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("domain", "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)
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)
#> Warning: taxonomizr is moving from data.table to SQLite databases to improve performance. This will require changing nodes and names processing. Please see ?read.names.sql or ?taxonomizrSwitch
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|\tdomain\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|\tdomain",
"131567\t|\t1\t|\tno rank"
)
writeLines(nodesText,tmpFile)
taxaNodes<-read.nodes(tmpFile)
#> Warning: taxonomizr is moving from data.table to SQLite databases to improve performance. This will require changing nodes and names processing. Please see ?read.nodes.sql or ?taxonomizrSwitch
getTaxonomy2(c(9606,9605),taxaNodes,taxaNames,mc.cores=1)
#> Warning: taxonomizr is moving from data.table to SQLite databases to improve performance. This will require changing nodes and names processing. Please see ?getTaxonomy or ?taxonomizrSwitch
#> domain phylum class order family genus
#> 9606 "Eukaryota" "Chordata" "Mammalia" "Primates" "Hominidae" "Homo"
#> 9605 "Eukaryota" "Chordata" "Mammalia" "Primates" "Hominidae" "Homo"
#> species
#> 9606 "Homo sapiens"
#> 9605 NA