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Copy pathGLASSgo2CopraRNA_balanced_ooi_selection.r
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GLASSgo2CopraRNA_balanced_ooi_selection.r
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# author Jens Georg
# selects candidates for copraRNA based on a phylogenetic tree of the input sRNAs
# selects a pre-defined set of organisms close to the organism of interest
#call: R --slave -f GLASSgo2CopraRNA_balanced_ooi_selection.r --args wildcard=NC_000913,NC_003197 exclude=NC_020260 max_number=15 outfile_prefix=sRNA ooi=NC_000913 sim=3
args <- commandArgs(trailingOnly = TRUE)
ooi<-"NZ_CP018205"
# Staphylococcus aureus, epidermidis, lugdunensis, warneri, capitis, pseudintermedius, saprophyticus
wildcard<-c("NC_007795", "NC_004461", "NC_013893", "NC_020164", "NZ_CP007601", "NC_014925", "NC_007350")
max_number<-20
outfile_prefix<-"sRNA"
exclude<-c()
sim<-3
for(i in 1:length(args)){
temp<-strsplit(args[i],"=")
temp<-temp[[1]]
temp1<-temp[1]
temp2<-temp[2]
assign(as.character(temp1),temp2)
}
wil<-grep(",",wildcard)
if(length(wil)>0){
wildcard<-strsplit(wildcard,",")[[1]]
}
max_number<-as.numeric(max_number)
sim<-as.numeric(sim)
require(ape)
load("refined_GLASSgo_table.Rdata")
temp<-coor2
if(length(exclude)>0){
temp_ex<-c()
for(i in 1:length(exclude)){
temp_ex1<-grep(exclude[i], coor2[,"fin"])
if(length(temp_ex1)>0){
temp_ex<-c(temp_ex,temp_ex1)
}
}
if(length(temp_ex)>0){
temp<-temp[-temp_ex,]
}
}
coor2<-temp
# clustal omega call with kimura distance matrix for tree generation
clustalo3<-function(coor, positions){
fasta<-c()
for(i in 1:length(positions)){
fasta<-c(fasta, paste(">",coor[positions[i],"fin"],sep=""))
fasta<-c(fasta, as.character(coor[positions[i],"sequence"]))
}
write.table(fasta, file="temp_fasta", row.names=F, col.names=F, quote=F)
wd<-getwd()
command<-paste("clustalo -i ", "temp_fasta", " --distmat-out=distmatout.txt --full --output-order=input-order --use-kimura --force --max-hmm-iterations=-1", sep="")
system(command)
na<-grep(">", fasta)
na<-gsub(">","",fasta[na])
temp<-read.delim("distmatout.txt",sep="",header=F, skip=1)
unlink("distmatout.txt")
unlink("temp_fasta")
temp<-temp[,2:ncol(temp)]
colnames(temp)<-na
rownames(temp)<-na
temp
}
# clustal omega call with percent identity matrix
clustalo4<-function(coor, positions){
wd<-getwd()
fasta<-c()
for(i in 1:length(positions)){
fasta<-c(fasta, paste(">",coor[positions[i],"fin"],sep=""))
fasta<-c(fasta, as.character(coor[positions[i],"sequence"]))
}
write.table(fasta, file="temp_fasta", row.names=F, col.names=F, quote=F)
command<-paste("clustalo -i ", "temp_fasta", " --distmat-out=distmatout.txt --full --percent-id --output-order=input-order --force --max-hmm-iterations=-1", sep="")
system(command)
na<-grep(">", fasta)
na<-gsub(">","",fasta[na])
temp<-read.delim("distmatout.txt",sep="",header=F, skip=1)
unlink("distmatout.txt")
temp<-temp[,2:ncol(temp)]
colnames(temp)<-na
rownames(temp)<-na
temp
}
if(nrow(coor2)<max_number){
ooi_pos<-grep(ooi, coor2[,"fin"])
fasta<-c()
if(length(ooi_pos)>0){
acc <- strsplit(coor2[ooi_pos,"fin"], "\\.")[[1]][1]
fasta<-c(paste(">",acc,sep=""), as.character(coor2[ooi_pos,"sequence"]))
coor2<-coor2[-ooi_pos,]
}
for(i in 1:nrow(coor2)){
acc <- strsplit(coor2[i,"fin"], "\\.")[[1]][1]
fasta<-c(fasta, paste(">",acc,sep=""))
fasta<-c(fasta, as.character(coor2[i,"sequence"]))
}
nam<-paste(outfile_prefix,"CopraRNA_input_balanced.fasta", sep="_" )
write.table(fasta, file=nam, row.names=F, col.names=F, quote=F)
}
if(nrow(coor2)>max_number){
wildcard<-c(ooi,wildcard)
pos_wild<-c()
pos_ooi<-grep(ooi,coor2[,"fin"])[1]
for(i in 1:length(wildcard)){
pos_wild<-c(pos_wild,grep(wildcard[i],coor2[,"fin"])[1])
}
pos_wild<-unique(na.omit(pos_wild))
max_number2<-max_number-sim-length(pos_wild)+1
pos<-seq(1,nrow(coor2))
if(length(pos_wild)>0){
pos<-pos[-pos_wild]
}
pos<-unique(c(pos_ooi,pos))
dis<-clustalo3(coor2, pos)
dis2<-clustalo4(coor2, pos)
dis<-as.dist(dis)
clus<-(hclust(dis,method="average"))
plot(clus)
knum<-min(max_number2,length(clus$labels)-1)
if(knum<2){
knum<-2
}
clus2<-rect.hclust(clus,k=knum)
out<-c()
for(i in 1:length(clus2)){
temp<-clus2[[i]]
temp_ooi<-grep(ooi,names(temp))
if(length(temp_ooi)==0){
temp2<-sample(length(temp),1)
out<-c(out, names(temp)[temp2])
}
}
ooil<-sort(dis2[grep(ooi, colnames(dis2)),], decreasing=T)
sel_ooi<-na.omit(match(out,names(ooil)))
if(length(sel_ooi)>0){
ooil<-ooil[-sel_ooi]
}
ident<-which(ooil==100)
if(length(ident)>0){
ooil<-ooil[-ident]
}
sel<-c()
close_orgs<-c()
iii<-0
while(length(close_orgs)<sim){
knum2<-min(max_number2,length(clus$labels)-1)-iii
if(knum2<2){
break
}
clus3<-rect.hclust(clus,k=knum2)
ooi1<-grep(ooi, names(unlist(clus3)))
len<-as.numeric(summary(clus3)[,1])
su<-0
ii<-1
while(su<ooi1){
su<-su+len[ii]
ii<-ii+1
}
ii<-ii-1
close_orgs<-sort(ooil[intersect(names(clus3[[ii]]),names(ooil))],decreasing=T)
iii<-iii+1
}
if(length(close_orgs)>sim){
n<-length(close_orgs)%/%sim
n<-seq(1,n*sim,by=n)
n<-names(close_orgs)[n]
sel<-unique(c(sel,n))
}
if(length(close_orgs)<=sim){
sel<-unique(c(sel,names(close_orgs)))
}
out_old<-out
out<-c(coor2[pos_wild,"fin"],sel,out)
out<-match(out,coor2[,"fin"])
fasta<-c()
for(i in 1:length(out)){
acc <- strsplit(coor2[out[i],"fin"], "\\.")[[1]][1]
fasta<-c(fasta, paste(">",acc,sep=""))
fasta<-c(fasta, as.character(coor2[out[i],"sequence"]))
}
nam<-paste(outfile_prefix,"CopraRNA_input_balanced_ooi_neighbourhood.fasta", sep="_" )
fasta<-gsub("\\..*","",fasta)
write.table(fasta, file=nam, row.names=F, col.names=F, quote=F)
dis<-clustalo3(coor2, seq(1,nrow(coor2)))
dis<-as.dist(dis)
clus<-(hclust(dis,method="average"))
clus<-as.phylo(clus)
lab<-clus$tip.label
nam_selected<-match(out_old,lab)
nam_wildcard<-match(coor2[pos_wild,"fin"],lab)
nam_neighbourhood<-match(sel,lab)
nam_ooi<-grep(ooi,lab)
lab<-match(lab,coor2[,"fin"])
lab<-coor2[lab,"nam2"]
clus$tip.label<-lab
nam<-paste(outfile_prefix,"tree_coprarna_candidates_balanced_ooi_neighbourhood.pdf", sep="_" )
pdf(nam)
colo<-rep("1",length(lab))
colo[nam_selected]<-"dodgerblue1"
colo[nam_wildcard]<-"olivedrab2"
colo[nam_neighbourhood]<-"orangered"
colo[nam_ooi]<-"purple1"
par(mar=c(3, 1, 1, 1), xpd=TRUE)
plot(clus,tip.color=colo, cex=0.5 )
legend("bottom", inset=c(-0.05),bty="n", legend=c("organism of interst (ooi)","pre-selected organisms","selected organisms","close to ooi"), text.col=c("purple1","olivedrab2","dodgerblue1","orangered"),cex=0.6)
par(xpd=FALSE)
dev.off()
}
unlink("Rplots.pdf")