Package 'taxonomizr' reference manual

Title:	Functions to Work with NCBI Accessions and Taxonomy
Description:	Functions for assigning taxonomy to NCBI accession numbers and taxon IDs based on NCBI's accession2taxid and taxdump files. This package allows the user to download NCBI data dumps and create a local database for fast and local taxonomic assignment.
Authors:	Scott Sherrill-Mix [aut, cre]
Maintainer:	Scott Sherrill-Mix <[email protected]>
License:	GPL (>=2) \| file LICENSE
Version:	0.10.6
Built:	2024-11-21 05:36:15 UTC
Source:	https://github.com/sherrillmix/taxonomizr

Convert accessions to taxa

Description

Convert a vector of NCBI accession numbers to their assigned taxonomy

Usage

accessionToTaxa(accessions, sqlFile, version = c("version", "base"))
accessionToTaxa(accessions, sqlFile, version = c("version", "base"))

Arguments

`accessions`	a vector of NCBI accession strings to convert to taxa
`sqlFile`	a string giving the path to a SQLite file screated by `read.accession2taxid`
`version`	either 'version' indicating that taxaids are versioned e.g. Z17427.1 or 'base' indicating that taxaids do not have version numbers e.g. Z17427

Value

a vector of NCBI taxa ids

References

https://ftp.ncbi.nih.gov/pub/taxonomy/accession2taxid/

Examples

taxa<-c(
 "accession\taccession.version\ttaxid\tgi",
 "Z17427\tZ17427.1\t3702\t16569",
 "Z17428\tZ17428.1\t3702\t16570",
 "Z17429\tZ17429.1\t3702\t16571",
 "Z17430\tZ17430.1\t3702\t16572",
 "X62402\tX62402.1\t9606\t30394"
)
inFile<-tempfile()
sqlFile<-tempfile()
writeLines(taxa,inFile)
read.accession2taxid(inFile,sqlFile,vocal=FALSE)
accessionToTaxa(c("Z17430.1","Z17429.1","X62402.1",'NOTREAL'),sqlFile)
taxa<-c(
 "accession\taccession.version\ttaxid\tgi",
 "Z17427\tZ17427.1\t3702\t16569",
 "Z17428\tZ17428.1\t3702\t16570",
 "Z17429\tZ17429.1\t3702\t16571",
 "Z17430\tZ17430.1\t3702\t16572",
 "X62402\tX62402.1\t9606\t30394"
)
inFile<-tempfile()
sqlFile<-tempfile()
writeLines(taxa,inFile)
read.accession2taxid(inFile,sqlFile,vocal=FALSE)
accessionToTaxa(c("Z17430.1","Z17429.1","X62402.1",'NOTREAL'),sqlFile)

Condense multiple taxonomic assignments to their most recent common branch

Description

Take a table of taxonomic assignments, e.g. assignments from hits to a read, and condense it to a single vector with NAs where there are disagreements between the hits.

Usage

condenseTaxa(taxaTable, groupings = rep(1, nrow(taxaTable)))
condenseTaxa(taxaTable, groupings = rep(1, nrow(taxaTable)))

Arguments

`taxaTable`	a matrix or data.frame with hits on the rows and various levels of taxonomy in the columns
`groupings`	a vector of groups e.g. read queries to condense taxa within

Value

a matrix with ncol(taxaTable) taxonomy columns with a row for each unique id (labelled on rownames) with NAs where there was not complete agreement for an id

Examples

taxas<-matrix(c(
 'a','b','c','e',
 'a','b','d','e'
),nrow=2,byrow=TRUE)
condenseTaxa(taxas)
condenseTaxa(taxas[c(1,2,2),],c(1,1,2))
taxas<-matrix(c(
 'a','b','c','e',
 'a','b','d','e'
),nrow=2,byrow=TRUE)
condenseTaxa(taxas)
condenseTaxa(taxas[c(1,2,2),],c(1,1,2))

Download accession2taxid files from NCBI

Description

Download a nucl_xxx.accession2taxid.gz from NCBI servers. These can then be used to create a SQLite datanase with read.accession2taxid. Note that if the files already exist in the target directory then this function will not redownload them. Delete the files if a fresh download is desired.

Usage

getAccession2taxid(
  outDir = ".",
  baseUrl = sprintf("%s://ftp.ncbi.nih.gov/pub/taxonomy/accession2taxid/", protocol),
  types = c("nucl_gb", "nucl_wgs"),
  protocol = "ftp",
  resume = TRUE
)
getAccession2taxid(
  outDir = ".",
  baseUrl = sprintf("%s://ftp.ncbi.nih.gov/pub/taxonomy/accession2taxid/", protocol),
  types = c("nucl_gb", "nucl_wgs"),
  protocol = "ftp",
  resume = TRUE
)

Arguments

`outDir`	the directory to put the accession2taxid.gz files in
`baseUrl`	the url of the directory where accession2taxid.gz files are located
`types`	the types if accession2taxid.gz files desired where type is the prefix of xxx.accession2taxid.gz. The default is to download all nucl_ accessions. For protein accessions, try `types=c('prot')`.
`protocol`	the protocol to be used for downloading. Probably either `'http'` or `'ftp'`. Overridden if `baseUrl` is provided directly
`resume`	if TRUE attempt to resume downloading an interrupted file without starting over from the beginning

Value

a vector of file path strings of the locations of the output files

References

https://ftp.ncbi.nih.gov/pub/taxonomy/, https://www.ncbi.nlm.nih.gov/genbank/acc_prefix/

Examples

## Not run: 
  if(readline(
    "This will download a lot data and take a while to process.
     Make sure you have space and bandwidth. Type y to continue: "
  )!='y')
    stop('This is a stop to make sure no one downloads a bunch of data unintentionally')

  getAccession2taxid()

## End(Not run)
## Not run: 
  if(readline(
    "This will download a lot data and take a while to process.
     Make sure you have space and bandwidth. Type y to continue: "
  )!='y')
    stop('This is a stop to make sure no one downloads a bunch of data unintentionally')

  getAccession2taxid()

## End(Not run)

Find all accessions for a taxa

Description

Find accessions numbers for a given taxa ID the NCBI taxonomy. This will be pretty slow unless the database was built with indexTaxa=TRUE since the database would not have an index for taxaId.

Usage

getAccessions(taxaId, sqlFile, version = c("version", "base"), limit = NULL)
getAccessions(taxaId, sqlFile, version = c("version", "base"), limit = NULL)

Arguments

`taxaId`	a vector of taxonomic IDs
`sqlFile`	a string giving the path to a SQLite file created by `read.accession2taxid`
`version`	either 'version' indicating that taxaids are versioned e.g. Z17427.1 or 'base' indicating that taxaids do not have version numbers e.g. Z17427
`limit`	return only this number of accessions or NULL for no limits

Value

a vector of character strings giving taxa IDs (potentially comma concatenated for any taxa with ambiguous names)

Examples

taxa<-c(
  "accession\taccession.version\ttaxid\tgi",
  "Z17427\tZ17427.1\t3702\t16569",
  "Z17428\tZ17428.1\t3702\t16570",
  "Z17429\tZ17429.1\t3702\t16571",
  "Z17430\tZ17430.1\t3702\t16572"
)
inFile<-tempfile()
sqlFile<-tempfile()
writeLines(taxa,inFile)
read.accession2taxid(inFile,sqlFile,vocal=FALSE)
getAccessions(3702,sqlFile)
taxa<-c(
  "accession\taccession.version\ttaxid\tgi",
  "Z17427\tZ17427.1\t3702\t16569",
  "Z17428\tZ17428.1\t3702\t16570",
  "Z17429\tZ17429.1\t3702\t16571",
  "Z17430\tZ17430.1\t3702\t16572"
)
inFile<-tempfile()
sqlFile<-tempfile()
writeLines(taxa,inFile)
read.accession2taxid(inFile,sqlFile,vocal=FALSE)
getAccessions(3702,sqlFile)

Find common names for a given taxa

Description

Find all common names recorded for a taxa in the NCBI taxonomy. Use getTaxonomy for scientific names.

Usage

getCommon(taxa, sqlFile = "nameNode.sqlite", types = NULL)
getCommon(taxa, sqlFile = "nameNode.sqlite", types = NULL)

Arguments

`taxa`	a vector of accession numbers
`sqlFile`	a string giving the path to a SQLite file containing a names tables
`types`	a vector of strings giving the type of names desired e.g. "common name". If NULL then all types are returned

Value

a named list of data.frames where each element corresponds to the query taxa IDs. Each data.frame contains columns name and type and each gives an available names and its name type

Examples

namesText<-"9894\t|\tGiraffa camelopardalis (Linnaeus, 1758)\t|\t\t|\tauthority\t|
9894\t|\tGiraffa camelopardalis\t|\t\t|\tscientific name\t|
9894\t|\tgiraffe\t|\t\t|\tgenbank common name\t|
9909\t|\taurochs\t|\t\t|\tgenbank common name\t|
9909\t|\tBos primigenius Bojanus, 1827\t|\t\t|\tauthority\t|
9909\t|\tBos primigenius\t|\t\t|\tscientific name\t|
9913\t|\tBos bovis\t|\t\t|\tsynonym\t|
9913\t|\tBos primigenius taurus\t|\t\t|\tsynonym\t|
9913\t|\tBos taurus Linnaeus, 1758\t|\t\t|\tauthority\t|
9913\t|\tBos taurus\t|\t\t|\tscientific name\t|
9913\t|\tBovidae sp. Adi Nefas\t|\t\t|\tincludes\t|
9913\t|\tbovine\t|\t\t|\tcommon name\t|
9913\t|\tcattle\t|\t\t|\tgenbank common name\t|
9913\t|\tcow\t|\t\t|\tcommon name\t|
9913\t|\tdairy cow\t|\t\t|\tcommon name\t|
9913\t|\tdomestic cattle\t|\t\t|\tcommon name\t|
9913\t|\tdomestic cow\t|\t\t|\tcommon name\t|
9913\t|\tox\t|\t\t|\tcommon name\t|
9913\t|\toxen\t|\t\t|\tcommon name\t|
9916\t|\tBoselaphus\t|\t\t|\tscientific name\t|"
tmpFile<-tempfile()
writeLines(namesText,tmpFile)
sqlFile<-tempfile()
read.names.sql(tmpFile,sqlFile)
getCommon(9909,sqlFile)
sapply(getCommon(c(9894,9913),sqlFile),function(xx)paste(xx$name,collapse='; '))
getCommon(c(9999999,9916,9894,9913),sqlFile,c("common name","genbank common name"))
namesText<-"9894\t|\tGiraffa camelopardalis (Linnaeus, 1758)\t|\t\t|\tauthority\t|
9894\t|\tGiraffa camelopardalis\t|\t\t|\tscientific name\t|
9894\t|\tgiraffe\t|\t\t|\tgenbank common name\t|
9909\t|\taurochs\t|\t\t|\tgenbank common name\t|
9909\t|\tBos primigenius Bojanus, 1827\t|\t\t|\tauthority\t|
9909\t|\tBos primigenius\t|\t\t|\tscientific name\t|
9913\t|\tBos bovis\t|\t\t|\tsynonym\t|
9913\t|\tBos primigenius taurus\t|\t\t|\tsynonym\t|
9913\t|\tBos taurus Linnaeus, 1758\t|\t\t|\tauthority\t|
9913\t|\tBos taurus\t|\t\t|\tscientific name\t|
9913\t|\tBovidae sp. Adi Nefas\t|\t\t|\tincludes\t|
9913\t|\tbovine\t|\t\t|\tcommon name\t|
9913\t|\tcattle\t|\t\t|\tgenbank common name\t|
9913\t|\tcow\t|\t\t|\tcommon name\t|
9913\t|\tdairy cow\t|\t\t|\tcommon name\t|
9913\t|\tdomestic cattle\t|\t\t|\tcommon name\t|
9913\t|\tdomestic cow\t|\t\t|\tcommon name\t|
9913\t|\tox\t|\t\t|\tcommon name\t|
9913\t|\toxen\t|\t\t|\tcommon name\t|
9916\t|\tBoselaphus\t|\t\t|\tscientific name\t|"
tmpFile<-tempfile()
writeLines(namesText,tmpFile)
sqlFile<-tempfile()
read.names.sql(tmpFile,sqlFile)
getCommon(9909,sqlFile)
sapply(getCommon(c(9894,9913),sqlFile),function(xx)paste(xx$name,collapse='; '))
getCommon(c(9999999,9916,9894,9913),sqlFile,c("common name","genbank common name"))

Get descendant ranks for a taxa

Description

Take a NCBI taxa ID and get the descendant taxa matching a given rank from a name and node SQLite database

Usage

getDescendants(ids, sqlFile = "nameNode.sqlite", desiredTaxa = "species")
getDescendants(ids, sqlFile = "nameNode.sqlite", desiredTaxa = "species")

Arguments

`ids`	a vector of ids to find descendants for
`sqlFile`	a string giving the path to a SQLite file containing names and nodes tables
`desiredTaxa`	a vector of strings giving the desired taxa levels

Value

a vector of strings giving the names a for each descendant taxa

Examples

sqlFile<-tempfile()
namesText<-c(
  "1\t|\troot\t|\t\t|\tscientific name\t|",
  "2\t|\tBacteria\t|\tBacteria <prokaryotes>\t|\tscientific name\t|",
  "2\t|\tProcaryotae\t|\tProcaryotae <Bacteria>\t|\tin-part\t|",
  "9606\t|\tHomo sapiens\t|\t\t|\tscientific name",
  "9605\t|\tHomo\t|\t\t|\tscientific name",
  "207598\t|\tHomininae\t|\t\t|\tscientific name",
  "9604\t|\tHominidae\t|\t\t|\tscientific name",
  "314295\t|\tHominoidea\t|\t\t|\tscientific name",
  "9526\t|\tCatarrhini\t|\t\t|\tscientific name",
  "314293\t|\tSimiiformes\t|\t\t|\tscientific name",
  "376913\t|\tHaplorrhini\t|\t\t|\tscientific name",
  "9443\t|\tPrimates\t|\t\t|\tscientific name",
  "314146\t|\tEuarchontoglires\t|\t\t|\tscientific name",
  "1437010\t|\tBoreoeutheria\t|\t\t|\tscientific name",
  "9347\t|\tEutheria\t|\t\t|\tscientific name",
  "32525\t|\tTheria\t|\t\t|\tscientific name",
  "40674\t|\tMammalia\t|\t\t|\tscientific name",
  "32524\t|\tAmniota\t|\t\t|\tscientific name",
  "32523\t|\tTetrapoda\t|\t\t|\tscientific name",
  "1338369\t|\tDipnotetrapodomorpha\t|\t\t|\tscientific name",
  "8287\t|\tSarcopterygii\t|\t\t|\tscientific name",
  "117571\t|\tEuteleostomi\t|\t\t|\tscientific name",
  "117570\t|\tTeleostomi\t|\t\t|\tscientific name",
  "7776\t|\tGnathostomata\t|\t\t|\tscientific name",
  "7742\t|\tVertebrata\t|\t\t|\tscientific name",
  "89593\t|\tCraniata\t|\t\t|\tscientific name",
  "7711\t|\tChordata\t|\t\t|\tscientific name",
  "33511\t|\tDeuterostomia\t|\t\t|\tscientific name",
  "33213\t|\tBilateria\t|\t\t|\tscientific name",
  "6072\t|\tEumetazoa\t|\t\t|\tscientific name",
  "33208\t|\tMetazoa\t|\t\t|\tscientific name",
  "33154\t|\tOpisthokonta\t|\t\t|\tscientific name",
  "2759\t|\tEukaryota\t|\t\t|\tscientific name",
  "131567\t|\tcellular organisms\t|\t\t|\tscientific name",
  "1425170\t|\tHomo heidelbergensis\t|\t\t|\tscientific name"
)
tmpFile<-tempfile()
writeLines(namesText,tmpFile)
taxaNames<-read.names.sql(tmpFile,sqlFile)
nodesText<-c(
 "1\t|\t1\t|\tno rank\t|\t\t|\t8\t|\t0\t|\t1\t|\t0\t|\t0\t|\t0\t|\t0\t|\t0\t|\t\t|",
  "2\t|\t131567\t|\tsuperkingdom\t|\t\t|\t0\t|\t0\t|\t11\t|\t0\t|\t0\t|\t0\t|\t0\t|\t0\t|\t\t|",
  "6\t|\t335928\t|\tgenus\t|\t\t|\t0\t|\t1\t|\t11\t|\t1\t|\t0\t|\t1\t|\t0\t|\t0\t|\t\t|",
  "7\t|\t6\t|\tspecies\t|\tAC\t|\t0\t|\t1\t|\t11\t|\t1\t|\t0\t|\t1\t|\t1\t|\t0\t|\t\t|",
  "9\t|\t32199\t|\tspecies\t|\tBA\t|\t0\t|\t1\t|\t11\t|\t1\t|\t0\t|\t1\t|\t1\t|\t0\t|\t\t|",
  "9606\t|\t9605\t|\tspecies", "9605\t|\t207598\t|\tgenus", "207598\t|\t9604\t|\tsubfamily",
  "9604\t|\t314295\t|\tfamily", "314295\t|\t9526\t|\tsuperfamily",
  "9526\t|\t314293\t|\tparvorder", "314293\t|\t376913\t|\tinfraorder",
  "376913\t|\t9443\t|\tsuborder", "9443\t|\t314146\t|\torder",
  "314146\t|\t1437010\t|\tsuperorder", "1437010\t|\t9347\t|\tno rank",
  "9347\t|\t32525\t|\tno rank", "32525\t|\t40674\t|\tno rank",
  "40674\t|\t32524\t|\tclass", "32524\t|\t32523\t|\tno rank", "32523\t|\t1338369\t|\tno rank",
  "1338369\t|\t8287\t|\tno rank", "8287\t|\t117571\t|\tno rank",
  "117571\t|\t117570\t|\tno rank", "117570\t|\t7776\t|\tno rank",
  "7776\t|\t7742\t|\tno rank", "7742\t|\t89593\t|\tno rank", "89593\t|\t7711\t|\tsubphylum",
  "7711\t|\t33511\t|\tphylum", "33511\t|\t33213\t|\tno rank", "33213\t|\t6072\t|\tno rank",
  "6072\t|\t33208\t|\tno rank", "33208\t|\t33154\t|\tkingdom",
  "33154\t|\t2759\t|\tno rank", "2759\t|\t131567\t|\tsuperkingdom",
  "131567\t|\t1\t|\tno rank", '1425170\t|\t9605\t|\tspecies'
)
writeLines(nodesText,tmpFile)
taxaNodes<-read.nodes.sql(tmpFile,sqlFile)
getDescendants(c(9604),sqlFile)
sqlFile<-tempfile()
namesText<-c(
  "1\t|\troot\t|\t\t|\tscientific name\t|",
  "2\t|\tBacteria\t|\tBacteria <prokaryotes>\t|\tscientific name\t|",
  "2\t|\tProcaryotae\t|\tProcaryotae <Bacteria>\t|\tin-part\t|",
  "9606\t|\tHomo sapiens\t|\t\t|\tscientific name",
  "9605\t|\tHomo\t|\t\t|\tscientific name",
  "207598\t|\tHomininae\t|\t\t|\tscientific name",
  "9604\t|\tHominidae\t|\t\t|\tscientific name",
  "314295\t|\tHominoidea\t|\t\t|\tscientific name",
  "9526\t|\tCatarrhini\t|\t\t|\tscientific name",
  "314293\t|\tSimiiformes\t|\t\t|\tscientific name",
  "376913\t|\tHaplorrhini\t|\t\t|\tscientific name",
  "9443\t|\tPrimates\t|\t\t|\tscientific name",
  "314146\t|\tEuarchontoglires\t|\t\t|\tscientific name",
  "1437010\t|\tBoreoeutheria\t|\t\t|\tscientific name",
  "9347\t|\tEutheria\t|\t\t|\tscientific name",
  "32525\t|\tTheria\t|\t\t|\tscientific name",
  "40674\t|\tMammalia\t|\t\t|\tscientific name",
  "32524\t|\tAmniota\t|\t\t|\tscientific name",
  "32523\t|\tTetrapoda\t|\t\t|\tscientific name",
  "1338369\t|\tDipnotetrapodomorpha\t|\t\t|\tscientific name",
  "8287\t|\tSarcopterygii\t|\t\t|\tscientific name",
  "117571\t|\tEuteleostomi\t|\t\t|\tscientific name",
  "117570\t|\tTeleostomi\t|\t\t|\tscientific name",
  "7776\t|\tGnathostomata\t|\t\t|\tscientific name",
  "7742\t|\tVertebrata\t|\t\t|\tscientific name",
  "89593\t|\tCraniata\t|\t\t|\tscientific name",
  "7711\t|\tChordata\t|\t\t|\tscientific name",
  "33511\t|\tDeuterostomia\t|\t\t|\tscientific name",
  "33213\t|\tBilateria\t|\t\t|\tscientific name",
  "6072\t|\tEumetazoa\t|\t\t|\tscientific name",
  "33208\t|\tMetazoa\t|\t\t|\tscientific name",
  "33154\t|\tOpisthokonta\t|\t\t|\tscientific name",
  "2759\t|\tEukaryota\t|\t\t|\tscientific name",
  "131567\t|\tcellular organisms\t|\t\t|\tscientific name",
  "1425170\t|\tHomo heidelbergensis\t|\t\t|\tscientific name"
)
tmpFile<-tempfile()
writeLines(namesText,tmpFile)
taxaNames<-read.names.sql(tmpFile,sqlFile)
nodesText<-c(
 "1\t|\t1\t|\tno rank\t|\t\t|\t8\t|\t0\t|\t1\t|\t0\t|\t0\t|\t0\t|\t0\t|\t0\t|\t\t|",
  "2\t|\t131567\t|\tsuperkingdom\t|\t\t|\t0\t|\t0\t|\t11\t|\t0\t|\t0\t|\t0\t|\t0\t|\t0\t|\t\t|",
  "6\t|\t335928\t|\tgenus\t|\t\t|\t0\t|\t1\t|\t11\t|\t1\t|\t0\t|\t1\t|\t0\t|\t0\t|\t\t|",
  "7\t|\t6\t|\tspecies\t|\tAC\t|\t0\t|\t1\t|\t11\t|\t1\t|\t0\t|\t1\t|\t1\t|\t0\t|\t\t|",
  "9\t|\t32199\t|\tspecies\t|\tBA\t|\t0\t|\t1\t|\t11\t|\t1\t|\t0\t|\t1\t|\t1\t|\t0\t|\t\t|",
  "9606\t|\t9605\t|\tspecies", "9605\t|\t207598\t|\tgenus", "207598\t|\t9604\t|\tsubfamily",
  "9604\t|\t314295\t|\tfamily", "314295\t|\t9526\t|\tsuperfamily",
  "9526\t|\t314293\t|\tparvorder", "314293\t|\t376913\t|\tinfraorder",
  "376913\t|\t9443\t|\tsuborder", "9443\t|\t314146\t|\torder",
  "314146\t|\t1437010\t|\tsuperorder", "1437010\t|\t9347\t|\tno rank",
  "9347\t|\t32525\t|\tno rank", "32525\t|\t40674\t|\tno rank",
  "40674\t|\t32524\t|\tclass", "32524\t|\t32523\t|\tno rank", "32523\t|\t1338369\t|\tno rank",
  "1338369\t|\t8287\t|\tno rank", "8287\t|\t117571\t|\tno rank",
  "117571\t|\t117570\t|\tno rank", "117570\t|\t7776\t|\tno rank",
  "7776\t|\t7742\t|\tno rank", "7742\t|\t89593\t|\tno rank", "89593\t|\t7711\t|\tsubphylum",
  "7711\t|\t33511\t|\tphylum", "33511\t|\t33213\t|\tno rank", "33213\t|\t6072\t|\tno rank",
  "6072\t|\t33208\t|\tno rank", "33208\t|\t33154\t|\tkingdom",
  "33154\t|\t2759\t|\tno rank", "2759\t|\t131567\t|\tsuperkingdom",
  "131567\t|\t1\t|\tno rank", '1425170\t|\t9605\t|\tspecies'
)
writeLines(nodesText,tmpFile)
taxaNodes<-read.nodes.sql(tmpFile,sqlFile)
getDescendants(c(9604),sqlFile)

Find a given taxa by name

Description

Find a taxa by string in the NCBI taxonomy. Note that NCBI species are stored as Genus species e.g. "Bos taurus". Ambiguous taxa names will return a comma concatenated string e.g. "123,234" and generate a warning.

Usage

getId(taxa, sqlFile = "nameNode.sqlite", onlyScientific = TRUE)
getId(taxa, sqlFile = "nameNode.sqlite", onlyScientific = TRUE)

Arguments

`taxa`	a vector of taxonomic names
`sqlFile`	a string giving the path to a SQLite file containing a names tables
`onlyScientific`	If TRUE then only match to scientific names. If FALSE use all names in database for matching (potentially increasing ambiguous matches).

Value

a vector of character strings giving taxa IDs (potentially comma concatenated for any taxa with ambiguous names)

Examples

namesText<-c(
  "1\t|\tall\t|\t\t|\tsynonym\t|",
  "1\t|\troot\t|\t\t|\tscientific name\t|",
  "3\t|\tMulti\t|\tBacteria <prokaryotes>\t|\tscientific name\t|",
  "4\t|\tMulti\t|\tBacteria <prokaryotes>\t|\tscientific name\t|",
  "2\t|\tBacteria\t|\tBacteria <prokaryotes>\t|\tscientific name\t|",
  "2\t|\tMonera\t|\tMonera <Bacteria>\t|\tin-part\t|",
  "2\t|\tProcaryotae\t|\tProcaryotae <Bacteria>\t|\tin-part\t|"
)
tmpFile<-tempfile()
writeLines(namesText,tmpFile)
sqlFile<-tempfile()
read.names.sql(tmpFile,sqlFile)
getId('Bacteria',sqlFile)
getId('Not a real name',sqlFile)
getId('Multi',sqlFile)
namesText<-c(
  "1\t|\tall\t|\t\t|\tsynonym\t|",
  "1\t|\troot\t|\t\t|\tscientific name\t|",
  "3\t|\tMulti\t|\tBacteria <prokaryotes>\t|\tscientific name\t|",
  "4\t|\tMulti\t|\tBacteria <prokaryotes>\t|\tscientific name\t|",
  "2\t|\tBacteria\t|\tBacteria <prokaryotes>\t|\tscientific name\t|",
  "2\t|\tMonera\t|\tMonera <Bacteria>\t|\tin-part\t|",
  "2\t|\tProcaryotae\t|\tProcaryotae <Bacteria>\t|\tin-part\t|"
)
tmpFile<-tempfile()
writeLines(namesText,tmpFile)
sqlFile<-tempfile()
read.names.sql(tmpFile,sqlFile)
getId('Bacteria',sqlFile)
getId('Not a real name',sqlFile)
getId('Multi',sqlFile)

Find a given taxa by name

Description

Usage

getId2(taxa, taxaNames)
getId2(taxa, taxaNames)

Arguments

`taxa`	a vector of taxonomic names
`taxaNames`	a names data.table from `read.names`

Value

a vector of character strings giving taxa IDs (potentially comma concatenated for any taxa with ambiguous names)

Examples

namesText<-c(
  "1\t|\tall\t|\t\t|\tsynonym\t|",
  "1\t|\troot\t|\t\t|\tscientific name\t|",
  "3\t|\tMulti\t|\tBacteria <prokaryotes>\t|\tscientific name\t|",
  "4\t|\tMulti\t|\tBacteria <prokaryotes>\t|\tscientific name\t|",
  "2\t|\tBacteria\t|\tBacteria <prokaryotes>\t|\tscientific name\t|",
  "2\t|\tMonera\t|\tMonera <Bacteria>\t|\tin-part\t|",
  "2\t|\tProcaryotae\t|\tProcaryotae <Bacteria>\t|\tin-part\t|"
)
tmpFile<-tempfile()
writeLines(namesText,tmpFile)
names<-read.names(tmpFile)
getId2('Bacteria',names)
getId2('Not a real name',names)
getId2('Multi',names)
namesText<-c(
  "1\t|\tall\t|\t\t|\tsynonym\t|",
  "1\t|\troot\t|\t\t|\tscientific name\t|",
  "3\t|\tMulti\t|\tBacteria <prokaryotes>\t|\tscientific name\t|",
  "4\t|\tMulti\t|\tBacteria <prokaryotes>\t|\tscientific name\t|",
  "2\t|\tBacteria\t|\tBacteria <prokaryotes>\t|\tscientific name\t|",
  "2\t|\tMonera\t|\tMonera <Bacteria>\t|\tin-part\t|",
  "2\t|\tProcaryotae\t|\tProcaryotae <Bacteria>\t|\tin-part\t|"
)
tmpFile<-tempfile()
writeLines(namesText,tmpFile)
names<-read.names(tmpFile)
getId2('Bacteria',names)
getId2('Not a real name',names)
getId2('Multi',names)

Download names and nodes files from NCBI

Description

Download a taxdump.tar.gz file from NCBI servers and extract the names.dmp and nodes.dmp files from it. These can then be used to create a SQLite database with read.names.sql and read.nodes.sql. Note that if the files already exist in the target directory then this function will not redownload them. Delete the files if a fresh download is desired.

Usage

getNamesAndNodes(
  outDir = ".",
  url = sprintf("%s://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz", protocol),
  fileNames = c("names.dmp", "nodes.dmp"),
  protocol = "ftp",
  resume = TRUE
)
getNamesAndNodes(
  outDir = ".",
  url = sprintf("%s://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz", protocol),
  fileNames = c("names.dmp", "nodes.dmp"),
  protocol = "ftp",
  resume = TRUE
)

Arguments

`outDir`	the directory to put names.dmp and nodes.dmp in
`url`	the url where taxdump.tar.gz is located
`fileNames`	the filenames desired from the tar.gz file
`protocol`	the protocol to be used for downloading. Probably either `'http'` or `'ftp'`. Overridden if `url` is provided directly
`resume`	if TRUE attempt to resume downloading an interrupted file without starting over from the beginning

Value

a vector of file path strings of the locations of the output files

References

https://ftp.ncbi.nih.gov/pub/taxonomy/, https://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/

Examples

## Not run: 
  getNamesAndNodes()

## End(Not run)
## Not run: 
  getNamesAndNodes()

## End(Not run)

Get all taxonomy for a taxa

Description

Take NCBI taxa IDs and get all taxonomic ranks from name and node SQLite database. Ranks that occur more than once are made unique with a postfix through make.unique

Usage

getRawTaxonomy(ids, sqlFile = "nameNode.sqlite")
getRawTaxonomy(ids, sqlFile = "nameNode.sqlite")

Arguments

`ids`	a vector of ids to find taxonomy for
`sqlFile`	a string giving the path to a SQLite file containing names and nodes tables

Value

a list of vectors with each element containing a vector of taxonomic strings with names corresponding to the taxonomic rank

Examples

sqlFile<-tempfile()
namesText<-c(
  "1\t|\tall\t|\t\t|\tsynonym\t|",
  "1\t|\troot\t|\t\t|\tscientific name\t|",
  "2\t|\tBacteria\t|\tBacteria <prokaryotes>\t|\tscientific name\t|",
  "2\t|\tMonera\t|\tMonera <Bacteria>\t|\tin-part\t|",
  "2\t|\tProcaryotae\t|\tProcaryotae <Bacteria>\t|\tin-part\t|",
  "9606\t|\tHomo sapiens\t|\t\t|\tscientific name",
  "9605\t|\tHomo\t|\t\t|\tscientific name",
  "207598\t|\tHomininae\t|\t\t|\tscientific name",
  "9604\t|\tHominidae\t|\t\t|\tscientific name",
  "314295\t|\tHominoidea\t|\t\t|\tscientific name",
  "9526\t|\tCatarrhini\t|\t\t|\tscientific name",
  "314293\t|\tSimiiformes\t|\t\t|\tscientific name",
  "376913\t|\tHaplorrhini\t|\t\t|\tscientific name",
  "9443\t|\tPrimates\t|\t\t|\tscientific name",
  "314146\t|\tEuarchontoglires\t|\t\t|\tscientific name",
  "1437010\t|\tBoreoeutheria\t|\t\t|\tscientific name",
  "9347\t|\tEutheria\t|\t\t|\tscientific name",
  "32525\t|\tTheria\t|\t\t|\tscientific name",
  "40674\t|\tMammalia\t|\t\t|\tscientific name",
  "32524\t|\tAmniota\t|\t\t|\tscientific name",
  "32523\t|\tTetrapoda\t|\t\t|\tscientific name",
  "1338369\t|\tDipnotetrapodomorpha\t|\t\t|\tscientific name",
  "8287\t|\tSarcopterygii\t|\t\t|\tscientific name",
  "117571\t|\tEuteleostomi\t|\t\t|\tscientific name",
  "117570\t|\tTeleostomi\t|\t\t|\tscientific name",
  "7776\t|\tGnathostomata\t|\t\t|\tscientific name",
  "7742\t|\tVertebrata\t|\t\t|\tscientific name",
  "89593\t|\tCraniata\t|\t\t|\tscientific name",
  "7711\t|\tChordata\t|\t\t|\tscientific name",
  "33511\t|\tDeuterostomia\t|\t\t|\tscientific name",
  "33213\t|\tBilateria\t|\t\t|\tscientific name",
  "6072\t|\tEumetazoa\t|\t\t|\tscientific name",
  "33208\t|\tMetazoa\t|\t\t|\tscientific name",
  "33154\t|\tOpisthokonta\t|\t\t|\tscientific name",
  "2759\t|\tEukaryota\t|\t\t|\tscientific name",
  "131567\t|\tcellular organisms\t|\t\t|\tscientific name"
)
tmpFile<-tempfile()
writeLines(namesText,tmpFile)
taxaNames<-read.names.sql(tmpFile,sqlFile)
nodesText<-c(
 "1\t|\t1\t|\tno rank\t|\t\t|\t8\t|\t0\t|\t1\t|\t0\t|\t0\t|\t0\t|\t0\t|\t0\t|\t\t|",
  "2\t|\t131567\t|\tsuperkingdom\t|\t\t|\t0\t|\t0\t|\t11\t|\t0\t|\t0\t|\t0\t|\t0\t|\t0\t|\t\t|",
  "6\t|\t335928\t|\tgenus\t|\t\t|\t0\t|\t1\t|\t11\t|\t1\t|\t0\t|\t1\t|\t0\t|\t0\t|\t\t|",
  "7\t|\t6\t|\tspecies\t|\tAC\t|\t0\t|\t1\t|\t11\t|\t1\t|\t0\t|\t1\t|\t1\t|\t0\t|\t\t|",
  "9\t|\t32199\t|\tspecies\t|\tBA\t|\t0\t|\t1\t|\t11\t|\t1\t|\t0\t|\t1\t|\t1\t|\t0\t|\t\t|",
  "9606\t|\t9605\t|\tspecies", "9605\t|\t207598\t|\tgenus", "207598\t|\t9604\t|\tsubfamily",
  "9604\t|\t314295\t|\tfamily", "314295\t|\t9526\t|\tsuperfamily",
  "9526\t|\t314293\t|\tparvorder", "314293\t|\t376913\t|\tinfraorder",
  "376913\t|\t9443\t|\tsuborder", "9443\t|\t314146\t|\torder",
  "314146\t|\t1437010\t|\tsuperorder", "1437010\t|\t9347\t|\tno rank",
  "9347\t|\t32525\t|\tno rank", "32525\t|\t40674\t|\tno rank",
  "40674\t|\t32524\t|\tclass", "32524\t|\t32523\t|\tno rank", "32523\t|\t1338369\t|\tno rank",
  "1338369\t|\t8287\t|\tno rank", "8287\t|\t117571\t|\tno rank",
  "117571\t|\t117570\t|\tno rank", "117570\t|\t7776\t|\tno rank",
  "7776\t|\t7742\t|\tno rank", "7742\t|\t89593\t|\tno rank", "89593\t|\t7711\t|\tsubphylum",
  "7711\t|\t33511\t|\tphylum", "33511\t|\t33213\t|\tno rank", "33213\t|\t6072\t|\tno rank",
  "6072\t|\t33208\t|\tno rank", "33208\t|\t33154\t|\tkingdom",
  "33154\t|\t2759\t|\tno rank", "2759\t|\t131567\t|\tsuperkingdom",
  "131567\t|\t1\t|\tno rank"
)
writeLines(nodesText,tmpFile)
taxaNodes<-read.nodes.sql(tmpFile,sqlFile)
getRawTaxonomy(c(9606,9605),sqlFile)
sqlFile<-tempfile()
namesText<-c(
  "1\t|\tall\t|\t\t|\tsynonym\t|",
  "1\t|\troot\t|\t\t|\tscientific name\t|",
  "2\t|\tBacteria\t|\tBacteria <prokaryotes>\t|\tscientific name\t|",
  "2\t|\tMonera\t|\tMonera <Bacteria>\t|\tin-part\t|",
  "2\t|\tProcaryotae\t|\tProcaryotae <Bacteria>\t|\tin-part\t|",
  "9606\t|\tHomo sapiens\t|\t\t|\tscientific name",
  "9605\t|\tHomo\t|\t\t|\tscientific name",
  "207598\t|\tHomininae\t|\t\t|\tscientific name",
  "9604\t|\tHominidae\t|\t\t|\tscientific name",
  "314295\t|\tHominoidea\t|\t\t|\tscientific name",
  "9526\t|\tCatarrhini\t|\t\t|\tscientific name",
  "314293\t|\tSimiiformes\t|\t\t|\tscientific name",
  "376913\t|\tHaplorrhini\t|\t\t|\tscientific name",
  "9443\t|\tPrimates\t|\t\t|\tscientific name",
  "314146\t|\tEuarchontoglires\t|\t\t|\tscientific name",
  "1437010\t|\tBoreoeutheria\t|\t\t|\tscientific name",
  "9347\t|\tEutheria\t|\t\t|\tscientific name",
  "32525\t|\tTheria\t|\t\t|\tscientific name",
  "40674\t|\tMammalia\t|\t\t|\tscientific name",
  "32524\t|\tAmniota\t|\t\t|\tscientific name",
  "32523\t|\tTetrapoda\t|\t\t|\tscientific name",
  "1338369\t|\tDipnotetrapodomorpha\t|\t\t|\tscientific name",
  "8287\t|\tSarcopterygii\t|\t\t|\tscientific name",
  "117571\t|\tEuteleostomi\t|\t\t|\tscientific name",
  "117570\t|\tTeleostomi\t|\t\t|\tscientific name",
  "7776\t|\tGnathostomata\t|\t\t|\tscientific name",
  "7742\t|\tVertebrata\t|\t\t|\tscientific name",
  "89593\t|\tCraniata\t|\t\t|\tscientific name",
  "7711\t|\tChordata\t|\t\t|\tscientific name",
  "33511\t|\tDeuterostomia\t|\t\t|\tscientific name",
  "33213\t|\tBilateria\t|\t\t|\tscientific name",
  "6072\t|\tEumetazoa\t|\t\t|\tscientific name",
  "33208\t|\tMetazoa\t|\t\t|\tscientific name",
  "33154\t|\tOpisthokonta\t|\t\t|\tscientific name",
  "2759\t|\tEukaryota\t|\t\t|\tscientific name",
  "131567\t|\tcellular organisms\t|\t\t|\tscientific name"
)
tmpFile<-tempfile()
writeLines(namesText,tmpFile)
taxaNames<-read.names.sql(tmpFile,sqlFile)
nodesText<-c(
 "1\t|\t1\t|\tno rank\t|\t\t|\t8\t|\t0\t|\t1\t|\t0\t|\t0\t|\t0\t|\t0\t|\t0\t|\t\t|",
  "2\t|\t131567\t|\tsuperkingdom\t|\t\t|\t0\t|\t0\t|\t11\t|\t0\t|\t0\t|\t0\t|\t0\t|\t0\t|\t\t|",
  "6\t|\t335928\t|\tgenus\t|\t\t|\t0\t|\t1\t|\t11\t|\t1\t|\t0\t|\t1\t|\t0\t|\t0\t|\t\t|",
  "7\t|\t6\t|\tspecies\t|\tAC\t|\t0\t|\t1\t|\t11\t|\t1\t|\t0\t|\t1\t|\t1\t|\t0\t|\t\t|",
  "9\t|\t32199\t|\tspecies\t|\tBA\t|\t0\t|\t1\t|\t11\t|\t1\t|\t0\t|\t1\t|\t1\t|\t0\t|\t\t|",
  "9606\t|\t9605\t|\tspecies", "9605\t|\t207598\t|\tgenus", "207598\t|\t9604\t|\tsubfamily",
  "9604\t|\t314295\t|\tfamily", "314295\t|\t9526\t|\tsuperfamily",
  "9526\t|\t314293\t|\tparvorder", "314293\t|\t376913\t|\tinfraorder",
  "376913\t|\t9443\t|\tsuborder", "9443\t|\t314146\t|\torder",
  "314146\t|\t1437010\t|\tsuperorder", "1437010\t|\t9347\t|\tno rank",
  "9347\t|\t32525\t|\tno rank", "32525\t|\t40674\t|\tno rank",
  "40674\t|\t32524\t|\tclass", "32524\t|\t32523\t|\tno rank", "32523\t|\t1338369\t|\tno rank",
  "1338369\t|\t8287\t|\tno rank", "8287\t|\t117571\t|\tno rank",
  "117571\t|\t117570\t|\tno rank", "117570\t|\t7776\t|\tno rank",
  "7776\t|\t7742\t|\tno rank", "7742\t|\t89593\t|\tno rank", "89593\t|\t7711\t|\tsubphylum",
  "7711\t|\t33511\t|\tphylum", "33511\t|\t33213\t|\tno rank", "33213\t|\t6072\t|\tno rank",
  "6072\t|\t33208\t|\tno rank", "33208\t|\t33154\t|\tkingdom",
  "33154\t|\t2759\t|\tno rank", "2759\t|\t131567\t|\tsuperkingdom",
  "131567\t|\t1\t|\tno rank"
)
writeLines(nodesText,tmpFile)
taxaNodes<-read.nodes.sql(tmpFile,sqlFile)
getRawTaxonomy(c(9606,9605),sqlFile)

Get taxonomic ranks for a taxa

Description

Take NCBI taxa IDs and get the corresponding taxa ranks from a name and node SQLite database

Usage

getTaxonomy(
  ids,
  sqlFile = "nameNode.sqlite",
  ...,
  desiredTaxa = c("superkingdom", "phylum", "class", "order", "family", "genus",
    "species")
)
getTaxonomy(
  ids,
  sqlFile = "nameNode.sqlite",
  ...,
  desiredTaxa = c("superkingdom", "phylum", "class", "order", "family", "genus",
    "species")
)

Arguments

`ids`	a vector of ids to find taxonomy for
`sqlFile`	a string giving the path to a SQLite file containing names and nodes tables
`...`	legacy additional arguments to original data.table based getTaxonomy function. Used only for support for deprecated function, do not use in new code.
`desiredTaxa`	a vector of strings giving the desired taxa levels

Value

a matrix of taxonomic strings with a row for each id and a column for each desiredTaxa rank

Examples

sqlFile<-tempfile()
namesText<-c(
  "1\t|\tall\t|\t\t|\tsynonym\t|",
  "1\t|\troot\t|\t\t|\tscientific name\t|",
  "2\t|\tBacteria\t|\tBacteria <prokaryotes>\t|\tscientific name\t|",
  "2\t|\tMonera\t|\tMonera <Bacteria>\t|\tin-part\t|",
  "2\t|\tProcaryotae\t|\tProcaryotae <Bacteria>\t|\tin-part\t|",
  "9606\t|\tHomo sapiens\t|\t\t|\tscientific name",
  "9605\t|\tHomo\t|\t\t|\tscientific name",
  "207598\t|\tHomininae\t|\t\t|\tscientific name",
  "9604\t|\tHominidae\t|\t\t|\tscientific name",
  "314295\t|\tHominoidea\t|\t\t|\tscientific name",
  "9526\t|\tCatarrhini\t|\t\t|\tscientific name",
  "314293\t|\tSimiiformes\t|\t\t|\tscientific name",
  "376913\t|\tHaplorrhini\t|\t\t|\tscientific name",
  "9443\t|\tPrimates\t|\t\t|\tscientific name",
  "314146\t|\tEuarchontoglires\t|\t\t|\tscientific name",
  "1437010\t|\tBoreoeutheria\t|\t\t|\tscientific name",
  "9347\t|\tEutheria\t|\t\t|\tscientific name",
  "32525\t|\tTheria\t|\t\t|\tscientific name",
  "40674\t|\tMammalia\t|\t\t|\tscientific name",
  "32524\t|\tAmniota\t|\t\t|\tscientific name",
  "32523\t|\tTetrapoda\t|\t\t|\tscientific name",
  "1338369\t|\tDipnotetrapodomorpha\t|\t\t|\tscientific name",
  "8287\t|\tSarcopterygii\t|\t\t|\tscientific name",
  "117571\t|\tEuteleostomi\t|\t\t|\tscientific name",
  "117570\t|\tTeleostomi\t|\t\t|\tscientific name",
  "7776\t|\tGnathostomata\t|\t\t|\tscientific name",
  "7742\t|\tVertebrata\t|\t\t|\tscientific name",
  "89593\t|\tCraniata\t|\t\t|\tscientific name",
  "7711\t|\tChordata\t|\t\t|\tscientific name",
  "33511\t|\tDeuterostomia\t|\t\t|\tscientific name",
  "33213\t|\tBilateria\t|\t\t|\tscientific name",
  "6072\t|\tEumetazoa\t|\t\t|\tscientific name",
  "33208\t|\tMetazoa\t|\t\t|\tscientific name",
  "33154\t|\tOpisthokonta\t|\t\t|\tscientific name",
  "2759\t|\tEukaryota\t|\t\t|\tscientific name",
  "131567\t|\tcellular organisms\t|\t\t|\tscientific name"
)
tmpFile<-tempfile()
writeLines(namesText,tmpFile)
taxaNames<-read.names.sql(tmpFile,sqlFile)
nodesText<-c(
 "1\t|\t1\t|\tno rank\t|\t\t|\t8\t|\t0\t|\t1\t|\t0\t|\t0\t|\t0\t|\t0\t|\t0\t|\t\t|",
  "2\t|\t131567\t|\tsuperkingdom\t|\t\t|\t0\t|\t0\t|\t11\t|\t0\t|\t0\t|\t0\t|\t0\t|\t0\t|\t\t|",
  "6\t|\t335928\t|\tgenus\t|\t\t|\t0\t|\t1\t|\t11\t|\t1\t|\t0\t|\t1\t|\t0\t|\t0\t|\t\t|",
  "7\t|\t6\t|\tspecies\t|\tAC\t|\t0\t|\t1\t|\t11\t|\t1\t|\t0\t|\t1\t|\t1\t|\t0\t|\t\t|",
  "9\t|\t32199\t|\tspecies\t|\tBA\t|\t0\t|\t1\t|\t11\t|\t1\t|\t0\t|\t1\t|\t1\t|\t0\t|\t\t|",
  "9606\t|\t9605\t|\tspecies", "9605\t|\t207598\t|\tgenus", "207598\t|\t9604\t|\tsubfamily",
  "9604\t|\t314295\t|\tfamily", "314295\t|\t9526\t|\tsuperfamily",
  "9526\t|\t314293\t|\tparvorder", "314293\t|\t376913\t|\tinfraorder",
  "376913\t|\t9443\t|\tsuborder", "9443\t|\t314146\t|\torder",
  "314146\t|\t1437010\t|\tsuperorder", "1437010\t|\t9347\t|\tno rank",
  "9347\t|\t32525\t|\tno rank", "32525\t|\t40674\t|\tno rank",
  "40674\t|\t32524\t|\tclass", "32524\t|\t32523\t|\tno rank", "32523\t|\t1338369\t|\tno rank",
  "1338369\t|\t8287\t|\tno rank", "8287\t|\t117571\t|\tno rank",
  "117571\t|\t117570\t|\tno rank", "117570\t|\t7776\t|\tno rank",
  "7776\t|\t7742\t|\tno rank", "7742\t|\t89593\t|\tno rank", "89593\t|\t7711\t|\tsubphylum",
  "7711\t|\t33511\t|\tphylum", "33511\t|\t33213\t|\tno rank", "33213\t|\t6072\t|\tno rank",
  "6072\t|\t33208\t|\tno rank", "33208\t|\t33154\t|\tkingdom",
  "33154\t|\t2759\t|\tno rank", "2759\t|\t131567\t|\tsuperkingdom",
  "131567\t|\t1\t|\tno rank"
)
writeLines(nodesText,tmpFile)
taxaNodes<-read.nodes.sql(tmpFile,sqlFile)
getTaxonomy(c(9606,9605),sqlFile)
sqlFile<-tempfile()
namesText<-c(
  "1\t|\tall\t|\t\t|\tsynonym\t|",
  "1\t|\troot\t|\t\t|\tscientific name\t|",
  "2\t|\tBacteria\t|\tBacteria <prokaryotes>\t|\tscientific name\t|",
  "2\t|\tMonera\t|\tMonera <Bacteria>\t|\tin-part\t|",
  "2\t|\tProcaryotae\t|\tProcaryotae <Bacteria>\t|\tin-part\t|",
  "9606\t|\tHomo sapiens\t|\t\t|\tscientific name",
  "9605\t|\tHomo\t|\t\t|\tscientific name",
  "207598\t|\tHomininae\t|\t\t|\tscientific name",
  "9604\t|\tHominidae\t|\t\t|\tscientific name",
  "314295\t|\tHominoidea\t|\t\t|\tscientific name",
  "9526\t|\tCatarrhini\t|\t\t|\tscientific name",
  "314293\t|\tSimiiformes\t|\t\t|\tscientific name",
  "376913\t|\tHaplorrhini\t|\t\t|\tscientific name",
  "9443\t|\tPrimates\t|\t\t|\tscientific name",
  "314146\t|\tEuarchontoglires\t|\t\t|\tscientific name",
  "1437010\t|\tBoreoeutheria\t|\t\t|\tscientific name",
  "9347\t|\tEutheria\t|\t\t|\tscientific name",
  "32525\t|\tTheria\t|\t\t|\tscientific name",
  "40674\t|\tMammalia\t|\t\t|\tscientific name",
  "32524\t|\tAmniota\t|\t\t|\tscientific name",
  "32523\t|\tTetrapoda\t|\t\t|\tscientific name",
  "1338369\t|\tDipnotetrapodomorpha\t|\t\t|\tscientific name",
  "8287\t|\tSarcopterygii\t|\t\t|\tscientific name",
  "117571\t|\tEuteleostomi\t|\t\t|\tscientific name",
  "117570\t|\tTeleostomi\t|\t\t|\tscientific name",
  "7776\t|\tGnathostomata\t|\t\t|\tscientific name",
  "7742\t|\tVertebrata\t|\t\t|\tscientific name",
  "89593\t|\tCraniata\t|\t\t|\tscientific name",
  "7711\t|\tChordata\t|\t\t|\tscientific name",
  "33511\t|\tDeuterostomia\t|\t\t|\tscientific name",
  "33213\t|\tBilateria\t|\t\t|\tscientific name",
  "6072\t|\tEumetazoa\t|\t\t|\tscientific name",
  "33208\t|\tMetazoa\t|\t\t|\tscientific name",
  "33154\t|\tOpisthokonta\t|\t\t|\tscientific name",
  "2759\t|\tEukaryota\t|\t\t|\tscientific name",
  "131567\t|\tcellular organisms\t|\t\t|\tscientific name"
)
tmpFile<-tempfile()
writeLines(namesText,tmpFile)
taxaNames<-read.names.sql(tmpFile,sqlFile)
nodesText<-c(
 "1\t|\t1\t|\tno rank\t|\t\t|\t8\t|\t0\t|\t1\t|\t0\t|\t0\t|\t0\t|\t0\t|\t0\t|\t\t|",
  "2\t|\t131567\t|\tsuperkingdom\t|\t\t|\t0\t|\t0\t|\t11\t|\t0\t|\t0\t|\t0\t|\t0\t|\t0\t|\t\t|",
  "6\t|\t335928\t|\tgenus\t|\t\t|\t0\t|\t1\t|\t11\t|\t1\t|\t0\t|\t1\t|\t0\t|\t0\t|\t\t|",
  "7\t|\t6\t|\tspecies\t|\tAC\t|\t0\t|\t1\t|\t11\t|\t1\t|\t0\t|\t1\t|\t1\t|\t0\t|\t\t|",
  "9\t|\t32199\t|\tspecies\t|\tBA\t|\t0\t|\t1\t|\t11\t|\t1\t|\t0\t|\t1\t|\t1\t|\t0\t|\t\t|",
  "9606\t|\t9605\t|\tspecies", "9605\t|\t207598\t|\tgenus", "207598\t|\t9604\t|\tsubfamily",
  "9604\t|\t314295\t|\tfamily", "314295\t|\t9526\t|\tsuperfamily",
  "9526\t|\t314293\t|\tparvorder", "314293\t|\t376913\t|\tinfraorder",
  "376913\t|\t9443\t|\tsuborder", "9443\t|\t314146\t|\torder",
  "314146\t|\t1437010\t|\tsuperorder", "1437010\t|\t9347\t|\tno rank",
  "9347\t|\t32525\t|\tno rank", "32525\t|\t40674\t|\tno rank",
  "40674\t|\t32524\t|\tclass", "32524\t|\t32523\t|\tno rank", "32523\t|\t1338369\t|\tno rank",
  "1338369\t|\t8287\t|\tno rank", "8287\t|\t117571\t|\tno rank",
  "117571\t|\t117570\t|\tno rank", "117570\t|\t7776\t|\tno rank",
  "7776\t|\t7742\t|\tno rank", "7742\t|\t89593\t|\tno rank", "89593\t|\t7711\t|\tsubphylum",
  "7711\t|\t33511\t|\tphylum", "33511\t|\t33213\t|\tno rank", "33213\t|\t6072\t|\tno rank",
  "6072\t|\t33208\t|\tno rank", "33208\t|\t33154\t|\tkingdom",
  "33154\t|\t2759\t|\tno rank", "2759\t|\t131567\t|\tsuperkingdom",
  "131567\t|\t1\t|\tno rank"
)
writeLines(nodesText,tmpFile)
taxaNodes<-read.nodes.sql(tmpFile,sqlFile)
getTaxonomy(c(9606,9605),sqlFile)

Get taxonomic ranks for a taxa

Description

Take NCBI taxa IDs and get the corresponding taxa ranks from name and node data.tables. NOTE: This function is now deprecated for getTaxonomy (using SQLite rather than data.table).

Usage

getTaxonomy2(
  ids,
  taxaNodes,
  taxaNames,
  desiredTaxa = c("superkingdom", "phylum", "class", "order", "family", "genus",
    "species"),
  mc.cores = 1,
  debug = FALSE
)
getTaxonomy2(
  ids,
  taxaNodes,
  taxaNames,
  desiredTaxa = c("superkingdom", "phylum", "class", "order", "family", "genus",
    "species"),
  mc.cores = 1,
  debug = FALSE
)

Arguments

`ids`	a vector of ids to find taxonomy for
`taxaNodes`	a nodes data.table from `read.nodes`
`taxaNames`	a names data.table from `read.names`
`desiredTaxa`	a vector of strings giving the desired taxa levels
`mc.cores`	DEPRECATED the number of cores to use when processing. Note this option is now deprecated and has no effect. Please switch to `getTaxonomy` (see taxonomizrSwitch) for much faster processing without requiring multiple cores.
`debug`	if TRUE output node and name vectors with dput for each id (probably useful only for development)

Value

a matrix of taxonomic strings with a row for each id and a column for each desiredTaxa rank

Examples

namesText<-c(
  "1\t|\tall\t|\t\t|\tsynonym\t|",
  "1\t|\troot\t|\t\t|\tscientific name\t|",
  "2\t|\tBacteria\t|\tBacteria <prokaryotes>\t|\tscientific name\t|",
  "2\t|\tMonera\t|\tMonera <Bacteria>\t|\tin-part\t|",
  "2\t|\tProcaryotae\t|\tProcaryotae <Bacteria>\t|\tin-part\t|",
  "9606\t|\tHomo sapiens\t|\t\t|\tscientific name",
  "9605\t|\tHomo\t|\t\t|\tscientific name",
  "207598\t|\tHomininae\t|\t\t|\tscientific name",
  "9604\t|\tHominidae\t|\t\t|\tscientific name",
  "314295\t|\tHominoidea\t|\t\t|\tscientific name",
  "9526\t|\tCatarrhini\t|\t\t|\tscientific name",
  "314293\t|\tSimiiformes\t|\t\t|\tscientific name",
  "376913\t|\tHaplorrhini\t|\t\t|\tscientific name",
  "9443\t|\tPrimates\t|\t\t|\tscientific name",
  "314146\t|\tEuarchontoglires\t|\t\t|\tscientific name",
  "1437010\t|\tBoreoeutheria\t|\t\t|\tscientific name",
  "9347\t|\tEutheria\t|\t\t|\tscientific name",
  "32525\t|\tTheria\t|\t\t|\tscientific name",
  "40674\t|\tMammalia\t|\t\t|\tscientific name",
  "32524\t|\tAmniota\t|\t\t|\tscientific name",
  "32523\t|\tTetrapoda\t|\t\t|\tscientific name",
  "1338369\t|\tDipnotetrapodomorpha\t|\t\t|\tscientific name",
  "8287\t|\tSarcopterygii\t|\t\t|\tscientific name",
  "117571\t|\tEuteleostomi\t|\t\t|\tscientific name",
  "117570\t|\tTeleostomi\t|\t\t|\tscientific name",
  "7776\t|\tGnathostomata\t|\t\t|\tscientific name",
  "7742\t|\tVertebrata\t|\t\t|\tscientific name",
  "89593\t|\tCraniata\t|\t\t|\tscientific name",
  "7711\t|\tChordata\t|\t\t|\tscientific name",
  "33511\t|\tDeuterostomia\t|\t\t|\tscientific name",
  "33213\t|\tBilateria\t|\t\t|\tscientific name",
  "6072\t|\tEumetazoa\t|\t\t|\tscientific name",
  "33208\t|\tMetazoa\t|\t\t|\tscientific name",
  "33154\t|\tOpisthokonta\t|\t\t|\tscientific name",
  "2759\t|\tEukaryota\t|\t\t|\tscientific name",
  "131567\t|\tcellular organisms\t|\t\t|\tscientific name"
)
tmpFile<-tempfile()
writeLines(namesText,tmpFile)
taxaNames<-read.names(tmpFile)
nodesText<-c(
 "1\t|\t1\t|\tno rank\t|\t\t|\t8\t|\t0\t|\t1\t|\t0\t|\t0\t|\t0\t|\t0\t|\t0\t|\t\t|",
  "2\t|\t131567\t|\tsuperkingdom\t|\t\t|\t0\t|\t0\t|\t11\t|\t0\t|\t0\t|\t0\t|\t0\t|\t0\t|\t\t|",
  "6\t|\t335928\t|\tgenus\t|\t\t|\t0\t|\t1\t|\t11\t|\t1\t|\t0\t|\t1\t|\t0\t|\t0\t|\t\t|",
  "7\t|\t6\t|\tspecies\t|\tAC\t|\t0\t|\t1\t|\t11\t|\t1\t|\t0\t|\t1\t|\t1\t|\t0\t|\t\t|",
  "9\t|\t32199\t|\tspecies\t|\tBA\t|\t0\t|\t1\t|\t11\t|\t1\t|\t0\t|\t1\t|\t1\t|\t0\t|\t\t|",
  "9606\t|\t9605\t|\tspecies", "9605\t|\t207598\t|\tgenus", "207598\t|\t9604\t|\tsubfamily",
  "9604\t|\t314295\t|\tfamily", "314295\t|\t9526\t|\tsuperfamily",
  "9526\t|\t314293\t|\tparvorder", "314293\t|\t376913\t|\tinfraorder",
  "376913\t|\t9443\t|\tsuborder", "9443\t|\t314146\t|\torder",
  "314146\t|\t1437010\t|\tsuperorder", "1437010\t|\t9347\t|\tno rank",
  "9347\t|\t32525\t|\tno rank", "32525\t|\t40674\t|\tno rank",
  "40674\t|\t32524\t|\tclass", "32524\t|\t32523\t|\tno rank", "32523\t|\t1338369\t|\tno rank",
  "1338369\t|\t8287\t|\tno rank", "8287\t|\t117571\t|\tno rank",
  "117571\t|\t117570\t|\tno rank", "117570\t|\t7776\t|\tno rank",
  "7776\t|\t7742\t|\tno rank", "7742\t|\t89593\t|\tno rank", "89593\t|\t7711\t|\tsubphylum",
  "7711\t|\t33511\t|\tphylum", "33511\t|\t33213\t|\tno rank", "33213\t|\t6072\t|\tno rank",
  "6072\t|\t33208\t|\tno rank", "33208\t|\t33154\t|\tkingdom",
  "33154\t|\t2759\t|\tno rank", "2759\t|\t131567\t|\tsuperkingdom",
  "131567\t|\t1\t|\tno rank"
)
writeLines(nodesText,tmpFile)
taxaNodes<-read.nodes(tmpFile)
getTaxonomy2(c(9606,9605),taxaNodes,taxaNames,mc.cores=1)
namesText<-c(
  "1\t|\tall\t|\t\t|\tsynonym\t|",
  "1\t|\troot\t|\t\t|\tscientific name\t|",
  "2\t|\tBacteria\t|\tBacteria <prokaryotes>\t|\tscientific name\t|",
  "2\t|\tMonera\t|\tMonera <Bacteria>\t|\tin-part\t|",
  "2\t|\tProcaryotae\t|\tProcaryotae <Bacteria>\t|\tin-part\t|",
  "9606\t|\tHomo sapiens\t|\t\t|\tscientific name",
  "9605\t|\tHomo\t|\t\t|\tscientific name",
  "207598\t|\tHomininae\t|\t\t|\tscientific name",
  "9604\t|\tHominidae\t|\t\t|\tscientific name",
  "314295\t|\tHominoidea\t|\t\t|\tscientific name",
  "9526\t|\tCatarrhini\t|\t\t|\tscientific name",
  "314293\t|\tSimiiformes\t|\t\t|\tscientific name",
  "376913\t|\tHaplorrhini\t|\t\t|\tscientific name",
  "9443\t|\tPrimates\t|\t\t|\tscientific name",
  "314146\t|\tEuarchontoglires\t|\t\t|\tscientific name",
  "1437010\t|\tBoreoeutheria\t|\t\t|\tscientific name",
  "9347\t|\tEutheria\t|\t\t|\tscientific name",
  "32525\t|\tTheria\t|\t\t|\tscientific name",
  "40674\t|\tMammalia\t|\t\t|\tscientific name",
  "32524\t|\tAmniota\t|\t\t|\tscientific name",
  "32523\t|\tTetrapoda\t|\t\t|\tscientific name",
  "1338369\t|\tDipnotetrapodomorpha\t|\t\t|\tscientific name",
  "8287\t|\tSarcopterygii\t|\t\t|\tscientific name",
  "117571\t|\tEuteleostomi\t|\t\t|\tscientific name",
  "117570\t|\tTeleostomi\t|\t\t|\tscientific name",
  "7776\t|\tGnathostomata\t|\t\t|\tscientific name",
  "7742\t|\tVertebrata\t|\t\t|\tscientific name",
  "89593\t|\tCraniata\t|\t\t|\tscientific name",
  "7711\t|\tChordata\t|\t\t|\tscientific name",
  "33511\t|\tDeuterostomia\t|\t\t|\tscientific name",
  "33213\t|\tBilateria\t|\t\t|\tscientific name",
  "6072\t|\tEumetazoa\t|\t\t|\tscientific name",
  "33208\t|\tMetazoa\t|\t\t|\tscientific name",
  "33154\t|\tOpisthokonta\t|\t\t|\tscientific name",
  "2759\t|\tEukaryota\t|\t\t|\tscientific name",
  "131567\t|\tcellular organisms\t|\t\t|\tscientific name"
)
tmpFile<-tempfile()
writeLines(namesText,tmpFile)
taxaNames<-read.names(tmpFile)
nodesText<-c(
 "1\t|\t1\t|\tno rank\t|\t\t|\t8\t|\t0\t|\t1\t|\t0\t|\t0\t|\t0\t|\t0\t|\t0\t|\t\t|",
  "2\t|\t131567\t|\tsuperkingdom\t|\t\t|\t0\t|\t0\t|\t11\t|\t0\t|\t0\t|\t0\t|\t0\t|\t0\t|\t\t|",
  "6\t|\t335928\t|\tgenus\t|\t\t|\t0\t|\t1\t|\t11\t|\t1\t|\t0\t|\t1\t|\t0\t|\t0\t|\t\t|",
  "7\t|\t6\t|\tspecies\t|\tAC\t|\t0\t|\t1\t|\t11\t|\t1\t|\t0\t|\t1\t|\t1\t|\t0\t|\t\t|",
  "9\t|\t32199\t|\tspecies\t|\tBA\t|\t0\t|\t1\t|\t11\t|\t1\t|\t0\t|\t1\t|\t1\t|\t0\t|\t\t|",
  "9606\t|\t9605\t|\tspecies", "9605\t|\t207598\t|\tgenus", "207598\t|\t9604\t|\tsubfamily",
  "9604\t|\t314295\t|\tfamily", "314295\t|\t9526\t|\tsuperfamily",
  "9526\t|\t314293\t|\tparvorder", "314293\t|\t376913\t|\tinfraorder",
  "376913\t|\t9443\t|\tsuborder", "9443\t|\t314146\t|\torder",
  "314146\t|\t1437010\t|\tsuperorder", "1437010\t|\t9347\t|\tno rank",
  "9347\t|\t32525\t|\tno rank", "32525\t|\t40674\t|\tno rank",
  "40674\t|\t32524\t|\tclass", "32524\t|\t32523\t|\tno rank", "32523\t|\t1338369\t|\tno rank",
  "1338369\t|\t8287\t|\tno rank", "8287\t|\t117571\t|\tno rank",
  "117571\t|\t117570\t|\tno rank", "117570\t|\t7776\t|\tno rank",
  "7776\t|\t7742\t|\tno rank", "7742\t|\t89593\t|\tno rank", "89593\t|\t7711\t|\tsubphylum",
  "7711\t|\t33511\t|\tphylum", "33511\t|\t33213\t|\tno rank", "33213\t|\t6072\t|\tno rank",
  "6072\t|\t33208\t|\tno rank", "33208\t|\t33154\t|\tkingdom",
  "33154\t|\t2759\t|\tno rank", "2759\t|\t131567\t|\tsuperkingdom",
  "131567\t|\t1\t|\tno rank"
)
writeLines(nodesText,tmpFile)
taxaNodes<-read.nodes(tmpFile)
getTaxonomy2(c(9606,9605),taxaNodes,taxaNames,mc.cores=1)

Return last not NA value

Description

A convenience function to return the last value which is not NA in a vector

Usage

lastNotNa(x, default = "Unknown")
lastNotNa(x, default = "Unknown")

Arguments

`x`	a vector to look for the last value in
`default`	a default value to use when all values are NA in a vector

Value

a single element from the last non NA value in x (or the default)

Examples

lastNotNa(c(1:4,NA,NA))
lastNotNa(c(letters[1:4],NA,'z',NA))
lastNotNa(c(NA,NA))
lastNotNa(c(1:4,NA,NA))
lastNotNa(c(letters[1:4],NA,'z',NA))
lastNotNa(c(NA,NA))

Create a Newick tree from taxonomy

Description

Create a Newick formatted tree from a data.frame of taxonomic assignments

Usage

makeNewick(
  taxa,
  naSub = "_",
  excludeTerminalNAs = FALSE,
  quote = NULL,
  terminator = ";"
)
makeNewick(
  taxa,
  naSub = "_",
  excludeTerminalNAs = FALSE,
  quote = NULL,
  terminator = ";"
)

Arguments

`taxa`	a matrix with a row for each leaf of the tree and a column for each taxonomic classification e.g. the output from getTaxonomy
`naSub`	a character string to substitute in place of NAs in the taxonomy
`excludeTerminalNAs`	If TRUE then do not output nodes downstream of the last named taxonomic level in a row
`quote`	If not NULL then wrap all entries with this character
`terminator`	If not NULL then add this character to the end of the tree

Value

a string giving a Newick formatted tree

Examples

taxa<-matrix(c('A','A','A','B','B','C','D','D','E','F','G','H'),nrow=3)
makeNewick(taxa)
taxa<-matrix(c('A','A','A','B',NA,'C','D','D',NA,'F','G',NA),nrow=3)
makeNewick(taxa)
makeNewick(taxa,excludeTerminalNAs=TRUE)
makeNewick(taxa,quote="'")
taxa<-matrix(c('A','A','A','B','B','C','D','D','E','F','G','H'),nrow=3)
makeNewick(taxa)
taxa<-matrix(c('A','A','A','B',NA,'C','D','D',NA,'F','G',NA),nrow=3)
makeNewick(taxa)
makeNewick(taxa,excludeTerminalNAs=TRUE)
makeNewick(taxa,quote="'")

Bring multiple raw taxonomies into alignment

Description

Combine the raw taxonomy of several taxa into a single matrix where each row corresponds to a taxa and each column a taxonomic level. Named taxonomic levels are aligned between taxa then any unspecified clades are combined between the named levels. Taxonomic levels between named levels are arbitrarily combined from most generic to most specific. Working from the data provided in the NCBI taxonomy results in ambiguities so results should be used with care.

Usage

normalizeTaxa(
  rawTaxa,
  cladeRegex = "^clade$|^clade\\.[0-9]+$|^$|no rank",
  rootFill = "_ROOT_",
  lineageOrder = c()
)
normalizeTaxa(
  rawTaxa,
  cladeRegex = "^clade$|^clade\\.[0-9]+$|^$|no rank",
  rootFill = "_ROOT_",
  lineageOrder = c()
)

Arguments

`rawTaxa`	A list of vectors with each vector containing a named character vector with entries specifying taxonomy for a clade and names giving the corresponding taxonomic levels e.g. the output from `getRawTaxonomy`
`cladeRegex`	A regex to identify ambiguous taxonomic levels. In the case of NCBI taxonomy, these unidentified levels are all labelled "clade" and `getRawTaxonomy` may attach a unique digit attach to the end for uniqueness.
`rootFill`	If a clade is upstream of the highest taxonomic level then it will be labeled with this prefix
`lineageOrder`	A vector giving an ordering for lineages from most specific to most generic. This should be unnecessary unless the taxonomy contains ambiguities e.g. one taxa goes from species to kingdom while another goes from genus to kingdom leaving it ambiguous whether genus or species is more specific

Value

a matrix with a row for each taxa and a column for each taxonomic level

Examples

rawTaxa<-list(
   '81907' = c(species = "Alectura lathami", genus = "Alectura",
     family = "Megapodiidae", order = "Galliformes", superorder = "Galloanserae",
     infraclass = "Neognathae", class = "Aves", clade = "Coelurosauria",
     clade.1 = "Theropoda", clade.2 = "Saurischia", clade.3 = "Dinosauria",
     clade.4 = "Archosauria", clade.5 = "Archelosauria", clade.6 = "Sauria",
     clade.7 = "Sauropsida", clade.8 = "Amniota", clade.9 = "Tetrapoda",
     clade.10 = "Dipnotetrapodomorpha", superclass = "Sarcopterygii",
     clade.11 = "Euteleostomi", clade.12 = "Teleostomi", clade.13 = "Gnathostomata",
     clade.14 = "Vertebrata", subphylum = "Craniata", phylum = "Chordata",
     clade.15 = "Deuterostomia", clade.16 = "Bilateria", clade.17 = "Eumetazoa",
     kingdom = "Metazoa", clade.18 = "Opisthokonta", superkingdom = "Eukaryota",
     'no rank' = "cellular organisms"),
   '8496' = c(species = "Alligator mississippiensis",
     genus = "Alligator", subfamily = "Alligatorinae", family = "Alligatoridae",
     order = "Crocodylia", clade = "Archosauria", clade.1 = "Archelosauria",
     clade.2 = "Sauria", clade.3 = "Sauropsida", clade.4 = "Amniota",
     clade.5 = "Tetrapoda", clade.6 = "Dipnotetrapodomorpha", superclass = "Sarcopterygii",
     clade.7 = "Euteleostomi", clade.8 = "Teleostomi", clade.9 = "Gnathostomata",
     clade.10 = "Vertebrata", subphylum = "Craniata", phylum = "Chordata",
     clade.11 = "Deuterostomia", clade.12 = "Bilateria", clade.13 = "Eumetazoa",
     kingdom = "Metazoa", clade.14 = "Opisthokonta", superkingdom = "Eukaryota",
     'no rank' = "cellular organisms"),
   '38654' = c(species = "Alligator sinensis",
     genus = "Alligator", subfamily = "Alligatorinae", family = "Alligatoridae",
     order = "Crocodylia", clade = "Archosauria", clade.1 = "Archelosauria",
     clade.2 = "Sauria", clade.3 = "Sauropsida", clade.4 = "Amniota",
     clade.5 = "Tetrapoda", clade.6 = "Dipnotetrapodomorpha", superclass = "Sarcopterygii",
     clade.7 = "Euteleostomi", clade.8 = "Teleostomi", clade.9 = "Gnathostomata",
     clade.10 = "Vertebrata", subphylum = "Craniata", phylum = "Chordata",
     clade.11 = "Deuterostomia", clade.12 = "Bilateria", clade.13 = "Eumetazoa",
     kingdom = "Metazoa", clade.14 = "Opisthokonta", superkingdom = "Eukaryota",
     'no rank' = "cellular organisms")
)
normalizeTaxa(rawTaxa)
rawTaxa<-list(
   '81907' = c(species = "Alectura lathami", genus = "Alectura",
     family = "Megapodiidae", order = "Galliformes", superorder = "Galloanserae",
     infraclass = "Neognathae", class = "Aves", clade = "Coelurosauria",
     clade.1 = "Theropoda", clade.2 = "Saurischia", clade.3 = "Dinosauria",
     clade.4 = "Archosauria", clade.5 = "Archelosauria", clade.6 = "Sauria",
     clade.7 = "Sauropsida", clade.8 = "Amniota", clade.9 = "Tetrapoda",
     clade.10 = "Dipnotetrapodomorpha", superclass = "Sarcopterygii",
     clade.11 = "Euteleostomi", clade.12 = "Teleostomi", clade.13 = "Gnathostomata",
     clade.14 = "Vertebrata", subphylum = "Craniata", phylum = "Chordata",
     clade.15 = "Deuterostomia", clade.16 = "Bilateria", clade.17 = "Eumetazoa",
     kingdom = "Metazoa", clade.18 = "Opisthokonta", superkingdom = "Eukaryota",
     'no rank' = "cellular organisms"),
   '8496' = c(species = "Alligator mississippiensis",
     genus = "Alligator", subfamily = "Alligatorinae", family = "Alligatoridae",
     order = "Crocodylia", clade = "Archosauria", clade.1 = "Archelosauria",
     clade.2 = "Sauria", clade.3 = "Sauropsida", clade.4 = "Amniota",
     clade.5 = "Tetrapoda", clade.6 = "Dipnotetrapodomorpha", superclass = "Sarcopterygii",
     clade.7 = "Euteleostomi", clade.8 = "Teleostomi", clade.9 = "Gnathostomata",
     clade.10 = "Vertebrata", subphylum = "Craniata", phylum = "Chordata",
     clade.11 = "Deuterostomia", clade.12 = "Bilateria", clade.13 = "Eumetazoa",
     kingdom = "Metazoa", clade.14 = "Opisthokonta", superkingdom = "Eukaryota",
     'no rank' = "cellular organisms"),
   '38654' = c(species = "Alligator sinensis",
     genus = "Alligator", subfamily = "Alligatorinae", family = "Alligatoridae",
     order = "Crocodylia", clade = "Archosauria", clade.1 = "Archelosauria",
     clade.2 = "Sauria", clade.3 = "Sauropsida", clade.4 = "Amniota",
     clade.5 = "Tetrapoda", clade.6 = "Dipnotetrapodomorpha", superclass = "Sarcopterygii",
     clade.7 = "Euteleostomi", clade.8 = "Teleostomi", clade.9 = "Gnathostomata",
     clade.10 = "Vertebrata", subphylum = "Craniata", phylum = "Chordata",
     clade.11 = "Deuterostomia", clade.12 = "Bilateria", clade.13 = "Eumetazoa",
     kingdom = "Metazoa", clade.14 = "Opisthokonta", superkingdom = "Eukaryota",
     'no rank' = "cellular organisms")
)
normalizeTaxa(rawTaxa)

Download data from NCBI and set up SQLite database

Description

Convenience function to do all necessary preparations downloading names, nodes and accession2taxid data from NCBI and preprocessing into a SQLite database for downstream use.

Usage

prepareDatabase(
  sqlFile = "nameNode.sqlite",
  tmpDir = ".",
  getAccessions = TRUE,
  vocal = TRUE,
  ...
)
prepareDatabase(
  sqlFile = "nameNode.sqlite",
  tmpDir = ".",
  getAccessions = TRUE,
  vocal = TRUE,
  ...
)

Arguments

`sqlFile`	character string giving the file location to store the SQLite database
`tmpDir`	location for storing the downloaded files from NCBI. (Note that it may be useful to store these somewhere convenient to avoid redownloading)
`getAccessions`	if TRUE download the very large accesssion2taxid files necessary to convert accessions to taxonomic IDs
`vocal`	if TRUE output messages describing progress
`...`	Arguments passed on to `getNamesAndNodes`, `getAccession2taxid`, `read.accession2taxid` `url` the url where taxdump.tar.gz is located `fileNames` the filenames desired from the tar.gz file `protocol` the protocol to be used for downloading. Probably either `'http'` or `'ftp'`. Overridden if `url` is provided directly `resume` if TRUE attempt to resume downloading an interrupted file without starting over from the beginning `baseUrl` the url of the directory where accession2taxid.gz files are located `types` the types if accession2taxid.gz files desired where type is the prefix of xxx.accession2taxid.gz. The default is to download all nucl_ accessions. For protein accessions, try `types=c('prot')`. `extraSqlCommand` for advanced use. A string giving a command to be called on the SQLite database before loading data. A couple potential uses: "PRAGMA temp_store_directory = '/MY/TMP/DIR'" to store SQLite temporary files in directory /MY/TMP/DIR. Useful if the temporary directory used by SQLite (which is not necessarily in the same location as R's) is small on your system "pragma temp_store = 2;" to keep all SQLite temp files in memory. Don't do this unless you have a lot (>100 Gb) of RAM `indexTaxa` if TRUE add an index for taxa ID. This would only be necessary if you want to look up accessions by taxa ID e.g. `getAccessions` `overwrite` If TRUE, delete accessionTaxa table in database if present and regenerate

Value

a vector of character string giving the path to the SQLite file

Examples

## Not run: 
  if(readline(
    "This will download a lot data and take a while to process.
     Make sure you have space and bandwidth. Type y to continue: "
  )!='y')
    stop('This is a stop to make sure no one downloads a bunch of data unintentionally')

  prepareDatabase()

## End(Not run)
## Not run: 
  if(readline(
    "This will download a lot data and take a while to process.
     Make sure you have space and bandwidth. Type y to continue: "
  )!='y')
    stop('This is a stop to make sure no one downloads a bunch of data unintentionally')

  prepareDatabase()

## End(Not run)

Read NCBI accession2taxid files

Description

Take NCBI accession2taxid files, keep only accession and taxa and save it as a SQLite database

Usage

read.accession2taxid(
  taxaFiles,
  sqlFile,
  vocal = TRUE,
  extraSqlCommand = "",
  indexTaxa = FALSE,
  overwrite = FALSE
)
read.accession2taxid(
  taxaFiles,
  sqlFile,
  vocal = TRUE,
  extraSqlCommand = "",
  indexTaxa = FALSE,
  overwrite = FALSE
)

Arguments

`taxaFiles`	a string or vector of strings giving the path(s) to files to be read in
`sqlFile`	a string giving the path where the output SQLite file should be saved
`vocal`	if TRUE output status messages
`extraSqlCommand`	for advanced use. A string giving a command to be called on the SQLite database before loading data. A couple potential uses: "PRAGMA temp_store_directory = '/MY/TMP/DIR'" to store SQLite temporary files in directory /MY/TMP/DIR. Useful if the temporary directory used by SQLite (which is not necessarily in the same location as R's) is small on your system "pragma temp_store = 2;" to keep all SQLite temp files in memory. Don't do this unless you have a lot (>100 Gb) of RAM
`indexTaxa`	if TRUE add an index for taxa ID. This would only be necessary if you want to look up accessions by taxa ID e.g. `getAccessions`
`overwrite`	If TRUE, delete accessionTaxa table in database if present and regenerate

Value

TRUE if sucessful

References

https://ftp.ncbi.nih.gov/pub/taxonomy/accession2taxid/

Examples

taxa<-c(
  "accession\taccession.version\ttaxid\tgi",
  "Z17427\tZ17427.1\t3702\t16569",
  "Z17428\tZ17428.1\t3702\t16570",
  "Z17429\tZ17429.1\t3702\t16571",
  "Z17430\tZ17430.1\t3702\t16572"
)
inFile<-tempfile()
sqlFile<-tempfile()
writeLines(taxa,inFile)
read.accession2taxid(inFile,sqlFile,vocal=FALSE)
db<-RSQLite::dbConnect(RSQLite::SQLite(),dbname=sqlFile)
RSQLite::dbGetQuery(db,'SELECT * FROM accessionTaxa')
RSQLite::dbDisconnect(db)
taxa<-c(
  "accession\taccession.version\ttaxid\tgi",
  "Z17427\tZ17427.1\t3702\t16569",
  "Z17428\tZ17428.1\t3702\t16570",
  "Z17429\tZ17429.1\t3702\t16571",
  "Z17430\tZ17430.1\t3702\t16572"
)
inFile<-tempfile()
sqlFile<-tempfile()
writeLines(taxa,inFile)
read.accession2taxid(inFile,sqlFile,vocal=FALSE)
db<-RSQLite::dbConnect(RSQLite::SQLite(),dbname=sqlFile)
RSQLite::dbGetQuery(db,'SELECT * FROM accessionTaxa')
RSQLite::dbDisconnect(db)

Read NCBI names file

Description

Take an NCBI names file, keep only scientific names and convert it to a data.table. NOTE: This function is now deprecated for read.names.sql (using SQLite rather than data.table).

Usage

read.names(nameFile, onlyScientific = TRUE)
read.names(nameFile, onlyScientific = TRUE)

Arguments

`nameFile`	string giving the path to an NCBI name file to read from (both gzipped or uncompressed files are ok)
`onlyScientific`	If TRUE, only store scientific names. If FALSE, synonyms and other types are included (increasing the potential for ambiguous taxonomic assignments).

Value

a data.table with columns id and name with a key on id

References

https://ftp.ncbi.nih.gov/pub/taxonomy/

Examples

namesText<-c(
  "1\t|\tall\t|\t\t|\tsynonym\t|",
  "1\t|\troot\t|\t\t|\tscientific name\t|",
  "2\t|\tBacteria\t|\tBacteria <prokaryotes>\t|\tscientific name\t|",
  "2\t|\tMonera\t|\tMonera <Bacteria>\t|\tin-part\t|",
  "2\t|\tProcaryotae\t|\tProcaryotae <Bacteria>\t|\tin-part\t|"
)
tmpFile<-tempfile()
writeLines(namesText,tmpFile)
read.names(tmpFile)
namesText<-c(
  "1\t|\tall\t|\t\t|\tsynonym\t|",
  "1\t|\troot\t|\t\t|\tscientific name\t|",
  "2\t|\tBacteria\t|\tBacteria <prokaryotes>\t|\tscientific name\t|",
  "2\t|\tMonera\t|\tMonera <Bacteria>\t|\tin-part\t|",
  "2\t|\tProcaryotae\t|\tProcaryotae <Bacteria>\t|\tin-part\t|"
)
tmpFile<-tempfile()
writeLines(namesText,tmpFile)
read.names(tmpFile)

Read NCBI names file

Description

Take an NCBI names file, keep only scientific names and convert it to a SQLite table

Usage

read.names.sql(nameFile, sqlFile = "nameNode.sqlite", overwrite = FALSE)
read.names.sql(nameFile, sqlFile = "nameNode.sqlite", overwrite = FALSE)

Arguments

`nameFile`	string giving the path to an NCBI name file to read from (both gzipped or uncompressed files are ok)
`sqlFile`	a string giving the path where the output SQLite file should be saved
`overwrite`	If TRUE, delete names table in database if present and regenerate

Value

invisibly returns a string with path to sqlfile

References

https://ftp.ncbi.nih.gov/pub/taxonomy/

Examples

namesText<-c(
  "1\t|\tall\t|\t\t|\tsynonym\t|",
  "1\t|\troot\t|\t\t|\tscientific name\t|",
  "2\t|\tBacteria\t|\tBacteria <prokaryotes>\t|\tscientific name\t|",
  "2\t|\tMonera\t|\tMonera <Bacteria>\t|\tin-part\t|",
  "2\t|\tProcaryotae\t|\tProcaryotae <Bacteria>\t|\tin-part\t|"
)
tmpFile<-tempfile()
writeLines(namesText,tmpFile)
sqlFile<-tempfile()
read.names.sql(tmpFile,sqlFile)
namesText<-c(
  "1\t|\tall\t|\t\t|\tsynonym\t|",
  "1\t|\troot\t|\t\t|\tscientific name\t|",
  "2\t|\tBacteria\t|\tBacteria <prokaryotes>\t|\tscientific name\t|",
  "2\t|\tMonera\t|\tMonera <Bacteria>\t|\tin-part\t|",
  "2\t|\tProcaryotae\t|\tProcaryotae <Bacteria>\t|\tin-part\t|"
)
tmpFile<-tempfile()
writeLines(namesText,tmpFile)
sqlFile<-tempfile()
read.names.sql(tmpFile,sqlFile)

Read NCBI nodes file

Description

Take an NCBI nodes file and convert it to a data.table. NOTE: This function is now deprecated for read.nodes.sql (using SQLite rather than data.table).

Usage

read.nodes(nodeFile)
read.nodes(nodeFile)

Arguments

nodeFile

string giving the path to an NCBI node file to read from (both gzipped or uncompressed files are ok)

Value

a data.table with columns id, parent and rank with a key on id

References

https://ftp.ncbi.nih.gov/pub/taxonomy/

Examples

nodes<-c(
 "1\t|\t1\t|\tno rank\t|\t\t|\t8\t|\t0\t|\t1\t|\t0\t|\t0\t|\t0\t|\t0\t|\t0\t|\t\t|",
 "2\t|\t131567\t|\tsuperkingdom\t|\t\t|\t0\t|\t0\t|\t11\t|\t0\t|\t0\t|\t0\t|\t0\t|\t0\t|\t\t|",
 "6\t|\t335928\t|\tgenus\t|\t\t|\t0\t|\t1\t|\t11\t|\t1\t|\t0\t|\t1\t|\t0\t|\t0\t|\t\t|",
 "7\t|\t6\t|\tspecies\t|\tAC\t|\t0\t|\t1\t|\t11\t|\t1\t|\t0\t|\t1\t|\t1\t|\t0\t|\t\t|",
 "9\t|\t32199\t|\tspecies\t|\tBA\t|\t0\t|\t1\t|\t11\t|\t1\t|\t0\t|\t1\t|\t1\t|\t0\t|\t\t|"
)
tmpFile<-tempfile()
writeLines(nodes,tmpFile)
read.nodes(tmpFile)
nodes<-c(
 "1\t|\t1\t|\tno rank\t|\t\t|\t8\t|\t0\t|\t1\t|\t0\t|\t0\t|\t0\t|\t0\t|\t0\t|\t\t|",
 "2\t|\t131567\t|\tsuperkingdom\t|\t\t|\t0\t|\t0\t|\t11\t|\t0\t|\t0\t|\t0\t|\t0\t|\t0\t|\t\t|",
 "6\t|\t335928\t|\tgenus\t|\t\t|\t0\t|\t1\t|\t11\t|\t1\t|\t0\t|\t1\t|\t0\t|\t0\t|\t\t|",
 "7\t|\t6\t|\tspecies\t|\tAC\t|\t0\t|\t1\t|\t11\t|\t1\t|\t0\t|\t1\t|\t1\t|\t0\t|\t\t|",
 "9\t|\t32199\t|\tspecies\t|\tBA\t|\t0\t|\t1\t|\t11\t|\t1\t|\t0\t|\t1\t|\t1\t|\t0\t|\t\t|"
)
tmpFile<-tempfile()
writeLines(nodes,tmpFile)
read.nodes(tmpFile)

Read NCBI nodes file

Description

Take an NCBI nodes file and convert it to a data.table

Usage

read.nodes.sql(nodeFile, sqlFile = "nameNode.sqlite", overwrite = FALSE)
read.nodes.sql(nodeFile, sqlFile = "nameNode.sqlite", overwrite = FALSE)

Arguments

`nodeFile`	string giving the path to an NCBI node file to read from (both gzipped or uncompressed files are ok)
`sqlFile`	a string giving the path where the output SQLite file should be saved
`overwrite`	If TRUE, delete nodes table in database if present and regenerate

Value

a data.table with columns id, parent and rank with a key on id

References

https://ftp.ncbi.nih.gov/pub/taxonomy/

Examples

nodes<-c(
 "1\t|\t1\t|\tno rank\t|\t\t|\t8\t|\t0\t|\t1\t|\t0\t|\t0\t|\t0\t|\t0\t|\t0\t|\t\t|",
 "2\t|\t131567\t|\tsuperkingdom\t|\t\t|\t0\t|\t0\t|\t11\t|\t0\t|\t0\t|\t0\t|\t0\t|\t0\t|\t\t|",
 "6\t|\t335928\t|\tgenus\t|\t\t|\t0\t|\t1\t|\t11\t|\t1\t|\t0\t|\t1\t|\t0\t|\t0\t|\t\t|",
 "7\t|\t6\t|\tspecies\t|\tAC\t|\t0\t|\t1\t|\t11\t|\t1\t|\t0\t|\t1\t|\t1\t|\t0\t|\t\t|",
 "9\t|\t32199\t|\tspecies\t|\tBA\t|\t0\t|\t1\t|\t11\t|\t1\t|\t0\t|\t1\t|\t1\t|\t0\t|\t\t|"
)
tmpFile<-tempfile()
sqlFile<-tempfile()
writeLines(nodes,tmpFile)
read.nodes.sql(tmpFile,sqlFile)
nodes<-c(
 "1\t|\t1\t|\tno rank\t|\t\t|\t8\t|\t0\t|\t1\t|\t0\t|\t0\t|\t0\t|\t0\t|\t0\t|\t\t|",
 "2\t|\t131567\t|\tsuperkingdom\t|\t\t|\t0\t|\t0\t|\t11\t|\t0\t|\t0\t|\t0\t|\t0\t|\t0\t|\t\t|",
 "6\t|\t335928\t|\tgenus\t|\t\t|\t0\t|\t1\t|\t11\t|\t1\t|\t0\t|\t1\t|\t0\t|\t0\t|\t\t|",
 "7\t|\t6\t|\tspecies\t|\tAC\t|\t0\t|\t1\t|\t11\t|\t1\t|\t0\t|\t1\t|\t1\t|\t0\t|\t\t|",
 "9\t|\t32199\t|\tspecies\t|\tBA\t|\t0\t|\t1\t|\t11\t|\t1\t|\t0\t|\t1\t|\t1\t|\t0\t|\t\t|"
)
tmpFile<-tempfile()
sqlFile<-tempfile()
writeLines(nodes,tmpFile)
read.nodes.sql(tmpFile,sqlFile)

Download file using curl allowing resumption of interrupted files

Description

A helper function that uses the curl package's multi_download to download a file using a temporary file to store progress and resume downloading on interruption.

Usage

resumableDownload(
  url,
  outFile = basename(url),
  tmpFile = sprintf("%s.__TMP__", outFile),
  quiet = FALSE,
  resume = TRUE,
  ...
)
resumableDownload(
  url,
  outFile = basename(url),
  tmpFile = sprintf("%s.__TMP__", outFile),
  quiet = FALSE,
  resume = TRUE,
  ...
)

Arguments

`url`	The address to download from
`outFile`	The file location to store final download at
`tmpFile`	The file location to store the intermediate download at
`quiet`	If TRUE show the progress reported by `multi_download`
`resume`	If TRUE try to resume interrupted downloads using intermediate file `tmpFile`. Otherwise delete `tempFile` on error
`...`	Additional arguments to `multi_download`

Value

invisibly return the output from multi_download

Examples

## Not run: 
  url<-'https://ftp.ncbi.nih.gov/pub/taxonomy/accession2taxid/prot.accession2taxid.FULL.1.gz'
  resumableDownload(url,'downloadedFile.gz')

## End(Not run)
## Not run: 
  url<-'https://ftp.ncbi.nih.gov/pub/taxonomy/accession2taxid/prot.accession2taxid.FULL.1.gz'
  resumableDownload(url,'downloadedFile.gz')

## End(Not run)

Process a large file piecewise

Description

A convenience function to read in a large file piece by piece, process it (hopefully reducing the size either by summarizing or removing extra rows or columns) and return the output

Usage

streamingRead(
  bigFile,
  n = 1e+06,
  FUN = function(xx) sub(",.*", "", xx),
  ...,
  vocal = FALSE
)
streamingRead(
  bigFile,
  n = 1e+06,
  FUN = function(xx) sub(",.*", "", xx),
  ...,
  vocal = FALSE
)

Arguments

`bigFile`	a string giving the path to a file to be read in or a connection opened with "r" mode
`n`	number of lines to read per chunk
`FUN`	a function taking the unparsed lines from a chunk of the bigfile as a single argument and returning the desired output
`...`	any additional arguments to FUN
`vocal`	if TRUE cat a "." as each chunk is processed

Value

a list containing the results from applying func to the multiple chunks of the file

Examples

tmpFile<-tempfile()
writeLines(LETTERS,tmpFile)
streamingRead(tmpFile,10,head,1)
writeLines(letters,tmpFile)
streamingRead(tmpFile,2,paste,collapse='',vocal=TRUE)
unlist(streamingRead(tmpFile,2,sample,1))
tmpFile<-tempfile()
writeLines(LETTERS,tmpFile)
streamingRead(tmpFile,10,head,1)
writeLines(letters,tmpFile)
streamingRead(tmpFile,2,paste,collapse='',vocal=TRUE)
unlist(streamingRead(tmpFile,2,sample,1))

Switch from data.table to SQLite

Description

In version 0.5.0, taxonomizr switched from data.table to SQLite name and node lookups. See below for more details.

Details

Version 0.5.0 marked a change for name and node lookups from using data.table to using SQLite. This was necessary to increase performance (10-100x speedup for getTaxonomy) and create a simpler interface (a single SQLite database contains all necessary data). Unfortunately, this switch requires a couple breaking changes:

getTaxonomy changes from getTaxonomy(ids,namesDT,nodesDT) to getTaxonomy(ids,sqlFile)
getId changes from getId(taxa,namesDT) to getId(taxa,sqlFile)
read.names is deprecated, instead use read.names.sql. For example, instead of calling names<-read.names('names.dmp') in every session, simply call read.names.sql('names.dmp','accessionTaxa.sql') once (or use the convenient prepareDatabase)).
read.nodes is deprecated, instead use read.names.sql. For example. instead of calling nodes<-read.names('nodes.dmp') in every session, simply call read.nodes.sql('nodes.dmp','accessionTaxa.sql') once (or use the convenient prepareDatabase).

I've tried to ease any problems with this by overloading getTaxonomy and getId to still function (with a warning) if passed a data.table names and nodes argument and providing a simpler prepareDatabase function for completing all setup steps (hopefully avoiding direct calls to read.names and read.nodes for most users).

I plan to eventually remove data.table functionality to avoid a split codebase so please switch to the new SQLite format in all new code.

Combine multiple sorted vectors into a single sorted vector

Description

Combine multiple sorted vectors into a single vector assuming there are no cycles or weird topologies. Where a global position is ambiguous, the result is placed arbitrarily.

Usage

topoSort(vectors, maxIter = 1000, errorIfAmbiguous = FALSE)
topoSort(vectors, maxIter = 1000, errorIfAmbiguous = FALSE)

Arguments

`vectors`	A list of vectors each vector containing sorted elements to be merged into a global sorted vector
`maxIter`	An integer specifying the maximum number of iterations before bailing out. This should be unnecessary and is just a safety feature in case of some unexpected input or bug.
`errorIfAmbiguous`	If TRUE then error if any ambiguities arise

Value

a vector with all unique elements sorted by the combined ordering provided by the input vectors

Examples

topoSort(list(c('a','b','f','g'),c('b','e','g','y','z'),c('b','d','e','f','y')))
topoSort(list(c('a','b','f','g'),c('b','e','g','y','z'),c('b','d','e','f','y')))

Trim columns from taxa file

Description

A simple script to delete the first row and then delete the first and fourth column of a four column tab delimited file and write to another file.

Usage

trimTaxa(inFile, outFile, desiredCols = c(2, 3))
trimTaxa(inFile, outFile, desiredCols = c(2, 3))

Arguments

`inFile`	a single string giving the 4 column tab separated file to read from
`outFile`	a single string giving the file path to write to
`desiredCols`	the integer IDs for columns to pull out from file

Package 'taxonomizr'

Help Index

Convert accessions to taxa

Description

Usage

Arguments

Value

References

See Also

Examples

Condense multiple taxonomic assignments to their most recent common branch

Description

Usage

Arguments

Value

Examples

Download accession2taxid files from NCBI

Description

Usage

Arguments

Value

References

See Also

Examples

Find all accessions for a taxa

Description

Usage

Arguments

Value

See Also

Examples

Find common names for a given taxa

Description

Usage

Arguments

Value

See Also

Examples

Get descendant ranks for a taxa

Description

Usage

Arguments

Value

See Also

Examples

Find a given taxa by name

Description

Usage

Arguments

Value

See Also

Examples

Find a given taxa by name

Description

Usage

Arguments

Value

See Also

Examples

Download names and nodes files from NCBI

Description

Usage

Arguments

Value

References

See Also

Examples

Get all taxonomy for a taxa

Description

Usage

Arguments

Value

See Also

Examples

Get taxonomic ranks for a taxa

Description

Usage

Arguments

Value

See Also