:field xpath="@ID" />
|
||||
</xs:key>
|
||||
|
||||
<xs:key name="abstractlocusid">
|
||||
<xs:selector xpath="./tns:metadata/tns:loci/tns:abstractlocus|./tns:metadata/tns:loci/tns:locus" />
|
||||
<xs:field xpath="@ID" />
|
||||
</xs:key>
|
||||
|
||||
<xs:key name="locusid">
|
||||
<xs:selector xpath="./tns:metadata/tns:loci/tns:locus" />
|
||||
<xs:field xpath="@ID" />
|
||||
</xs:key>
|
||||
|
||||
<xs:key name="primerid">
|
||||
<xs:selector xpath="./tns:primers/tns:primer" />
|
||||
<xs:field xpath="@ID" />
|
||||
</xs:key>
|
||||
|
||||
<xs:key name="biblioid">
|
||||
<xs:selector xpath="./tns:bibliography/mods:mods" />
|
||||
<xs:field xpath="@ID" />
|
||||
</xs:key>
|
||||
|
||||
<xs:key name="roottaxid">
|
||||
<xs:selector xpath="./tns:taxonomy/tns:taxon|./tns:taxonomy/tns:root" />
|
||||
<xs:field xpath="@ID" />
|
||||
</xs:key>
|
||||
|
||||
<xs:key name="taxid">
|
||||
<xs:selector xpath="./tns:taxonomy/tns:taxon" />
|
||||
<xs:field xpath="@ID" />
|
||||
</xs:key>
|
||||
|
||||
|
||||
|
||||
<!-- Foreign key constaints -->
|
||||
|
||||
<!-- Constraint on forward and reverse primers -->
|
||||
|
||||
<xs:keyref name="forward_ref" refer="tns:primerid">
|
||||
<xs:selector xpath="./tns:metabarcodes/tns:metabarcode"></xs:selector>
|
||||
<xs:field xpath="tns:forward"></xs:field>
|
||||
</xs:keyref>
|
||||
|
||||
<xs:keyref name="reverse_ref" refer="tns:primerid">
|
||||
<xs:selector xpath="./tns:metabarcodes/tns:metabarcode"></xs:selector>
|
||||
<xs:field xpath="tns:reverse"></xs:field>
|
||||
</xs:keyref>
|
||||
|
||||
<xs:keyref name="target_ref" refer="tns:taxid">
|
||||
<xs:selector xpath="./tns:metabarcodes/tns:metabarcode"></xs:selector>
|
||||
<xs:field xpath="tns:targettaxon"></xs:field>
|
||||
</xs:keyref>
|
||||
|
||||
<xs:keyref name="excluded_ref" refer="tns:taxid">
|
||||
<xs:selector xpath="./tns:metabarcodes/tns:metabarcode"></xs:selector>
|
||||
<xs:field xpath="tns:excludedtaxon"></xs:field>
|
||||
</xs:keyref>
|
||||
|
||||
<xs:keyref name="describedin_ref" refer="tns:biblioid">
|
||||
<xs:selector
|
||||
xpath="./tns:metabarcodes/tns:metabarcode/tns:references/tns:describedin"></xs:selector>
|
||||
<xs:field xpath="@biblioid"></xs:field>
|
||||
</xs:keyref>
|
||||
|
||||
<xs:keyref name="usedin_ref" refer="tns:biblioid">
|
||||
<xs:selector
|
||||
xpath="./tns:metabarcodes/tns:metabarcode/tns:references/tns:usedin"></xs:selector>
|
||||
<xs:field xpath="@biblioid"></xs:field>
|
||||
</xs:keyref>
|
||||
|
||||
<xs:keyref name="partof_ref" refer="tns:abstractlocusid">
|
||||
<xs:selector
|
||||
xpath="./tns:metadata/tns:loci/tns:abstractlocus|./tns:metadata/tns:loci/tns:locus"></xs:selector>
|
||||
<xs:field xpath="tns:partof"></xs:field>
|
||||
</xs:keyref>
|
||||
|
||||
<xs:keyref name="barcodelocus_ref" refer="tns:locusid">
|
||||
<xs:selector
|
||||
xpath="./tns:metabarcodes/tns:metabarcode"></xs:selector>
|
||||
<xs:field xpath="tns:locus"></xs:field>
|
||||
</xs:keyref>
|
||||
|
||||
<xs:keyref name="taxopartof_ref" refer="tns:roottaxid">
|
||||
<xs:selector xpath="./tns:metabarcodes/tns:taxonomy/tns:taxon"></xs:selector>
|
||||
<xs:field xpath="@ID"></xs:field>
|
||||
</xs:keyref>
|
||||
|
||||
</xs:element>
|
||||
|
||||
<!-- *************************************************************
|
||||
|
||||
Declaration of the root element of the document
|
||||
|
||||
************************************************************* -->
|
||||
|
||||
<xs:complexType name="abstractlocus_t">
|
||||
<xs:sequence>
|
||||
<xs:element name="name" type="xs:string" maxOccurs="1" minOccurs="1"></xs:element>
|
||||
<xs:element name="partof" type="tns:locusid_t" maxOccurs="1"
|
||||
minOccurs="0">
|
||||
</xs:element>
|
||||
<xs:element name="documentation" type="tns:documentation_t"
|
||||
maxOccurs="1" minOccurs="0">
|
||||
</xs:element>
|
||||
</xs:sequence>
|
||||
<xs:attribute name="ID" type="tns:locusid_t" use="required"></xs:attribute>
|
||||
</xs:complexType>
|
||||
|
||||
|
||||
<xs:complexType name="computedproperties_t">
|
||||
</xs:complexType>
|
||||
|
||||
<xs:complexType name="computedproperty_t"></xs:complexType>
|
||||
|
||||
|
||||
<xs:complexType name="interval_t">
|
||||
<xs:sequence>
|
||||
<xs:element name="min" type="xs:positiveInteger" maxOccurs="1" minOccurs="1"></xs:element>
|
||||
<xs:element name="max" type="xs:positiveInteger" maxOccurs="1" minOccurs="1"></xs:element>
|
||||
</xs:sequence>
|
||||
</xs:complexType>
|
||||
</xs:schema>
|
||||
Vendored
+730
@@ -0,0 +1,730 @@
|
||||
<?xml version="1.0" encoding="UTF-8"?>
|
||||
<obimetabarcodedb xmlns="http://metabarcoding.org/OBIMetabarcodes" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:mods="http://www.loc.gov/mods/v3" xsi:schemaLocation="http://metabarcoding.org/OBIMetabarcodes OBIMetabarcodes.xsd">
|
||||
<metadata>
|
||||
<loci>
|
||||
<abstractlocus ID="LO.RRNA">
|
||||
<name>mRNA</name>
|
||||
</abstractlocus>
|
||||
<abstractlocus ID="LO.MRRNA">
|
||||
<name>Mitochondrial mRNA</name>
|
||||
<partof>LO.RRNA</partof>
|
||||
</abstractlocus>
|
||||
<abstractlocus ID="LO.ITS">
|
||||
<name>Internal Transcribed Spacer (ITS)</name>
|
||||
</abstractlocus>
|
||||
<locus ID="LO.M16SRRNA">
|
||||
<name>16S rRNA</name>
|
||||
<partof>LO.MRRNA</partof>
|
||||
<organelle>mitochondria</organelle>
|
||||
</locus>
|
||||
<locus ID="LO.M12SRRNA">
|
||||
<name>12S rRNA</name>
|
||||
<partof>LO.MRRNA</partof>
|
||||
<organelle>mitochondria</organelle>
|
||||
</locus>
|
||||
<locus ID="LO.P6_LOOP">
|
||||
<name>P6-Loop trnL</name>
|
||||
<organelle>chloroplast</organelle>
|
||||
</locus>
|
||||
<locus ID="LO.ITS1">
|
||||
<name>ITS1</name>
|
||||
<partof>LO.ITS</partof>
|
||||
<organelle>nucleus</organelle>
|
||||
</locus>
|
||||
</loci>
|
||||
</metadata>
|
||||
<taxonomy>
|
||||
<root ID="TX.1">
|
||||
<name>Root</name>
|
||||
<rank>no rank</rank>
|
||||
</root><taxon ID="TX.2759"><name>Eukaryota</name><rank>superkingdom</rank><partof>TX.131567</partof></taxon><taxon ID="TX.3193"><name>Embryophyta</name><rank>no rank</rank><partof>TX.131221</partof></taxon><taxon ID="TX.3208"><name>Bryophyta</name><rank>no rank</rank><partof>TX.3193</partof></taxon><taxon ID="TX.4751"><name>Fungi</name><rank>kingdom</rank><partof>TX.33154</partof></taxon><taxon ID="TX.6072"><name>Eumetazoa</name><rank>no rank</rank><partof>TX.33208</partof></taxon><taxon ID="TX.6340"><name>Annelida</name><rank>phylum</rank><partof>TX.193545</partof></taxon><taxon ID="TX.6381"><name>Oligochaeta</name><rank>subclass</rank><partof>TX.42113</partof></taxon><taxon ID="TX.6382"><name>Haplotaxida</name><rank>order</rank><partof>TX.6381</partof></taxon><taxon ID="TX.6383"><name>Tubificina</name><rank>suborder</rank><partof>TX.6382</partof></taxon><taxon ID="TX.6388"><name>Enchytraeidae</name><rank>family</rank><partof>TX.6383</partof></taxon><taxon ID="TX.6656"><name>Arthropoda</name><rank>phylum</rank><partof>TX.88770</partof></taxon><taxon ID="TX.6960"><name>Hexapoda</name><rank>superclass</rank><partof>TX.197562</partof></taxon><taxon ID="TX.7041"><name>Coleoptera</name><rank>order</rank><partof>TX.33392</partof></taxon><taxon ID="TX.7496"><name>Pterygota</name><rank>no rank</rank><partof>TX.85512</partof></taxon><taxon ID="TX.7711"><name>Chordata</name><rank>phylum</rank><partof>TX.33511</partof></taxon><taxon ID="TX.7742"><name>Vertebrata</name><rank>no rank</rank><partof>TX.89593</partof></taxon><taxon ID="TX.7776"><name>Gnathostomata</name><rank>superclass</rank><partof>TX.7742</partof></taxon><taxon ID="TX.8287"><name>Sarcopterygii</name><rank>no rank</rank><partof>TX.117571</partof></taxon><taxon ID="TX.8457"><name>Sauropsida</name><rank>no rank</rank><partof>TX.32524</partof></taxon><taxon ID="TX.8492"><name>Archosauria</name><rank>no rank</rank><partof>TX.32561</partof></taxon><taxon ID="TX.8782"><name>Aves</name><rank>class</rank><partof>TX.436492</partof></taxon><taxon ID="TX.32523"><name>Tetrapoda</name><rank>no rank</rank><partof>TX.8287</partof></taxon><taxon ID="TX.32524"><name>Amniota</name><rank>no rank</rank><partof>TX.32523</partof></taxon><taxon ID="TX.32561"><name>Sauria</name><rank>no rank</rank><partof>TX.8457</partof></taxon><taxon ID="TX.33090"><name>Viridiplantae</name><rank>kingdom</rank><partof>TX.2759</partof></taxon><taxon ID="TX.33154"><name>Opisthokonta</name><rank>no rank</rank><partof>TX.2759</partof></taxon><taxon ID="TX.33208"><name>Metazoa</name><rank>kingdom</rank><partof>TX.33154</partof></taxon><taxon ID="TX.33213"><name>Bilateria</name><rank>no rank</rank><partof>TX.6072</partof></taxon><taxon ID="TX.33316"><name>Coelomata</name><rank>no rank</rank><partof>TX.33213</partof></taxon><taxon ID="TX.33317"><name>Protostomia</name><rank>no rank</rank><partof>TX.33316</partof></taxon><taxon ID="TX.33340"><name>Neoptera</name><rank>subclass</rank><partof>TX.7496</partof></taxon><taxon ID="TX.33392"><name>Endopterygota</name><rank>infraclass</rank><partof>TX.33340</partof></taxon><taxon ID="TX.33511"><name>Deuterostomia</name><rank>no rank</rank><partof>TX.33316</partof></taxon><taxon ID="TX.35493"><name>Streptophyta</name><rank>phylum</rank><partof>TX.33090</partof></taxon><taxon ID="TX.42113"><name>Clitellata</name><rank>no rank</rank><partof>TX.6340</partof></taxon><taxon ID="TX.50557"><name>Insecta</name><rank>class</rank><partof>TX.6960</partof></taxon><taxon ID="TX.85512"><name>Dicondylia</name><rank>no rank</rank><partof>TX.50557</partof></taxon><taxon ID="TX.88770"><name>Panarthropoda</name><rank>no rank</rank><partof>TX.33317</partof></taxon><taxon ID="TX.89593"><name>Craniata</name><rank>subphylum</rank><partof>TX.7711</partof></taxon><taxon ID="TX.117570"><name>Teleostomi</name><rank>no rank</rank><partof>TX.7776</partof></taxon><taxon ID="TX.117571"><name>Euteleostomi</name><rank>no rank</rank><partof>TX.117570</partof></taxon><taxon ID="TX.131221"><name>Streptophytina</name><rank>no rank</rank><partof>TX.35493</partof></taxon><taxon ID="TX.131567"><name>cellular organisms</name><rank>no rank</rank><partof>TX.1</partof></taxon><taxon ID="TX.193545"><name>Annelida/Echiura/Pogonophora group</name><rank>no rank</rank><partof>TX.33317</partof></taxon><taxon ID="TX.197562"><name>Pancrustacea</name><rank>no rank</rank><partof>TX.197563</partof></taxon><taxon ID="TX.197563"><name>Mandibulata</name><rank>no rank</rank><partof>TX.6656</partof></taxon><taxon ID="TX.436486"><name>Dinosauria</name><rank>no rank</rank><partof>TX.8492</partof></taxon><taxon ID="TX.436489"><name>Saurischia</name><rank>no rank</rank><partof>TX.436486</partof></taxon><taxon ID="TX.436491"><name>Theropoda</name><rank>no rank</rank><partof>TX.436489</partof></taxon><taxon ID="TX.436492"><name>Coelurosauria</name><rank>no rank</rank><partof>TX.436491</partof></taxon></taxonomy>
|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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||||
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||||
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||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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||||
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||||
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||||
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||||
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||||
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||||
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|
||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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|
||||
</mods:originInfo>
|
||||
<mods:typeOfResource>text</mods:typeOfResource>
|
||||
<mods:genre>journal article</mods:genre>
|
||||
<mods:relatedItem type="host">
|
||||
<mods:titleInfo>
|
||||
<mods:title>BMC Microbiology</mods:title>
|
||||
</mods:titleInfo>
|
||||
<mods:originInfo>
|
||||
<mods:issuance>continuing</mods:issuance>
|
||||
</mods:originInfo>
|
||||
<mods:genre authority="marcgt">periodical</mods:genre>
|
||||
<mods:genre>academic journal</mods:genre>
|
||||
</mods:relatedItem>
|
||||
<mods:identifier type="citekey">Bellemain:10:00</mods:identifier>
|
||||
<mods:part>
|
||||
<mods:date>2010</mods:date>
|
||||
<mods:detail type="volume"><mods:number>10</mods:number></mods:detail>
|
||||
<mods:detail type="page"><mods:number>189</mods:number></mods:detail>
|
||||
</mods:part>
|
||||
</mods:mods></bibliography>
|
||||
</obimetabarcodedb>
|
||||
Vendored
+22
@@ -0,0 +1,22 @@
|
||||
<?xml version="1.0" encoding="UTF-8"?>
|
||||
|
||||
<obimetabarcodedb
|
||||
xmlns="http://metabarcoding.org/OBIMetabarcodes"
|
||||
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
|
||||
xmlns:mods="http://www.loc.gov/mods/v3"
|
||||
xsi:schemaLocation="http://metabarcoding.org/OBIMetabarcodes OBIMetabarcodes.xsd">
|
||||
<metadata>
|
||||
<loci>
|
||||
</loci>
|
||||
</metadata>
|
||||
<taxonomy>
|
||||
<root ID="TX.1">
|
||||
<name>Root</name>
|
||||
<rank>no rank</rank>
|
||||
</root>
|
||||
</taxonomy>
|
||||
<primers>
|
||||
</primers>
|
||||
<metabarcodes>
|
||||
</metabarcodes>
|
||||
</obimetabarcodedb>
|
||||
Vendored
+1
File diff suppressed because one or more lines are too long
Vendored
+24
@@ -0,0 +1,24 @@
|
||||
<?xml version="1.0" encoding="UTF-8"?>
|
||||
|
||||
<obimetabarcodedb
|
||||
xmlns="http://metabarcoding.org/OBIMetabarcodes"
|
||||
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
|
||||
xmlns:mods="http://www.loc.gov/mods/v3"
|
||||
xsi:schemaLocation="http://metabarcoding.org/OBIMetabarcodes OBIMetabarcodes.xsd">
|
||||
<metadata>
|
||||
<loci>
|
||||
</loci>
|
||||
</metadata>
|
||||
<taxonomy>
|
||||
<root ID="TX.1">
|
||||
<name>Root</name>
|
||||
<rank>no rank</rank>
|
||||
</root>
|
||||
</taxonomy>
|
||||
<primers>
|
||||
</primers>
|
||||
<metabarcodes>
|
||||
</metabarcodes>
|
||||
<bibliography>
|
||||
</bibliography>
|
||||
</obimetabarcodedb>
|
||||
Vendored
+9
@@ -0,0 +1,9 @@
|
||||
|
||||
@article{Taberlet:07:00,
|
||||
Author = {Taberlet, Pierre and Coissac, E and Pompanon, Francois and Gielly, Ludovic and Miquel, Christian and Valentini, Alice and Vermat, Thierry and Corthier, Gerard and Brochmann, Christian and Willerslev, Eske},
|
||||
Journal = {Nucleic Acids Res},
|
||||
Number = {3},
|
||||
Pages = {e14},
|
||||
Title = {Power and limitations of the chloroplast trnL (UAA) intron for plant DNA barcoding.},
|
||||
Volume = {35},
|
||||
Year = {2007}}
|
||||
Vendored
+100
@@ -0,0 +1,100 @@
|
||||
<?xml version="1.0" encoding="UTF-8"?>
|
||||
<modsCollection xmlns="http://www.loc.gov/mods/v3">
|
||||
<mods ID="Taberlet:07:00">
|
||||
<titleInfo>
|
||||
<title>Power and limitations of the chloroplast trnL (UAA) intron for plant DNA barcoding.</title>
|
||||
</titleInfo>
|
||||
<name type="personal">
|
||||
<namePart type="given">Pierre</namePart>
|
||||
<namePart type="family">Taberlet</namePart>
|
||||
<role>
|
||||
<roleTerm authority="marcrelator" type="text">author</roleTerm>
|
||||
</role>
|
||||
</name>
|
||||
<name type="personal">
|
||||
<namePart type="given">E</namePart>
|
||||
<namePart type="family">Coissac</namePart>
|
||||
<role>
|
||||
<roleTerm authority="marcrelator" type="text">author</roleTerm>
|
||||
</role>
|
||||
</name>
|
||||
<name type="personal">
|
||||
<namePart type="given">Francois</namePart>
|
||||
<namePart type="family">Pompanon</namePart>
|
||||
<role>
|
||||
<roleTerm authority="marcrelator" type="text">author</roleTerm>
|
||||
</role>
|
||||
</name>
|
||||
<name type="personal">
|
||||
<namePart type="given">Ludovic</namePart>
|
||||
<namePart type="family">Gielly</namePart>
|
||||
<role>
|
||||
<roleTerm authority="marcrelator" type="text">author</roleTerm>
|
||||
</role>
|
||||
</name>
|
||||
<name type="personal">
|
||||
<namePart type="given">Christian</namePart>
|
||||
<namePart type="family">Miquel</namePart>
|
||||
<role>
|
||||
<roleTerm authority="marcrelator" type="text">author</roleTerm>
|
||||
</role>
|
||||
</name>
|
||||
<name type="personal">
|
||||
<namePart type="given">Alice</namePart>
|
||||
<namePart type="family">Valentini</namePart>
|
||||
<role>
|
||||
<roleTerm authority="marcrelator" type="text">author</roleTerm>
|
||||
</role>
|
||||
</name>
|
||||
<name type="personal">
|
||||
<namePart type="given">Thierry</namePart>
|
||||
<namePart type="family">Vermat</namePart>
|
||||
<role>
|
||||
<roleTerm authority="marcrelator" type="text">author</roleTerm>
|
||||
</role>
|
||||
</name>
|
||||
<name type="personal">
|
||||
<namePart type="given">Gerard</namePart>
|
||||
<namePart type="family">Corthier</namePart>
|
||||
<role>
|
||||
<roleTerm authority="marcrelator" type="text">author</roleTerm>
|
||||
</role>
|
||||
</name>
|
||||
<name type="personal">
|
||||
<namePart type="given">Christian</namePart>
|
||||
<namePart type="family">Brochmann</namePart>
|
||||
<role>
|
||||
<roleTerm authority="marcrelator" type="text">author</roleTerm>
|
||||
</role>
|
||||
</name>
|
||||
<name type="personal">
|
||||
<namePart type="given">Eske</namePart>
|
||||
<namePart type="family">Willerslev</namePart>
|
||||
<role>
|
||||
<roleTerm authority="marcrelator" type="text">author</roleTerm>
|
||||
</role>
|
||||
</name>
|
||||
<originInfo>
|
||||
<dateIssued>2007</dateIssued>
|
||||
</originInfo>
|
||||
<typeOfResource>text</typeOfResource>
|
||||
<genre>journal article</genre>
|
||||
<relatedItem type="host">
|
||||
<titleInfo>
|
||||
<title>Nucleic Acids Res</title>
|
||||
</titleInfo>
|
||||
<originInfo>
|
||||
<issuance>continuing</issuance>
|
||||
</originInfo>
|
||||
<genre authority="marcgt">periodical</genre>
|
||||
<genre>academic journal</genre>
|
||||
</relatedItem>
|
||||
<identifier type="citekey">Taberlet:07:00</identifier>
|
||||
<part>
|
||||
<date>2007</date>
|
||||
<detail type="volume"><number>35</number></detail>
|
||||
<detail type="issue"><number>3</number></detail>
|
||||
<detail type="page"><number>e14</number></detail>
|
||||
</part>
|
||||
</mods>
|
||||
</modsCollection>
|
||||
Vendored
+10
@@ -0,0 +1,10 @@
|
||||
|
||||
@article{Yoccoz:12:00,
|
||||
Author = {Yoccoz, N G and Br{\aa}then, K A and Gielly, L and Haile, J and Edwards, M E and Goslar, T and Von Stedingk, H and Brysting, A K and Coissac, E and Pompanon, F and S{\o}nsteb{\o}, J H and Miquel, C and Valentini, A and De Bello, F and Chave, J and Thuiller, W and Wincker, P and Cruaud, C and Gavory, F and Rasmussen, M and Gilbert, M T P and Orlando, L and Brochmann, C and Willerslev, E and Taberlet, P},
|
||||
Journal = {Mol Ecol},
|
||||
Month = {Aug},
|
||||
Number = {15},
|
||||
Pages = {3647-55},
|
||||
Title = {DNA from soil mirrors plant taxonomic and growth form diversity},
|
||||
Volume = {21},
|
||||
Year = {2012}}
|
||||
Executable
BIN
Binary file not shown.
@@ -0,0 +1,26 @@
|
||||
#include "ecoPCR.h"
|
||||
#include <stdio.h>
|
||||
#include <stdlib.h>
|
||||
|
||||
/*
|
||||
* print the message given as argument and exit the program
|
||||
* @param error error number
|
||||
* @param message the text explaining what's going on
|
||||
* @param filename the file source where the program failed
|
||||
* @param linenumber the line where it has failed
|
||||
* filename and linenumber are written at pre-processing
|
||||
* time by a macro
|
||||
*/
|
||||
void ecoError(int32_t error,
|
||||
const char* message,
|
||||
const char * filename,
|
||||
int linenumber)
|
||||
{
|
||||
fprintf(stderr,"Error %d in file %s line %d : %s\n",
|
||||
error,
|
||||
filename,
|
||||
linenumber,
|
||||
message);
|
||||
|
||||
abort();
|
||||
}
|
||||
Binary file not shown.
@@ -0,0 +1,122 @@
|
||||
#include "ecoPCR.h"
|
||||
#include <stdio.h>
|
||||
#include <stdlib.h>
|
||||
|
||||
#define SWAPINT32(x) ((((x) << 24) & 0xFF000000) | (((x) << 8) & 0xFF0000) | \
|
||||
(((x) >> 8) & 0xFF00) | (((x) >> 24) & 0xFF))
|
||||
|
||||
|
||||
int32_t is_big_endian()
|
||||
{
|
||||
int32_t i=1;
|
||||
|
||||
return (int32_t)((char*)&i)[0];
|
||||
}
|
||||
|
||||
|
||||
|
||||
|
||||
int32_t swap_int32_t(int32_t i)
|
||||
{
|
||||
return SWAPINT32(i);
|
||||
}
|
||||
|
||||
|
||||
/**
|
||||
* Read part of the file
|
||||
* @param *f the database
|
||||
* @param recordSize the size to be read
|
||||
*
|
||||
* @return buffer
|
||||
*/
|
||||
void *read_ecorecord(FILE *f,int32_t *recordSize)
|
||||
{
|
||||
static void *buffer =NULL;
|
||||
int32_t buffersize=0;
|
||||
int32_t read;
|
||||
|
||||
if (!recordSize)
|
||||
ECOERROR(ECO_ASSERT_ERROR,
|
||||
"recordSize cannot be NULL");
|
||||
|
||||
read = fread(recordSize,
|
||||
1,
|
||||
sizeof(int32_t),
|
||||
f);
|
||||
|
||||
if (feof(f))
|
||||
return NULL;
|
||||
|
||||
if (read != sizeof(int32_t))
|
||||
ECOERROR(ECO_IO_ERROR,"Reading record size error");
|
||||
|
||||
if (is_big_endian())
|
||||
*recordSize=swap_int32_t(*recordSize);
|
||||
|
||||
if (buffersize < *recordSize)
|
||||
{
|
||||
if (buffer)
|
||||
buffer = ECOREALLOC(buffer,*recordSize,
|
||||
"Increase size of record buffer");
|
||||
else
|
||||
buffer = ECOMALLOC(*recordSize,
|
||||
"Allocate record buffer");
|
||||
}
|
||||
|
||||
read = fread(buffer,
|
||||
1,
|
||||
*recordSize,
|
||||
f);
|
||||
|
||||
if (read != *recordSize)
|
||||
ECOERROR(ECO_IO_ERROR,"Reading record data error");
|
||||
|
||||
return buffer;
|
||||
};
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
/**
|
||||
* Open the database and check it's readable
|
||||
* @param filename name of the database (.sdx, .rdx, .tbx)
|
||||
* @param sequencecount buffer - pointer to variable storing the number of occurence
|
||||
* @param abort_on_open_error boolean to define the behaviour in case of error
|
||||
* while opening the database
|
||||
* @return FILE type
|
||||
**/
|
||||
FILE *open_ecorecorddb(const char *filename,
|
||||
int32_t *sequencecount,
|
||||
int32_t abort_on_open_error)
|
||||
{
|
||||
FILE *f;
|
||||
int32_t read;
|
||||
|
||||
f = fopen(filename,"rb");
|
||||
|
||||
if (!f)
|
||||
{
|
||||
if (abort_on_open_error)
|
||||
ECOERROR(ECO_IO_ERROR,"Cannot open file");
|
||||
else
|
||||
{
|
||||
*sequencecount=0;
|
||||
return NULL;
|
||||
}
|
||||
}
|
||||
|
||||
read = fread(sequencecount,
|
||||
1,
|
||||
sizeof(int32_t),
|
||||
f);
|
||||
|
||||
if (read != sizeof(int32_t))
|
||||
ECOERROR(ECO_IO_ERROR,"Reading record size error");
|
||||
|
||||
if (is_big_endian())
|
||||
*sequencecount=swap_int32_t(*sequencecount);
|
||||
|
||||
return f;
|
||||
}
|
||||
|
||||
Binary file not shown.
@@ -0,0 +1,79 @@
|
||||
#include "ecoPCR.h"
|
||||
#include <stdlib.h>
|
||||
|
||||
static int eco_log_malloc = 0;
|
||||
|
||||
void eco_trace_memory_allocation()
|
||||
{
|
||||
eco_log_malloc=1;
|
||||
}
|
||||
|
||||
void eco_untrace_memory_allocation()
|
||||
{
|
||||
eco_log_malloc=0;
|
||||
}
|
||||
|
||||
|
||||
void *eco_malloc(int32_t chunksize,
|
||||
const char *error_message,
|
||||
const char *filename,
|
||||
int32_t line)
|
||||
{
|
||||
void * chunk;
|
||||
|
||||
chunk = calloc(1,chunksize);
|
||||
|
||||
if (!chunk)
|
||||
ecoError(ECO_MEM_ERROR,error_message,filename,line);
|
||||
|
||||
if (eco_log_malloc)
|
||||
fprintf(stderr,
|
||||
"Memory segment located at %p of size %d is allocated (file : %s [%d])",
|
||||
chunk,
|
||||
chunksize,
|
||||
filename,
|
||||
line);
|
||||
|
||||
return chunk;
|
||||
}
|
||||
|
||||
void *eco_realloc(void *chunk,
|
||||
int32_t newsize,
|
||||
const char *error_message,
|
||||
const char *filename,
|
||||
int32_t line)
|
||||
{
|
||||
void *newchunk;
|
||||
|
||||
newchunk = realloc(chunk,newsize);
|
||||
|
||||
if (!newchunk)
|
||||
ecoError(ECO_MEM_ERROR,error_message,filename,line);
|
||||
|
||||
if (eco_log_malloc)
|
||||
fprintf(stderr,
|
||||
"Old memory segment %p is reallocated at %p with a size of %d (file : %s [%d])",
|
||||
chunk,
|
||||
newchunk,
|
||||
newsize,
|
||||
filename,
|
||||
line);
|
||||
|
||||
return newchunk;
|
||||
}
|
||||
|
||||
void eco_free(void *chunk,
|
||||
const char *error_message,
|
||||
const char *filename,
|
||||
int32_t line)
|
||||
{
|
||||
free(chunk);
|
||||
|
||||
if (eco_log_malloc)
|
||||
fprintf(stderr,
|
||||
"Memory segment %p is released => %s (file : %s [%d])",
|
||||
chunk,
|
||||
error_message,
|
||||
filename,
|
||||
line);
|
||||
}
|
||||
Binary file not shown.
+283
@@ -0,0 +1,283 @@
|
||||
#ifndef ECOPCR_H_
|
||||
#define ECOPCR_H_
|
||||
|
||||
#include <stdio.h>
|
||||
#include <inttypes.h>
|
||||
|
||||
#include <R.h>
|
||||
#include <Rinternals.h>
|
||||
#include <Rdefines.h>
|
||||
|
||||
|
||||
//#ifndef H_apat
|
||||
//#include "../libapat/apat.h"
|
||||
//#endif
|
||||
|
||||
/*****************************************************
|
||||
*
|
||||
* Data type declarations
|
||||
*
|
||||
*****************************************************/
|
||||
|
||||
/*
|
||||
*
|
||||
* Sequence types
|
||||
*
|
||||
*/
|
||||
|
||||
typedef struct {
|
||||
|
||||
int32_t taxid;
|
||||
char AC[20];
|
||||
int32_t DE_length;
|
||||
int32_t SQ_length;
|
||||
int32_t CSQ_length;
|
||||
|
||||
char data[1];
|
||||
|
||||
} ecoseqformat_t;
|
||||
|
||||
typedef struct {
|
||||
int32_t taxid;
|
||||
int32_t SQ_length;
|
||||
char *AC;
|
||||
char *DE;
|
||||
char *SQ;
|
||||
} ecoseq_t;
|
||||
|
||||
/*
|
||||
*
|
||||
* Taxonomy taxon types
|
||||
*
|
||||
*/
|
||||
|
||||
|
||||
typedef struct {
|
||||
int32_t taxid;
|
||||
int32_t rank;
|
||||
int32_t parent;
|
||||
int32_t namelength;
|
||||
char name[1];
|
||||
|
||||
} ecotxformat_t;
|
||||
|
||||
typedef struct ecotxnode {
|
||||
int32_t taxid;
|
||||
int32_t rank;
|
||||
int32_t farest;
|
||||
struct ecotxnode *parent;
|
||||
char *name;
|
||||
} ecotx_t;
|
||||
|
||||
typedef struct {
|
||||
int32_t count;
|
||||
int32_t maxtaxid;
|
||||
int32_t buffersize;
|
||||
ecotx_t taxon[1];
|
||||
} ecotxidx_t;
|
||||
|
||||
|
||||
/*
|
||||
*
|
||||
* Taxonomy rank types
|
||||
*
|
||||
*/
|
||||
|
||||
typedef struct {
|
||||
int32_t count;
|
||||
char* label[1];
|
||||
} ecorankidx_t;
|
||||
|
||||
/*
|
||||
*
|
||||
* Taxonomy name types
|
||||
*
|
||||
*/
|
||||
|
||||
typedef struct {
|
||||
int32_t is_scientificname;
|
||||
int32_t namelength;
|
||||
int32_t classlength;
|
||||
int32_t taxid;
|
||||
char names[1];
|
||||
} econameformat_t;
|
||||
|
||||
|
||||
typedef struct {
|
||||
char *name;
|
||||
char *classname;
|
||||
int32_t is_scientificname;
|
||||
struct ecotxnode *taxon;
|
||||
} econame_t;
|
||||
|
||||
|
||||
typedef struct {
|
||||
int32_t count;
|
||||
econame_t names[1];
|
||||
} econameidx_t;
|
||||
|
||||
|
||||
typedef struct {
|
||||
ecorankidx_t *ranks;
|
||||
econameidx_t *names;
|
||||
ecotxidx_t *taxons;
|
||||
} ecotaxonomy_t;
|
||||
|
||||
|
||||
/*****************************************************
|
||||
*
|
||||
* Function declarations
|
||||
*
|
||||
*****************************************************/
|
||||
|
||||
/*
|
||||
*
|
||||
* Low level system functions
|
||||
*
|
||||
*/
|
||||
|
||||
int32_t is_big_endian();
|
||||
int32_t swap_int32_t(int32_t);
|
||||
|
||||
void *eco_malloc(int32_t chunksize,
|
||||
const char *error_message,
|
||||
const char *filename,
|
||||
int32_t line);
|
||||
|
||||
|
||||
void *eco_realloc(void *chunk,
|
||||
int32_t chunksize,
|
||||
const char *error_message,
|
||||
const char *filename,
|
||||
int32_t line);
|
||||
|
||||
void eco_free(void *chunk,
|
||||
const char *error_message,
|
||||
const char *filename,
|
||||
int32_t line);
|
||||
|
||||
void eco_trace_memory_allocation();
|
||||
void eco_untrace_memory_allocation();
|
||||
|
||||
#define ECOMALLOC(size,error_message) \
|
||||
eco_malloc((size),(error_message),__FILE__,__LINE__)
|
||||
|
||||
#define ECOREALLOC(chunk,size,error_message) \
|
||||
eco_realloc((chunk),(size),(error_message),__FILE__,__LINE__)
|
||||
|
||||
#define ECOFREE(chunk,error_message) \
|
||||
eco_free((chunk),(error_message),__FILE__,__LINE__)
|
||||
|
||||
|
||||
|
||||
|
||||
/*
|
||||
*
|
||||
* Error managment
|
||||
*
|
||||
*/
|
||||
|
||||
|
||||
void ecoError(int32_t,const char*,const char *,int);
|
||||
|
||||
#define ECOERROR(code,message) ecoError((code),(message),__FILE__,__LINE__)
|
||||
|
||||
#define ECO_IO_ERROR (1)
|
||||
#define ECO_MEM_ERROR (2)
|
||||
#define ECO_ASSERT_ERROR (3)
|
||||
#define ECO_NOTFOUND_ERROR (4)
|
||||
|
||||
|
||||
/*
|
||||
*
|
||||
* Low level Disk access functions
|
||||
*
|
||||
*/
|
||||
|
||||
FILE *open_ecorecorddb(const char *filename,
|
||||
int32_t *sequencecount,
|
||||
int32_t abort_on_open_error);
|
||||
|
||||
void *read_ecorecord(FILE *,int32_t *recordSize);
|
||||
|
||||
|
||||
|
||||
/*
|
||||
* Read function in internal binary format
|
||||
*/
|
||||
|
||||
FILE *open_ecoseqdb(const char *filename,
|
||||
int32_t *sequencecount);
|
||||
|
||||
ecoseq_t *readnext_ecoseq(FILE *);
|
||||
|
||||
ecorankidx_t *read_rankidx(const char *filename);
|
||||
|
||||
econameidx_t *read_nameidx(const char *filename,ecotaxonomy_t *taxonomy);
|
||||
|
||||
|
||||
|
||||
/**
|
||||
* Read taxonomy data as formated by the ecoPCRFormat.py script.
|
||||
*
|
||||
* This function is normaly uses internaly by the read_taxonomy
|
||||
* function and should not be called directly.
|
||||
*
|
||||
* @arg filename path to the *.tdx file of the reformated db
|
||||
*
|
||||
* @return pointer to a taxonomy index structure
|
||||
*/
|
||||
|
||||
ecotxidx_t *read_taxonomyidx(const char *filename,const char *filename2);
|
||||
|
||||
ecotaxonomy_t *read_taxonomy(const char *prefix,int32_t readAlternativeName);
|
||||
|
||||
ecotx_t *eco_findtaxonatrank(ecotx_t *taxon, int32_t rankidx);
|
||||
|
||||
ecotx_t *eco_findtaxonbytaxid(ecotaxonomy_t *taxonomy, int32_t taxid);
|
||||
|
||||
int eco_isundertaxon(ecotx_t *taxon, int other_taxid);
|
||||
|
||||
ecoseq_t *ecoseq_iterator(const char *prefix);
|
||||
|
||||
|
||||
|
||||
ecoseq_t *new_ecoseq();
|
||||
int32_t delete_ecoseq(ecoseq_t *);
|
||||
ecoseq_t *new_ecoseq_with_data( char *AC,
|
||||
char *DE,
|
||||
char *SQ,
|
||||
int32_t taxid
|
||||
);
|
||||
|
||||
|
||||
int32_t delete_taxon(ecotx_t *taxon);
|
||||
int32_t delete_taxonomy(ecotxidx_t *index);
|
||||
int32_t delete_ecotaxonomy(ecotaxonomy_t *taxonomy);
|
||||
|
||||
|
||||
int32_t rank_index(const char* label,ecorankidx_t* ranks);
|
||||
|
||||
//int32_t delete_apatseq(SeqPtr pseq);
|
||||
//PatternPtr buildPattern(const char *pat, int32_t error_max);
|
||||
//PatternPtr complementPattern(PatternPtr pat);
|
||||
//
|
||||
//SeqPtr ecoseq2apatseq(ecoseq_t *in,SeqPtr out,int32_t circular);
|
||||
|
||||
//char *ecoComplementPattern(char *nucAcSeq);
|
||||
//char *ecoComplementSequence(char *nucAcSeq);
|
||||
//char *getSubSequence(char* nucAcSeq,int32_t begin,int32_t end);
|
||||
|
||||
ecotx_t *eco_getspecies(ecotx_t *taxon,ecotaxonomy_t *taxonomy);
|
||||
ecotx_t *eco_getgenus(ecotx_t *taxon,ecotaxonomy_t *taxonomy);
|
||||
ecotx_t *eco_getfamily(ecotx_t *taxon,ecotaxonomy_t *taxonomy);
|
||||
ecotx_t *eco_getkingdom(ecotx_t *taxon,ecotaxonomy_t *taxonomy);
|
||||
ecotx_t *eco_getsuperkingdom(ecotx_t *taxon,ecotaxonomy_t *taxonomy);
|
||||
|
||||
//int eco_is_taxid_ignored(int32_t *ignored_taxid, int32_t tab_len, int32_t taxid);
|
||||
//int eco_is_taxid_included(ecotaxonomy_t *taxonomy, int32_t *included_taxid, int32_t tab_len, int32_t taxid);
|
||||
|
||||
|
||||
ecotaxonomy_t *getTaxPointer(SEXP Rtaxonomy);
|
||||
|
||||
#endif /*ECOPCR_H_*/
|
||||
@@ -0,0 +1,64 @@
|
||||
#include "ecoPCR.h"
|
||||
#include <string.h>
|
||||
#include <stdlib.h>
|
||||
|
||||
static econame_t *readnext_econame(FILE *f,econame_t *name,ecotaxonomy_t *taxonomy);
|
||||
|
||||
econameidx_t *read_nameidx(const char *filename,ecotaxonomy_t *taxonomy)
|
||||
{
|
||||
|
||||
int32_t count;
|
||||
FILE *f;
|
||||
econameidx_t *indexname;
|
||||
int32_t i;
|
||||
|
||||
f = open_ecorecorddb(filename,&count,0);
|
||||
|
||||
if (f==NULL)
|
||||
return NULL;
|
||||
|
||||
indexname = (econameidx_t*) ECOMALLOC(sizeof(econameidx_t) + sizeof(econame_t) * (count-1),"Allocate names");
|
||||
|
||||
indexname->count=count;
|
||||
|
||||
for (i=0; i < count; i++){
|
||||
readnext_econame(f,(indexname->names)+i,taxonomy);
|
||||
}
|
||||
|
||||
return indexname;
|
||||
}
|
||||
|
||||
econame_t *readnext_econame(FILE *f,econame_t *name,ecotaxonomy_t *taxonomy)
|
||||
{
|
||||
|
||||
econameformat_t *raw;
|
||||
int32_t rs;
|
||||
|
||||
raw = read_ecorecord(f,&rs);
|
||||
|
||||
if (!raw)
|
||||
return NULL;
|
||||
|
||||
if (is_big_endian())
|
||||
{
|
||||
raw->is_scientificname = swap_int32_t(raw->is_scientificname);
|
||||
raw->namelength = swap_int32_t(raw->namelength);
|
||||
raw->classlength = swap_int32_t(raw->classlength);
|
||||
raw->taxid = swap_int32_t(raw->taxid);
|
||||
}
|
||||
|
||||
name->is_scientificname=raw->is_scientificname;
|
||||
|
||||
name->name = ECOMALLOC((raw->namelength+1) * sizeof(char),"Allocate name");
|
||||
strncpy(name->name,raw->names,raw->namelength);
|
||||
name->name[raw->namelength]=0;
|
||||
|
||||
name->classname = ECOMALLOC((raw->classlength+1) * sizeof(char),"Allocate classname");
|
||||
strncpy(name->classname,(raw->names+raw->namelength),raw->classlength);
|
||||
name->classname[raw->classlength]=0;
|
||||
|
||||
name->taxon = taxonomy->taxons->taxon + raw->taxid;
|
||||
|
||||
return name;
|
||||
}
|
||||
|
||||
Binary file not shown.
@@ -0,0 +1,55 @@
|
||||
#include "ecoPCR.h"
|
||||
#include <string.h>
|
||||
#include <stdlib.h>
|
||||
|
||||
static int compareRankLabel(const void *label1, const void *label2);
|
||||
|
||||
ecorankidx_t *read_rankidx(const char *filename)
|
||||
{
|
||||
int32_t count;
|
||||
FILE *f;
|
||||
ecorankidx_t *index;
|
||||
int32_t i;
|
||||
int32_t rs;
|
||||
char *buffer;
|
||||
|
||||
f = open_ecorecorddb(filename,&count,0);
|
||||
|
||||
if (f==NULL)
|
||||
return NULL;
|
||||
|
||||
index = (ecorankidx_t*) ECOMALLOC(sizeof(ecorankidx_t) + sizeof(char*) * (count-1),
|
||||
"Allocate rank index");
|
||||
|
||||
index->count=count;
|
||||
|
||||
for (i=0; i < count; i++)
|
||||
{
|
||||
buffer = read_ecorecord(f,&rs);
|
||||
index->label[i]=(char*) ECOMALLOC(rs+1,
|
||||
"Allocate rank label");
|
||||
strncpy(index->label[i],buffer,rs);
|
||||
}
|
||||
|
||||
return index;
|
||||
}
|
||||
|
||||
int32_t rank_index(const char* label,ecorankidx_t* ranks)
|
||||
{
|
||||
char **rep;
|
||||
|
||||
rep = bsearch(label,ranks->label,ranks->count,sizeof(char*),compareRankLabel);
|
||||
|
||||
if (rep)
|
||||
return rep-ranks->label;
|
||||
// else
|
||||
// ECOERROR(ECO_NOTFOUND_ERROR,"Rank label not found");
|
||||
|
||||
return -1;
|
||||
}
|
||||
|
||||
|
||||
int compareRankLabel(const void *label1, const void *label2)
|
||||
{
|
||||
return strcmp((const char*)label1,*(const char**)label2);
|
||||
}
|
||||
Binary file not shown.
+422
@@ -0,0 +1,422 @@
|
||||
#include "ecoPCR.h"
|
||||
#include <string.h>
|
||||
#include <stdlib.h>
|
||||
#include <stdio.h>
|
||||
|
||||
#include <R.h>
|
||||
|
||||
#ifndef MAX
|
||||
#define MAX(x,y) (((x)>(y)) ? (x):(y))
|
||||
#endif
|
||||
|
||||
static ecotx_t *readnext_ecotaxon(FILE *f,ecotx_t *taxon);
|
||||
|
||||
/**
|
||||
* Open the taxonomy database
|
||||
* @param pointer to the database (.tdx file)
|
||||
* @return a ecotxidx_t structure
|
||||
*/
|
||||
ecotxidx_t *read_taxonomyidx(const char *filename,const char *filename2)
|
||||
{
|
||||
int32_t count;
|
||||
int32_t count2;
|
||||
FILE *f;
|
||||
FILE *f2;
|
||||
ecotxidx_t *index;
|
||||
struct ecotxnode *t;
|
||||
int32_t i;
|
||||
int32_t j;
|
||||
|
||||
f = open_ecorecorddb(filename,&count,0);
|
||||
|
||||
if (f==NULL) return NULL;
|
||||
|
||||
f2 = open_ecorecorddb(filename2,&count2,0);
|
||||
|
||||
index = (ecotxidx_t*) ECOMALLOC(sizeof(ecotxidx_t) + sizeof(ecotx_t) * (count+count2-1),
|
||||
"Allocate taxonomy");
|
||||
|
||||
index->count=count+count2;
|
||||
index->buffersize = index->count;
|
||||
|
||||
index->maxtaxid=0;
|
||||
REprintf("Readind %d taxa...\n",count);
|
||||
for (i=0; i < count; i++){
|
||||
readnext_ecotaxon(f,&(index->taxon[i]));
|
||||
index->taxon[i].parent=index->taxon + (size_t)index->taxon[i].parent;
|
||||
index->taxon[i].parent->farest=0;
|
||||
if (index->taxon[i].taxid > index->maxtaxid)
|
||||
index->maxtaxid=index->taxon[i].taxid;
|
||||
}
|
||||
|
||||
|
||||
if (count2>0)
|
||||
REprintf("Readind %d local taxa...\n",count2);
|
||||
else
|
||||
REprintf("No local taxon\n");
|
||||
|
||||
count = index->count;
|
||||
|
||||
for (; i < count; i++){
|
||||
readnext_ecotaxon(f2,&(index->taxon[i]));
|
||||
index->taxon[i].parent=index->taxon + (size_t)index->taxon[i].parent;
|
||||
index->taxon[i].parent->farest=0;
|
||||
if (index->taxon[i].taxid > index->maxtaxid)
|
||||
index->maxtaxid=index->taxon[i].taxid;
|
||||
}
|
||||
|
||||
REprintf("Computing longest branches...\n",count);
|
||||
|
||||
for (i=0; i < count; i++){
|
||||
t=index->taxon+i;
|
||||
if (t->farest==-1)
|
||||
{
|
||||
t->farest=0;
|
||||
while(t->parent != t)
|
||||
{
|
||||
j = t->farest + 1;
|
||||
if (j > t->parent->farest)
|
||||
{
|
||||
t->parent->farest = j;
|
||||
t=t->parent;
|
||||
}
|
||||
else
|
||||
t=index->taxon;
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
return index;
|
||||
}
|
||||
|
||||
|
||||
int32_t delete_taxonomy(ecotxidx_t *index)
|
||||
{
|
||||
int32_t i;
|
||||
|
||||
if (index)
|
||||
{
|
||||
for (i=0; i< index->count; i++)
|
||||
if (index->taxon[i].name)
|
||||
ECOFREE(index->taxon[i].name,"Free scientific name");
|
||||
|
||||
ECOFREE(index,"Free Taxonomy");
|
||||
|
||||
return 0;
|
||||
}
|
||||
|
||||
return 1;
|
||||
}
|
||||
|
||||
|
||||
|
||||
int32_t delete_taxon(ecotx_t *taxon)
|
||||
{
|
||||
if (taxon)
|
||||
{
|
||||
if (taxon->name)
|
||||
ECOFREE(taxon->name,"Free scientific name");
|
||||
|
||||
ECOFREE(taxon,"Free Taxon");
|
||||
|
||||
return 0;
|
||||
}
|
||||
|
||||
return 1;
|
||||
}
|
||||
|
||||
|
||||
/**
|
||||
* Read the database for a given taxon a save the data
|
||||
* into the taxon structure(if any found)
|
||||
* @param *f pointer to FILE type returned by fopen
|
||||
* @param *taxon pointer to the structure
|
||||
*
|
||||
* @return a ecotx_t structure if any taxon found else NULL
|
||||
*/
|
||||
ecotx_t *readnext_ecotaxon(FILE *f,ecotx_t *taxon)
|
||||
{
|
||||
|
||||
ecotxformat_t *raw;
|
||||
int32_t rs;
|
||||
|
||||
raw = read_ecorecord(f,&rs);
|
||||
|
||||
if (!raw)
|
||||
return NULL;
|
||||
|
||||
if (is_big_endian())
|
||||
{
|
||||
raw->namelength = swap_int32_t(raw->namelength);
|
||||
raw->parent = swap_int32_t(raw->parent);
|
||||
raw->rank = swap_int32_t(raw->rank);
|
||||
raw->taxid = swap_int32_t(raw->taxid);
|
||||
}
|
||||
|
||||
taxon->parent = (ecotx_t*)((size_t)raw->parent);
|
||||
taxon->taxid = raw->taxid;
|
||||
taxon->rank = raw->rank;
|
||||
taxon->farest = -1;
|
||||
|
||||
taxon->name = ECOMALLOC((raw->namelength+1) * sizeof(char),
|
||||
"Allocate taxon scientific name");
|
||||
|
||||
strncpy(taxon->name,raw->name,raw->namelength);
|
||||
|
||||
return taxon;
|
||||
}
|
||||
|
||||
|
||||
ecotaxonomy_t *read_taxonomy(const char *prefix,int32_t readAlternativeName)
|
||||
{
|
||||
ecotaxonomy_t *tax;
|
||||
char *filename;
|
||||
char *filename2;
|
||||
int buffsize;
|
||||
|
||||
tax = ECOMALLOC(sizeof(ecotaxonomy_t),
|
||||
"Allocate taxonomy structure");
|
||||
|
||||
tax->ranks =NULL;
|
||||
tax->taxons=NULL;
|
||||
tax->names =NULL;
|
||||
|
||||
buffsize = strlen(prefix)+10;
|
||||
|
||||
filename = ECOMALLOC(buffsize,
|
||||
"Allocate filename");
|
||||
filename2= ECOMALLOC(buffsize,
|
||||
"Allocate filename");
|
||||
|
||||
snprintf(filename,buffsize,"%s.rdx",prefix);
|
||||
|
||||
tax->ranks = read_rankidx(filename);
|
||||
|
||||
if (tax->ranks == NULL)
|
||||
{
|
||||
ECOFREE(filename,"Desallocate filename 1");
|
||||
ECOFREE(filename2,"Desallocate filename 2");
|
||||
|
||||
delete_ecotaxonomy(tax);
|
||||
return NULL;
|
||||
}
|
||||
|
||||
snprintf(filename,buffsize,"%s.tdx",prefix);
|
||||
snprintf(filename2,buffsize,"%s.ldx",prefix);
|
||||
|
||||
tax->taxons = read_taxonomyidx(filename,filename2);
|
||||
|
||||
if (tax->taxons == NULL)
|
||||
{
|
||||
ECOFREE(filename,"Desallocate filename 1");
|
||||
ECOFREE(filename,"Desallocate filename 2");
|
||||
|
||||
delete_ecotaxonomy(tax);
|
||||
return NULL;
|
||||
}
|
||||
|
||||
if (readAlternativeName)
|
||||
{
|
||||
snprintf(filename,buffsize,"%s.ndx",prefix);
|
||||
tax->names=read_nameidx(filename,tax);
|
||||
}
|
||||
else
|
||||
tax->names=NULL;
|
||||
|
||||
ECOFREE(filename,"Desallocate filename 1");
|
||||
ECOFREE(filename2,"Desallocate filename 2");
|
||||
|
||||
return tax;
|
||||
|
||||
}
|
||||
|
||||
|
||||
|
||||
int32_t delete_ecotaxonomy(ecotaxonomy_t *taxonomy)
|
||||
{
|
||||
if (taxonomy)
|
||||
{
|
||||
if (taxonomy->ranks)
|
||||
ECOFREE(taxonomy->ranks,"Free rank index");
|
||||
|
||||
if (taxonomy->names)
|
||||
ECOFREE(taxonomy->names,"Free names index");
|
||||
|
||||
if (taxonomy->taxons)
|
||||
ECOFREE(taxonomy->taxons,"Free taxon index");
|
||||
|
||||
ECOFREE(taxonomy,"Free taxonomy structure");
|
||||
|
||||
return 0;
|
||||
}
|
||||
|
||||
return 1;
|
||||
}
|
||||
|
||||
ecotx_t *eco_findtaxonatrank(ecotx_t *taxon,
|
||||
int32_t rankidx)
|
||||
{
|
||||
ecotx_t *current_taxon;
|
||||
ecotx_t *next_taxon;
|
||||
|
||||
current_taxon = taxon;
|
||||
next_taxon = current_taxon->parent;
|
||||
|
||||
while ((current_taxon!=next_taxon) && // I' am the root node
|
||||
(current_taxon->rank!=rankidx))
|
||||
{
|
||||
current_taxon = next_taxon;
|
||||
next_taxon = current_taxon->parent;
|
||||
}
|
||||
|
||||
if (current_taxon->rank==rankidx)
|
||||
return current_taxon;
|
||||
else
|
||||
return NULL;
|
||||
}
|
||||
|
||||
/**
|
||||
* Get back information concerning a taxon from a taxonomic id
|
||||
* @param *taxonomy the taxonomy database
|
||||
* @param taxid the taxonomic id
|
||||
*
|
||||
* @result a ecotx_t structure containing the taxonimic information
|
||||
**/
|
||||
ecotx_t *eco_findtaxonbytaxid(ecotaxonomy_t *taxonomy,
|
||||
int32_t taxid)
|
||||
{
|
||||
ecotx_t *current_taxon;
|
||||
int32_t taxoncount;
|
||||
int32_t i;
|
||||
|
||||
taxoncount=taxonomy->taxons->count;
|
||||
|
||||
for (current_taxon=taxonomy->taxons->taxon,
|
||||
i=0;
|
||||
i < taxoncount;
|
||||
i++,
|
||||
current_taxon++){
|
||||
if (current_taxon->taxid==taxid){
|
||||
return current_taxon;
|
||||
}
|
||||
}
|
||||
|
||||
return (ecotx_t*)NULL;
|
||||
}
|
||||
|
||||
/**
|
||||
* Find out if taxon is son of other taxon (identified by its taxid)
|
||||
* @param *taxon son taxon
|
||||
* @param parent_taxid taxonomic id of the other taxon
|
||||
*
|
||||
* @return 1 is the other taxid math a parent taxid, else 0
|
||||
**/
|
||||
int eco_isundertaxon(ecotx_t *taxon,
|
||||
int other_taxid)
|
||||
{
|
||||
ecotx_t *next_parent;
|
||||
|
||||
next_parent = taxon->parent;
|
||||
|
||||
while ( (other_taxid != next_parent->taxid) &&
|
||||
(strcmp(next_parent->name, "root")) )
|
||||
{
|
||||
next_parent = next_parent->parent;
|
||||
}
|
||||
|
||||
if (other_taxid == next_parent->taxid)
|
||||
return 1;
|
||||
else
|
||||
return 0;
|
||||
}
|
||||
|
||||
ecotx_t *eco_getspecies(ecotx_t *taxon,
|
||||
ecotaxonomy_t *taxonomy)
|
||||
{
|
||||
static ecotaxonomy_t *tax=NULL;
|
||||
static int32_t rankindex=-1;
|
||||
|
||||
if (taxonomy && tax!=taxonomy)
|
||||
{
|
||||
rankindex = rank_index("species",taxonomy->ranks);
|
||||
tax=taxonomy;
|
||||
}
|
||||
|
||||
if (!tax || rankindex < 0)
|
||||
ECOERROR(ECO_ASSERT_ERROR,"No taxonomy defined");
|
||||
|
||||
return eco_findtaxonatrank(taxon,rankindex);
|
||||
}
|
||||
|
||||
ecotx_t *eco_getgenus(ecotx_t *taxon,
|
||||
ecotaxonomy_t *taxonomy)
|
||||
{
|
||||
static ecotaxonomy_t *tax=NULL;
|
||||
static int32_t rankindex=-1;
|
||||
|
||||
if (taxonomy && tax!=taxonomy)
|
||||
{
|
||||
rankindex = rank_index("genus",taxonomy->ranks);
|
||||
tax=taxonomy;
|
||||
}
|
||||
|
||||
if (!tax || rankindex < 0)
|
||||
ECOERROR(ECO_ASSERT_ERROR,"No taxonomy defined");
|
||||
|
||||
return eco_findtaxonatrank(taxon,rankindex);
|
||||
}
|
||||
|
||||
|
||||
ecotx_t *eco_getfamily(ecotx_t *taxon,
|
||||
ecotaxonomy_t *taxonomy)
|
||||
{
|
||||
static ecotaxonomy_t *tax=NULL;
|
||||
static int32_t rankindex=-1;
|
||||
|
||||
if (taxonomy && tax!=taxonomy)
|
||||
{
|
||||
rankindex = rank_index("family",taxonomy->ranks);
|
||||
tax=taxonomy;
|
||||
}
|
||||
|
||||
if (!tax || rankindex < 0)
|
||||
ECOERROR(ECO_ASSERT_ERROR,"No taxonomy defined");
|
||||
|
||||
return eco_findtaxonatrank(taxon,rankindex);
|
||||
}
|
||||
|
||||
ecotx_t *eco_getkingdom(ecotx_t *taxon,
|
||||
ecotaxonomy_t *taxonomy)
|
||||
{
|
||||
static ecotaxonomy_t *tax=NULL;
|
||||
static int32_t rankindex=-1;
|
||||
|
||||
if (taxonomy && tax!=taxonomy)
|
||||
{
|
||||
rankindex = rank_index("kingdom",taxonomy->ranks);
|
||||
tax=taxonomy;
|
||||
}
|
||||
|
||||
if (!tax || rankindex < 0)
|
||||
ECOERROR(ECO_ASSERT_ERROR,"No taxonomy defined");
|
||||
|
||||
return eco_findtaxonatrank(taxon,rankindex);
|
||||
}
|
||||
|
||||
ecotx_t *eco_getsuperkingdom(ecotx_t *taxon,
|
||||
ecotaxonomy_t *taxonomy)
|
||||
{
|
||||
static ecotaxonomy_t *tax=NULL;
|
||||
static int32_t rankindex=-1;
|
||||
|
||||
if (taxonomy && tax!=taxonomy)
|
||||
{
|
||||
rankindex = rank_index("superkingdom",taxonomy->ranks);
|
||||
tax=taxonomy;
|
||||
}
|
||||
|
||||
if (!tax || rankindex < 0)
|
||||
ECOERROR(ECO_ASSERT_ERROR,"No taxonomy defined");
|
||||
|
||||
return eco_findtaxonatrank(taxon,rankindex);
|
||||
}
|
||||
Binary file not shown.
@@ -0,0 +1,6 @@
|
||||
#include "ecoPCR.h"
|
||||
|
||||
|
||||
ecotaxonomy_t *getTaxPointer(SEXP Rtaxonomy);
|
||||
SEXP R_delete_taxonomy(SEXP Rtaxonomy);
|
||||
|
||||
+199
@@ -0,0 +1,199 @@
|
||||
/*
|
||||
* taxonomy.c
|
||||
*
|
||||
* Created on: 17 janv. 2013
|
||||
* Author: coissac
|
||||
*/
|
||||
|
||||
#include "robitax.h"
|
||||
|
||||
|
||||
static ecorankidx_t *new_bdbecorankidx(void);
|
||||
static ecotxidx_t *new_bdbecotxidx(int nbtaxa, int rootrank);
|
||||
|
||||
static ecorankidx_t *new_bdbecorankidx(void)
|
||||
{
|
||||
ecorankidx_t *index;
|
||||
int i;
|
||||
size_t size;
|
||||
char* rank[]={"class", "family", "forma",
|
||||
"genus", "infraclass", "infraorder",
|
||||
"kingdom", "motu", "no rank",
|
||||
"order", "parvorder", "phylum",
|
||||
"species", "species group", "species subgroup",
|
||||
"subclass", "subfamily", "subgenus",
|
||||
"subkingdom", "suborder", "subphylum",
|
||||
"subspecies", "subtribe", "superclass",
|
||||
"superfamily","superkingdom", "superorder",
|
||||
"superphylum","tribe", "varietas"};
|
||||
|
||||
|
||||
|
||||
index = (ecorankidx_t*) ECOMALLOC(sizeof(ecorankidx_t) + sizeof(char*) * (29),
|
||||
"Allocate rank index");
|
||||
|
||||
index->count=30;
|
||||
for (i=0; i < index->count; i++)
|
||||
{
|
||||
size = strlen(rank[i]);
|
||||
index->label[i]=(char*) ECOMALLOC(size+1,
|
||||
"Allocate rank label");
|
||||
strcpy(index->label[i],rank[i]);
|
||||
}
|
||||
|
||||
return index;
|
||||
}
|
||||
|
||||
static ecotxidx_t *new_bdbecotxidx(int nbtaxa, int rootrank) {
|
||||
|
||||
ecotxidx_t *index;
|
||||
int rootnamelen = 4; // "rootname="root"
|
||||
|
||||
index = (ecotxidx_t*) ECOMALLOC(sizeof(ecotxidx_t) + sizeof(ecotx_t) * (nbtaxa),
|
||||
"Allocate taxonomy");
|
||||
|
||||
//initialize the taxonomy with the root taxon
|
||||
index->count=nbtaxa+1;
|
||||
index->maxtaxid=1;
|
||||
index->buffersize=nbtaxa+1;
|
||||
|
||||
// Create the root taxon
|
||||
index->taxon[0].taxid=1;
|
||||
index->taxon[0].rank=rootrank;
|
||||
index->taxon[0].farest=0;
|
||||
index->taxon[0].parent=(ecotx_t*)1;
|
||||
|
||||
index->taxon[0].name= (char*) ECOMALLOC(sizeof(char) * rootnamelen +1,
|
||||
"Allocate taxonomy root name");
|
||||
|
||||
strcpy(index->taxon[0].name, "root");
|
||||
|
||||
return index;
|
||||
|
||||
}
|
||||
|
||||
static int cmptaxid(const void* t1, const void* t2) {
|
||||
int et1 = ((ecotx_t*)t1)->taxid;
|
||||
int et2 = ((ecotx_t*)t2)->taxid;
|
||||
|
||||
if (et1 < et2)
|
||||
return -1;
|
||||
|
||||
if (et2 < et1)
|
||||
return 1;
|
||||
|
||||
return 0;
|
||||
}
|
||||
|
||||
static int findparentcmp(const void* p, const void* t) {
|
||||
int parent = (int)p;
|
||||
int et = ((ecotx_t*)t)->taxid;
|
||||
|
||||
if (parent < et)
|
||||
return -1;
|
||||
|
||||
if (et < parent)
|
||||
return 1;
|
||||
|
||||
return 0;
|
||||
}
|
||||
|
||||
SEXP R_buildbarcodetaxo(SEXP rdata) {
|
||||
SEXP names;
|
||||
SEXP taxids;
|
||||
SEXP ranks;
|
||||
SEXP partofs;
|
||||
SEXP Rtax;
|
||||
|
||||
int nbtaxa;
|
||||
int rootrank;
|
||||
int i;
|
||||
|
||||
int taxid;
|
||||
char *name;
|
||||
int rank;
|
||||
int partof;
|
||||
|
||||
ecotxidx_t* parent;
|
||||
|
||||
taxids = getAttrib(rdata, R_RowNamesSymbol);
|
||||
names = VECTOR_ELT(rdata, 0);
|
||||
ranks = VECTOR_ELT(rdata, 1);
|
||||
partofs= VECTOR_ELT(rdata, 2);
|
||||
|
||||
nbtaxa = GET_LENGTH(taxids);
|
||||
|
||||
ecotaxonomy_t *tax;
|
||||
|
||||
tax = ECOMALLOC(sizeof(ecotaxonomy_t),
|
||||
"Allocate taxonomy structure");
|
||||
|
||||
tax->ranks =new_bdbecorankidx();
|
||||
|
||||
rootrank = rank_index("no rank",tax->ranks);
|
||||
|
||||
tax->taxons=new_bdbecotxidx(nbtaxa,rootrank);
|
||||
tax->names =NULL;
|
||||
|
||||
|
||||
for (i=0; i< nbtaxa; i++) {
|
||||
taxid = atol(CHAR(STRING_ELT(taxids, i)) + 3);
|
||||
name = (char*) CHAR(STRING_ELT(names, i));
|
||||
rank = rank_index(CHAR(STRING_ELT(ranks, i)),tax->ranks);
|
||||
partof = atol(CHAR(STRING_ELT(partofs, i)) + 3);
|
||||
|
||||
if (taxid > tax->taxons->maxtaxid)
|
||||
tax->taxons->maxtaxid=taxid;
|
||||
|
||||
tax->taxons->taxon[i+1].taxid=taxid;
|
||||
tax->taxons->taxon[i+1].rank=rootrank;
|
||||
tax->taxons->taxon[i+1].farest=0;
|
||||
tax->taxons->taxon[i+1].parent=(ecotx_t*)((size_t)partof);
|
||||
|
||||
tax->taxons->taxon[i+1].name= (char*) ECOMALLOC(sizeof(char) * strlen(name) +1,
|
||||
"Allocate taxonomy root name");
|
||||
|
||||
strcpy(tax->taxons->taxon[i+1].name, name);
|
||||
}
|
||||
|
||||
qsort((void*)tax->taxons->taxon,nbtaxa+1,sizeof(ecotx_t),cmptaxid);
|
||||
|
||||
for (i=0; i< nbtaxa+1; i++) {
|
||||
parent = (ecotxidx_t*) bsearch((void*)(tax->taxons->taxon[i].parent),
|
||||
(void*)(tax->taxons->taxon),
|
||||
nbtaxa+1,
|
||||
sizeof(ecotx_t),
|
||||
findparentcmp);
|
||||
|
||||
|
||||
if (parent==NULL)
|
||||
error("Error during taxonomy indexing");
|
||||
|
||||
tax->taxons->taxon[i].parent=(struct ecotxnode *)parent;
|
||||
}
|
||||
|
||||
Rtax = PROTECT(R_MakeExternalPtr(tax, mkString("ROBITools NCBI Taxonomy pointer"), R_NilValue));
|
||||
R_RegisterCFinalizerEx(Rtax, (R_CFinalizer_t)R_delete_taxonomy,TRUE);
|
||||
|
||||
UNPROTECT(1);
|
||||
|
||||
return Rtax;
|
||||
|
||||
}
|
||||
|
||||
|
||||
SEXP R_delete_taxonomy(SEXP Rtaxonomy)
|
||||
{
|
||||
ecotaxonomy_t *ptax;
|
||||
SEXP pointer;
|
||||
|
||||
ptax = (ecotaxonomy_t *) R_ExternalPtrAddr(Rtaxonomy);
|
||||
|
||||
(void) delete_ecotaxonomy(ptax);
|
||||
|
||||
// Clear the external pointer
|
||||
R_ClearExternalPtr(Rtaxonomy);
|
||||
|
||||
return R_NilValue;
|
||||
|
||||
}
|
||||
Binary file not shown.
Reference in New Issue
Block a user