initial commit

.gitignore

+/man/
+/vignettes/
+/Read-and-delete-me

DESCRIPTION

+Package: ROBITaxonomy
+Type: Package
+Title: Metabarcoding data biodiversity analysis
+Version: 0.1
+Date: 2012-08-23
+Author: LECA - Laboratoire d'ecologie alpine
+Maintainer: LECA OBITools team <obitools@metabarcoding.org>
+Description: More about what it does (maybe more than one line)
+License: CeCILL v2.0
+LazyLoad: yes
+Roxygen: list(wrap = FALSE)
+Collate:
+    'ROBITaxonomy.R'
+    'taxonomy.R'
+    'basic.R'
+    'default.R'
+    'distance.R'
+    'lca.R'
+    'rank.R'
+RoxygenNote: 5.0.1

NAMESPACE

+# Generated by roxygen2: do not edit by hand
+
+export(default.taxonomy)
+export(distance.taxonomy)
+export(ecofind)
+export(family)
+export(genus)
+export(is.obitools.taxonomy)
+export(is.subcladeof)
+export(kingdom)
+export(length.obitools.taxonomy)
+export(longest.path)
+export(lowest.common.ancestor)
+export(max.obitools.taxonomy)
+export(parent)
+export(path)
+export(rank.list)
+export(read.taxonomy)
+export(scientificname)
+export(species)
+export(superkingdom)
+export(taxid.list)
+export(taxonatrank)
+export(taxonomicrank)
+export(validate)
+exportClasses(obitools.taxonomy)
+exportClasses(obitools.taxonomyOrNULL)
+useDynLib(ROBITaxonomy)

R/default.R

+#' @include taxonomy.R
+NULL
+
+
+#
+#
+# Manage le loading of the default taxonomy
+#
+#
+
+.__default__taxonomy__ = NULL
+
+#' Returns the default taxonomy
+#' 
+#' Returns a \code{\linkS4class{obitools.taxonomy}} instance corresponding
+#' to a NCBI taxonomy included by default in the \pkg{\link{ROBITaxonomy}} package.
+#' 
+#' @return a \code{\linkS4class{obitools.taxonomy}} instance.
+#' 
+#' @examples
+#' 
+#' # Load the default taxonomy
+#' taxo = default.taxonomy()
+#' 
+#' # and use it for requesting a scientific name
+#' scientificname(taxo,7742)
+#' 
+#' @seealso \code{\linkS4class{obitools.taxonomy}}
+#' 
+#' @author Eric Coissac
+#' @keywords taxonomy
+#' @export
+#' 
+default.taxonomy = function() {
+  if (is.null(get(".__default__taxonomy__",envir = environment())))
+    assign(".__default__taxonomy__", 
+           read.taxonomy(paste(system.file("extdata", 
+                                           package="ROBITaxonomy"),
+                                           'ncbitaxo',
+                                        sep='/')), 
+           envir=globalenv())
+  
+  return(get(".__default__taxonomy__",envir = globalenv()))
+}
+
+
+#' @export
+#' 
+is.obitools.taxonomy = function(taxonomy) {
+  class(t)[1] == "obitools.taxonomy"
+}
+

R/distance.R

+#' @include taxonomy.R
+NULL
+
+#' @export
+setGeneric("longest.path", function(taxonomy,taxid) {
+  return(standardGeneric("longest.path"))
+})
+
+#' Returns the longuest path from a taxon.
+#' 
+#' The method \code{longest.path} returns the length of the
+#' path linking a taxid to the farest leaf belonging this taxid.
+#' 
+#' @param taxonomy the \code{\linkS4class{obitools.taxonomy}} to use.
+#' 
+#' @param taxid an \code{integer} vector containing the list of taxids.
+#' 
+#' @return an \code{integer} vector containing the list length.
+#' 
+#' @examples
+#' # loads the default taxonomy database
+#' taxo=default.taxonomy()
+#' 
+#' # returns the longest path in the taxonomy (from the root node)
+#' longest.path(taxo,1)
+#' 
+#' 
+#' @seealso \code{\linkS4class{obitools.taxonomy}}
+#' 
+#' @author Eric Coissac
+#' @keywords taxonomy
+#' @docType methods
+#' @rdname longest.path-method
+#' @aliases longest.path,obitools.taxonomy
+#' 
+setMethod("longest.path", "obitools.taxonomy",
+          function(taxonomy,taxid) {
+            getp = function(t)   {	
+              if (is.na(t))
+                return(NA)
+              else
+                return(.Call('R_longest_path',
+                             taxonomy,
+                             t,
+                             PACKAGE="ROBITaxonomy"))
+            }
+            
+            taxid = as.integer(taxid)
+            sapply(taxid,getp)
+          })
+
+
+#' @export
+setGeneric("distance.taxonomy", function(taxonomy,taxid1,taxid2=NULL,name=F) {
+  return(standardGeneric("distance.taxonomy"))
+})
+
+
+#' Computes a distance matrix between taxids
+#' 
+#' The method \code{taxonomy.distance} computes a distance matrix between a
+#' set of taxids. The distance between two taxa is based on the topology of
+#' the taxonomomy tree.
+#' 
+#' \deqn{ d(Taxon_A,Taxon_B) = \frac{longest.path(lca(Taxon_A,Taxon_B))}{max(longest.path(Taxon_A),longest.path(Taxon_B))}}
+#'                                  { longest.path(lca(Taxon_A,Taxon_B)) / max(longest.path(Taxon_A),longest.path(Taxon_B)) }
+#' 
+#' 
+#' @param taxonomy the \code{\linkS4class{obitools.taxonomy}} to use.
+#' 
+#' @param taxid1 an \code{integer} vector containing a list of taxids.
+#' 
+#' @param taxid2 an \code{integer} vector containing a list of taxids.
+#'               If \code{taxid2} is set to \code{NULL} (it's default value)
+#'               then the \code{taxid2} list is considered as equal to 
+#'               \code{taxid1} list. 
+#' @param name  A logical value \code{TRUE} or \code{FALSE} indicating 
+#'          if the method return distance matrix annotated by taxids or 
+#'          by scientific names.
+#'          
+#' @return the distance matrix between taxids specified in the \code{taxid1}
+#'         set and the \code{taxid2} set.
+#'         
+#' @examples
+#' # loads the default taxonomy database
+#' taxo=default.taxonomy()
+#' 
+#' # build a vector of 6 taxids corresponding to species
+#' sp.taxid=c(7000,7004,7007,7009,7010,7011)
+#' 
+#' # computes the distance matrix between taxids
+#' distance.taxonomy(taxo,sp.taxid)
+#' 
+#' # Same thing but the matrix is annotated by scientific names
+#' distance.taxonomy(taxo,sp.taxid,name=TRUE)
+#' 
+#' @seealso \code{\link{longest.path}}
+#' 
+#' @author Eric Coissac
+#' @keywords taxonomy
+#' @docType methods
+#' @rdname distance.taxonomy-method
+#' @aliases taxonomy.distance,obitools.taxonomy
+#' 
+setMethod("distance.taxonomy", "obitools.taxonomy",
+          function(taxonomy,taxid1,taxid2=NULL,name=F) {
+            taxdist = function(r)
+            {	
+              t1=r[1]
+              t2=r[2]
+              if (is.na(t1) | is.na(t2))
+                return(NA)
+              
+              p1 = path(taxonomy,t1)
+              p2 = path(taxonomy,t2)
+              
+              minp = min(length(p1),length(p2))
+              common = sum(p1[1:minp] == p2[1:minp])
+              lca = p1[common]
+              lp = longest.path(taxonomy,lca)
+              return(lp/(lp+common))
+            }
+            
+            multitaxdist=function(t1,t2) {
+              apply(data.frame(t1,t2),1,taxdist)
+            }
+            
+            taxid1 = taxid1[! is.na(validate(taxonomy,taxid1))]
+            t1 = path(taxonomy,taxid1)
+            
+            same = is.null(taxid2)
+            
+            if (same)
+            {
+              ntaxon = length(taxid1) 
+              t2 = t1[unlist(sapply(2:ntaxon,
+                                    function(x) x:ntaxon))]
+              t1 = t1[rep(1:(ntaxon-1),(ntaxon-1):1)]
+            }
+            else
+            {
+              taxid2 = taxid2[! is.na(validate(taxonomy,taxid2))]
+              t2 = path(taxonomy,taxid2)
+              nt1 = length(taxid1)
+              nt2 = length(taxid2)
+              t1 = t1[rep(1:nt1,nt2)]
+              t2 = t2[rep(1:nt2,rep(nt1,nt2))]
+            }
+            
+            lmin = mapply(function(a,b) min(length(a),length(b)),
+                          t1,
+                          t2)
+            
+            llca = mapply(function(x,y,l) sum(x[1:l]==y[1:l]),
+                          t1,
+                          t2,
+                          lmin)
+            
+            lb   = longest.path(taxonomy,mapply(function(x,y) x[y],t1,llca))
+            d    = as.double(lb / (lb + llca))
+            
+            if (same) {
+              attr(d, "Size") <- ntaxon
+              if (name)
+                attr(d, "Labels") <- scientificname(taxonomy,taxid1)
+              else
+                attr(d, "Labels") <- as.character(taxid1)
+              attr(d, "Diag") <- FALSE
+              attr(d, "Upper") <- FALSE
+              attr(d, "method") <- NULL
+              attr(d, "call") <- match.call()
+              class(d) <- "dist"
+            }
+            else {
+              if (name)
+                d = matrix(d,nt1,nt2,
+                           dimnames=list(scientificname(taxonomy,taxid1),
+                                         scientificname(taxonomy,taxid2)))
+              else
+                d = matrix(d,nt1,nt2,
+                           dimnames=list(as.character(taxid1),
+                                         as.character(taxid2)))
+              
+            }
+            
+            return(d)
+          })
+
+

R/lca.R

+#' @include taxonomy.R
+NULL
+
+#' @export
+setGeneric("lowest.common.ancestor", function(taxonomy,taxid,threshold=1.0,error=0,name=FALSE) {
+  return(standardGeneric("lowest.common.ancestor"))
+})
+
+#' Computes the lowest common ancestor in the taxonomy tree between a set of taxa
+#' 
+#' The \code{lowest.common.ancestor} function in package \pkg{ROBITaxonomy} computes
+#' the lowest common ancestor of a set of taxids. The lowest common ancestor (LCA)
+#' is the most precise taxonomic group shared by all the considered taxa. Tha
+#' \code{lowest.common.ancestor} function implemented in the \pkg{ROBITaxonomy}
+#' package, considers a fuzzy definition of the LCA as the most precise
+#' taxonomic group shared by a quorum of the considered taxa.
+#' 
+#' @param taxonomy an instance of \code{\linkS4class{obitools.taxonomy}}
+#' @param taxid an integer value or a vector of integer representing NCBI 
+#'   taxonomic identifiers.
+#' @param threshold a numeric value between 0.0 and 1.0 indicating the minimum 
+#' quorum of taxid that must belong the LCA.
+#' @param error an integer value indicating the maximum count of taxids that 
+#' have not to belong the returned taxid. A \code{threshold} below 1.0 have
+#'  priority on the \code{error} parameter.
+#' @param name A logical value \code{TRUE} or \code{FALSE} indicating if the
+#' method return a \emph{taxid} or a scientific name.
+#' 
+#' @return Depending on the value of the \code{name} argument, set by default 
+#'         to \code{FALSE} the method returns :
+#'    \describe{  
+#'           \item{If \code{name==FALSE}}{ the taxid of the taxon corresponding 
+#'             to the LCA as an integer value}
+#'           \item{If \code{name==TRUE}}{ the scientific name of the taxon 
+#'                 corresponding to the LCA as a string}
+#'          }
+#'          
+#' @examples
+#' require(ROBITaxonomy)
+#'
+#' \dontshow{# switch the working directory to the data package directory}
+#' \dontshow{setwd(system.file("extdata", package="ROBITaxonomy"))}
+#'   
+#' # read the taxonomy database
+#'   
+#' taxo=read.taxonomy('ncbitaxo')
+#' 
+#' # build a vector of 6 taxids corresponding to species
+#' 
+#' sp.taxid=c(7000,7004,7007,7009,7010,7011)
+#' 
+#' # look for the lowest common ancestor taxids
+#' 
+#' lowest.common.ancestor(taxo,sp.taxid)
+#' 
+#' # same thing but returns results as a vector of scientific names
+#' lowest.common.ancestor(taxo,sp.taxid,name=TRUE)
+#' 
+#' # If we accept than 2 or 1 taxa do not belong the LCA
+#' lowest.common.ancestor(taxo,sp.taxid,name=TRUE,error=2)
+#' lowest.common.ancestor(taxo,sp.taxid,name=TRUE,error=1)
+#' 
+#' # Partial LCA can also be speciefied as the minimal frequency of
+#' # taxa belonging the LCA 
+#' lowest.common.ancestor(taxo,sp.taxid,name=TRUE,threshold=0.8)
+#' 
+#' @seealso class \code{\linkS4class{obitools.taxonomy}},
+#' and methods \code{\link{path}}, \code{\link{parent}},
+#' 
+#' @author Eric Coissac
+#' @keywords taxonomy
+#' @docType methods
+#' @rdname lowest.common.ancestor-method
+#' @aliases lowest.common.ancestor,obitools.taxonomy
+#' 
+setMethod("lowest.common.ancestor", "obitools.taxonomy",
+          function(taxonomy,taxid,threshold=1.0,error=0,name=FALSE) {
+            
+            if (threshold != 1.0)
+              error=as.integer(floor(length(taxid) * (1-threshold)))
+            
+            
+            #
+            # Remove nod valid taxid
+            #
+            
+            taxid = validate(taxonomy,taxid)
+            if (any(is.na(taxid)))
+              return(NA)
+                      
+            ntaxid=length(taxid)
+            nok = ntaxid - error
+            if (ntaxid==1)
+              return(taxid)
+            
+            allpath  = path(taxonomy,taxid)
+            minlength= min(vapply(allpath,length,0))
+                        
+            lca=NA
+            for (i in 1:minlength) {
+              
+              n = vapply(allpath,function(x) x[i],0)
+              nt = table(n)
+              mt = max(nt)
+              if (mt >= nok) {
+                p = nt[nt==mt]
+                if (length(p)==1)
+                  lca=as.integer(names(p)[1])
+                else
+                  break
+              }
+              else
+                  break
+            }
+            
+            if (name)
+              return(scientificname(taxonomy,lca))
+            else
+              return(lca)
+          })
+
+

R/taxonomy.R

+#' @include ROBITaxonomy.R
+#' @useDynLib ROBITaxonomy
+NULL
+
+#' Gives access to a taxonomy preformated by OBITools
+#' 
+#' A S4 class describing a taxonomy. It allows access to 
+#' taxonomy formated for OBITools.
+#'
+#' @references \describe{
+#'  \item{NCBI Taxonomy : }{\url{http://www.ncbi.nlm.nih.gov/taxonomy}}
+#'  \item{OBITools : }{\url{http://metabarcoding/obitools/doc}}
+#'  }
+#'  
+#' @seealso \code{\link{read.taxonomy}}
+#'  
+#' @name obitools.taxonomy
+#' @rdname obitools-taxonomy-class
+#' @keywords taxonomy
+#' @author Eric Coissac
+#' @exportClass obitools.taxonomy
+#' 
+setClass("obitools.taxonomy",
+         
+         
+         #
+         # Attribute declaration
+         #
+         
+         # data.frame containing the counts of reads per samples
+         #      1 samples per line
+         #      1 sequence per column
+         
+         representation(
+           
+           # An external pointer structure to 
+           # the C taxonomy structure
+           
+           pointer    = "externalptr",
+           
+           # the name of the database on the hard disk
+           
+           dbname     = 'character',
+           
+           # the working directory when the taxonomy
+           # object is created. 
+           # This inforation combined with bname allows
+           # to reload taxonomy from disk
+           
+           workingdir = 'character',
+           
+           # Indicate if the taxonomy is saved in a file
+           # Taxonomy created in R or modified in R are
+           # not saved ==> This have to be take into 
+           # consideration but how ???
+           saved = 'logical'
+         ),
+         
+         #
+         # Check object structure 
+         #
+         
+         validity = function(object) { 			
+           return(TRUE)
+         }
+)
+
+
+
+#' obitools.taxonomy constructor
+#' 
+#' --> this constructor have not to be called directly
+#'     use the read.obitools.taxonomy function to
+#'     create a new instance of taxonomy
+#'
+#' @docType methods
+#' @rdname initialize-methods-obitools.taxonomy
+#' @aliases initialize-methods,obitools.taxonomy
+setMethod("initialize",
+          "obitools.taxonomy",
+          function(.Object, pointer,dbname,workingdir,saved) {
+            .Object@pointer    <- pointer
+            .Object@dbname     <- dbname
+            .Object@workingdir <- workingdir
+            .Object@saved      <- saved
+            
+            validObject(.Object) ## valide l'objet
+            return(.Object)
+          })
+
+
+#' @exportClass obitools.taxonomyOrNULL
+setClassUnion("obitools.taxonomyOrNULL",c("obitools.taxonomy","NULL"))
+
+
+#' @export
+setGeneric("path", function(taxonomy,taxid,name=FALSE) {
+  return(standardGeneric("path"))
+})
+
+
+
+setMethod("path", "obitools.taxonomy",function(taxonomy,taxid,name=FALSE) {
+  getp = function(t)	 {	
+    if (is.na(t))
+      return(NA)
+    else
+    {
+      path=c()
+      
+      t=.Call('R_validate_taxid',
+              taxonomy,
+              as.integer(t),
+              PACKAGE="ROBITaxonomy")
+      
+      if (is.na(t))
+        return(NA)
+      
+      repeat {
+        if (name)
+          path = c(scientificname(taxonomy,t),path)
+        else
+          path = c(t,path)
+        
+        t = .Call('R_get_parent',
+                  taxonomy,
+                  t,
+                  FALSE,
+                  PACKAGE="ROBITaxonomy")
+        if (is.na(t))
+          break
+      }
+      
+      return(path)
+    }
+  }
+  
+  taxid=as.integer(taxid)
+  name=as.logical(name)
+  
+  p = lapply(taxid,getp)
+  d = dim(p)
+  
+  if (!is.null(d))
+    if (d[2]==1)
+      p = as.vector(p)
+  
+  return(p)
+})
+
+
+#' @export
+setGeneric("is.subcladeof", function(taxonomy,taxid,parent) {
+  return(standardGeneric("is.subcladeof"))
+})
+
+setMethod("is.subcladeof", "obitools.taxonomy",function(taxonomy,taxid,parent) {
+  taxid = as.integer(taxid)
+  parent= as.integer(parent)
+  return(.Call('R_is_under_taxon',
+               taxonomy,
+               taxid,
+               parent,
+               PACKAGE="ROBITaxonomy"))
+})
+
+
+
+build.taxonomy = function(pointer,dbname,workingdir,saved) {
+  rd <- new('obitools.taxonomy',
+            pointer=pointer,
+            dbname=dbname,
+            workingdir=workingdir,
+            saved=saved
+  )
+  return(rd)
+}
+
+
+#' Reads a taxonomy
+#' 
+#' \code{read.taxonomy} reads a taxonomy formated by OBITools.
+#' NCBI taxonomy can be download from the NCBI FTP site in taxdump format.
+#' The taxdump must be formated using the obitaxonomy command from OBITools
+#' before being used in R. A OBITools formated taxonomy is composed of 3 files 
+#' with the same prefix name and suffixes .tdx, .rdx, .ndx, two extra files 
+#' suffixed .adx and .ldx can also be present. 
+#' 
+#' @param  dbname A character string containing the file name of the database
+#' 
+#' @return an instance of the class \code{\linkS4class{obitools.taxonomy}}
+#' 
+#' @examples
+#' 
+#' \dontshow{# switch the working directory to the data package directory}
+#' \dontshow{setwd(system.file("extdata", package="ROBITaxonomy"))}
+#'
+#' # read the taxonomy ncbi
+#' ncbi = read.taxonomy("ncbitaxo")
+#' 
+#' # and use it for requesting a scientific name
+#' scientificname(ncbi,7742)
+#' 
+#' @seealso \code{\linkS4class{obitools.taxonomy}}
+#' 
+#' @author Eric Coissac
+#' @keywords taxonomy
+#' @export
+
+read.taxonomy = function(dbname) {
+  t <- .Call('R_read_taxonomy',dbname,TRUE,PACKAGE="ROBITaxonomy")	
+  
+  return(build.taxonomy(t,dbname,getwd(),TRUE))
+}
+
+

ROBITaxonomy.Rproj

+Version: 1.0
+
+RestoreWorkspace: Default
+SaveWorkspace: Default
+AlwaysSaveHistory: Default
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
+Encoding: UTF-8
+
+RnwWeave: knitr
+LaTeX: pdfLaTeX
+
+AutoAppendNewline: Yes
+
+BuildType: Package
+PackageUseDevtools: Yes
+PackageInstallArgs: --no-multiarch --with-keep.source
+PackageRoxygenize: rd,collate,namespace

src/ecoError.c

+#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 errorcode,
+              const char* message,
+              const char * filename,
+              int linenumber)
+{
+  error("Error %d in file %s line %d : %s",
+                 errorcode,
+	               filename,
+	               linenumber,
+	               message);
+}

src/ecoIOUtils.c

+#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,