R/ExampleRankSeq.R

In bomeara/sleq: sleq

# Other example Latrodectus hesperus 
#accession.number<-c("KP656931","DQ127326","KP656707","KC414081","KC414080")
#library(ape)
#seqs.onespecies<- read.GenBank(access.nb=accession.number, species.names=TRUE,gene.names=TRUE, as.character=TRUE)

#seqs.onespeciesv2<- read.GenBank(access.nb=accession.number, species.names=TRUE,gene.names=TRUE, as.character=FALSE)

#no.sites<-500
#no.seqs<-5

#sequences.example2<-rbind(seqs.onespecies[[1]][1:500], seqs.onespecies[[2]][1:500], seqs.onespecies[[3]][1:500], seqs.onespecies[[4]][1:500],seqs.onespecies[[5]][1:500] )

#summary.example2<-SingleTaxonCompare(sequences.example2)#

#print(summary.example2[1:10])
#3 474
#
#percentage.rankmatrix<-matrix(rep(0,no.sites*4), nrow=4)
#nucleotide.rankmatrix<-matrix(rep("l",no.sites*4),nrow=4)
#rank.qualityseq<-rep(0,no.seqs)

#for(i in 1:10){
#aux<-sort(summary.example2[[i]][1:4,2],decreasing=TRUE)
#percentage.rankmatrix[,i]<-aux
#nucleotide.rankmatrix[,i]<-names(aux)

#aux1<-match(percentage.rankmatrix[,i],percentage.rankmatrix[,i])
#aux2<-which(aux1==1)
#target.nucleotide<-nucleotide.rankmatrix[aux2,i]
#case.number<-length(target.nucleotide)
#if(case.number==1){
#		penalty.value<-1
#}else{
#	if(case.number==2){
#		penalty.value<-0.5
#	}else{
#		if(case.number==3){
#			penalty.value=0.3
#		}else{ 
#			penalty.value=0
#		}
#	}	
#}

#target.seqsite<-which(sequences.example2[,i]%in%target.nucleotide)
#rank.qualityseq[target.seqsite]<-rank.qualityseq[target.seqsite]+penalty.value
#}



#a=percentage.rankmatrix[,3]
#match(a,a)
#summary.example2[1:5]