library(taxonomizr)

# read.names.sql('names.dmp','accessionTaxa.sql')

# read.nodes.sql('nodes.dmp','accessionTaxa.sql')

# read.accession2taxid('~/prot.accession2taxid.gz','accessionTaxa.sql')

# prepareDatabase('accessionTaxa.sql')

path <- "/home/liu507/zhao/12.20-accnumber"

path2 <- "/home/liu507/zhao/12.20-nr-annotation"

fileName <- dir(path)

for(k in 1:length(fileName)){

? blastAccessions<-read.table(file=paste(path,fileName[k],sep ="/"))

? blastAccessions<-as.character(blastAccessions$V1)

? ids<-accessionToTaxa(blastAccessions,'~/taxdump/accessionTaxa.sql')

? tax = getTaxonomy(ids,'~/taxdump/accessionTaxa.sql')

? write.table(tax,file=paste(path2,fileName[k],sep="/"),sep="\t",quote = F)

}

blastAccessions<-read.table(""file=paste(path,fileName[k],sep ="/"))

blastAccessions<-as.character(blastAccessions$V1)

ids<-accessionToTaxa("WP_059424346.1",'~/taxdump/accessionTaxa.sql')

tax = getTaxonomy(ids,'~/taxdump/accessionTaxa.sql')

write.table(tax,file=paste(path2,fileName[k],sep="/"),sep=";",quote = F,col.names = F)