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seqSerotyper.R
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# File seqSerotyper.R
# Author: Andries J. van Tonder
#
# Copyright (C) 2016 University of Oxford
#
# This is free software; you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License as
# published by the Free Software Foundation; either version 2
# of the License, or (at your option) any later version.
#
# This is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public
# License along with this software package; if not, write to the
# Free Software Foundation, Inc., 51 Franklin St, Fifth Floor,
# Boston, MA 02110-1301 USA
###############################
## Output of seqSerotyper -help
###############################
help <- paste(
"",
"seqSerotyper.R assigns serotypes to pneumococcal WGS",
"Author: Andries J. van Tonder",
"",
"Usage: Rscript seqSerotyper.R -dataFile -srcDir",
" e.g. Rscript seqSerotyper.R -dataFile pneumo_fasta_ids.txt -srcDir /home/user/Software/avt_scripts/seqSerotyper/bin",
"",
"Options:",
"",
"-dataFile",
" The path of a file containing sample ids and file paths to fasta files",
"-srcDir",
" Path of the directory that contains the reference files and related scripts",
"",
sep="\n"
)
##########################################################################################
## Create tmp directory to work in and save main seqSerotyper directory to seqSerotyperDir
##########################################################################################
system2("mkdir", "tmp")
seqSerotyperDir <- getwd()
###################################
## Make executable files executable
###################################
system2("chmod",args=c("+x","bin/blat","bin/mview","bin/blastall","bin/transeq"))
######################
## Load seqinr library
######################
library(seqinr)
###################
## Define functions
###################
####################################################
## Format the dir appropriately.
## @dir: The directory path to be formated properly.
####################################################
formatDir = function(dir = NULL){
dirLength = nchar(dir)
if(substr(dir, dirLength, dirLength) !='/'){
dir = paste(dir,"/",sep="")
}
return(dir)
}
################################################
## checkExist: checks file paths exist
## @filePath: the path of the file to be checked
################################################
checkExist <- function(filePath = NULL){
message(filePath)
message(class(filePath))
doesNotExist = which(!file.exists(filePath))
message("Done!")
if(length(doesNotExist) > 0){
stop(paste("The file", filePath[doesNotExist]," does not exist!", collapse="\n", sep=""))
}
}
####################################################
## Turn command line inputs into a n x 2 matrix
## @args: A string vector of command line arguments.
####################################################
getCommandLineInputMatrix = function(args = NULL){
argsCount = length(args)/2
inputs = matrix(nrow=argsCount, ncol=2)
inputs[,1] = args[c(1:argsCount)*2 -1]
if(length(which(regexpr("-",inputs[,1]) != 1)) > 0){
stop("Argument names must start with '-'! E.g. -dataFile.")
}
inputs[,1] = gsub("-", "", inputs[,1])
inputs[,2] = args[c(1:argsCount)*2]
return(inputs)
}
#####################################################################################
## Extract input arguments.
## @argName: Name of the argument to be extracted
## @commandLineInputs: A n x 2 matrix, where n is the number of command line inputs.
## @default: default value of the input argument if not provided
## The first column of the matrix contains the names of the arguments, and the second
## column contains the arguments values.
#####################################################################################
extractInputArgument = function(argName = NULL, commandLineInputs = NULL,
default = NULL, canBeNULL = FALSE){
argIndex = which(commandLineInputs[,1] == argName)
argIndexCount = length(argIndex)
if(argIndexCount == 0){
if(canBeNULL | !is.null(default)){
return(default)
}else{
stop(paste(c("The argument", argName, "must be specified!"), collapse=" "))
}
}else if(argIndexCount > 1){
stop(paste(c("The argument", argName, "has been specified multiple times!"), collapse=" "))
}else{
return(commandLineInputs[argIndex,2])
}
}
###########################################################################
## RunBlat: runs blat using appropriate query and reference sequences
## @querySeqs: sequence/s to be compared against reference sequence
## @refNuc: reference sequence against which query sequences compared
## @blatOutput: name/s of blat output files in standard blast output format
###########################################################################
RunBlat <- function(querySeqs, refNuc, blatOutput) {
system2(paste(blatPath),args=c("-t=dna",querySeqs,"-q=dna", refNuc, blatOutput,"out=blast"))
}
###########################################################################
## RunBlatBlast8: runs blat using appropriate query and reference sequences
## @querySeqs: sequence/s to be compared against reference sequence
## @refNuc: reference sequence against which query sequences compared
## @blatOutput: name/s of blat output files in blast8 output format
###########################################################################
RunBlatBlast8 <- function(querySeqs, refNuc, blatOutput) {
system2(paste(blatPath),args=c("-t=dna",querySeqs,"-q=dna", refNuc, blatOutput,"out=blast8"))
}
#############################################################################
## RunBlastall: runs blastall using appropriate query and reference sequences
## @BARef: reference sequence against which query sequences compared
## @BAquerySeqs: sequence/s to be compared against reference sequence
## @blastAllOut: names of blastall output files
#############################################################################
RunBlastall <- function(BARef, BAquerySeqs, blastAllOut) {
system2(paste(blastallPath),args=c("-p blastn", "-d", BARef, "-i", BAquerySeqs,"-m 8","-o",blastAllOut))
}
##########################################################################
## runMview: runs mview which extracts sequence from blast output as fasta
## @mviewIn: input file in blast format
## @mviewOut: output file in pearson (fasta) format
##########################################################################
runMview <- function(mviewIn, mviewOut) {
system2(paste(mviewPath),args=c("-in","blast",mviewIn,"-out","pearson", "-top", "1", ">",mviewOut))
}
#############################################################################
## runSplitMultifasta: splits multifasta file into individual fasta sequences
## @multifasta: multifasta file to be split
## @outDir: output directory for individual fasta files
#############################################################################
runSplitMultifasta <- function(multifasta, outDir) {
system2("perl",args=c(splitMultifastapath,"-i", multifasta,"-o",outDir))
}
##############################################################################
## runTranseq: runs transeq which translates nucleotide sequence to amino acid
## @TranseqIn: fasta nucleotide sequences
## @TranseqOut: fasta amino acid sequences
##############################################################################
runTranseq <- function(TranseqIn, TranseqOut) {
system2(paste(transeqPath),args=c("-sequence", TranseqIn, "-outseq", TranseqOut))
}
###############################################
## Read in the arguments from the command line
###############################################
args <- commandArgs(trailingOnly = TRUE)
if(length(args!=0)){
if(args[1]=="-help" | args[1]=="-h"){
cat(help,sep="\n")
q("no")
}
}
if((length(args)%%2)!=0 | length(args)==0) {
cat(help,sep="\n")
stop("\nIncorrect usage\n")
}
####################################
## Get inputs from the command line
####################################
message("Arg length:")
message(length(args))
inputs <- getCommandLineInputMatrix(args = args)
message(nrow(inputs))
message(ncol(inputs))
############################
## Input arguments required
############################
dataFilePath <- extractInputArgument(argName = "dataFile", commandLineInputs = inputs)
srcDir <- formatDir(extractInputArgument(argName = "srcDir", commandLineInputs = inputs, default = getwd()))
message("Input arguments have been read.")
###########################
## Reference files location
###########################
cat(paste0("Reference directory: ",srcDir))
#######################################
## Get the paths of the reference files
#######################################
assign11Eref <- paste(srcDir, "11A_wcjE_nuc.fas", sep="")
assign11ADref <- paste(srcDir, "11A_wcrL_nuc.fas", sep="")
assign18BCref <- paste(srcDir, "18B_18C_wciX_nuc.fas", sep="")
assign20ABref <- paste(srcDir, "20B_whaF_nuc.fas", sep="")
assign22AFref <- paste(srcDir, "22F_wcwA_nuc.fas", sep="")
assign25AFref <- paste(srcDir, "25F_wzg_nuc.fas", sep="")
assign33AFref <- paste(srcDir, "33A_33F_wcjE_nuc.fas", sep="")
assign37ref <- paste(srcDir, "37_tts_nuc.fas", sep="")
assign6ABref <- paste(srcDir, "6A_6B_wciP_nuc.fas", sep="")
assign6CEGref <- paste(srcDir, "6A_6B_wzy_nuc.fas", sep="")
assign6Fref <- paste(srcDir, "6A_wciN_alpha_nuc.fas", sep="")
assign6CDref <- paste(srcDir, "6D_wciN_beta_nuc.fas", sep="")
assign7AFref <- paste(srcDir, "7A_7F_wcwD_nuc.fas", sep="")
assign9AVref <- paste(srcDir, "9A_9V_wcjE_nuc.fas", sep="")
mainRefPath <- paste(srcDir, "Pneumo_serotypes.fasta", sep="")
splitMultifastapath <- paste(srcDir, "split_multifasta.pl", sep="")
blatPath <- paste(srcDir, "blat", sep="")
blastallPath <- paste(srcDir, "blastall", sep="")
transeqPath <- paste(srcDir, "transeq", sep="")
mviewPath <- paste(srcDir, "mview", sep="")
##############################
## Check reference files exist
###############################
checkExist(c(assign11Eref, assign11ADref, assign18BCref, assign20ABref, assign22AFref, assign25AFref, assign33AFref,
assign37ref, assign6ABref, assign6CEGref, assign6CEGref, assign6Fref, assign6CDref, assign7AFref, assign9AVref,
mainRefPath, splitMultifastapath, blatPath, blastallPath, transeqPath, mviewPath))
############################################################
## Read in data file and sort alphabetically based on the id
############################################################
data.df <- read.table(file=dataFilePath, header=T, as.is=T)
orderdata.df <- data.df[order(data.df$id),]
fastaFile <- orderdata.df$filePath
fastaID <- orderdata.df$id
numberSeqs <- length(fastaFile)
message(paste(numberSeqs, "sequence files found.", "\n"))
###############################
## Set working directory to tmp
###############################
setwd("tmp")
######################################################################
## Use blat to compare each genome sequence to serotype reference file
######################################################################
fastaFileTab <- paste(fastaID,".tab",sep="")
for (i in 1:length(fastaID)) {
RunBlatBlast8(querySeqs = fastaFile[[i]], refNuc = mainRefPath, blatOutput = fastaFileTab[[i]])
}
#############################
## Process blat output files
#############################
blatTabOut <- NULL
for (i in 1:length(fastaFileTab)) blatTabOut[[i]] <- read.delim(fastaFileTab[i],header=F,sep="\t")
sortBlatTabOut <- NULL
for (i in 1:length(blatTabOut)) sortBlatTabOut[[i]] <- blatTabOut[[i]][order(-blatTabOut[[i]]$V12),]
topBlatHit <- NULL
for (i in 1:length(sortBlatTabOut)) topBlatHit[[i]] <- sortBlatTabOut[[i]][1,]
######################################
## Write out best hits for each genome
######################################
topBlatHitOut <- file("topBlatHit.out",open="a")
for (i in 1:length(topBlatHit)) {
write.table(topBlatHit[[i]],file=topBlatHitOut,sep="\t",row.names=FALSE,col.names=FALSE,quote=FALSE)
}
close(topBlatHitOut)
###########################################################
## Read best hits file and process by serotype and best hit
###########################################################
blatResults <- read.delim("topBlatHit.out",header=F,sep="\t")
addtopBlatHitData <- cbind(orderdata.df,blatResults)
fastablatID <- addtopBlatHitData$id
####################################################################
## Assign NT if length of alignment is <3000 i.e. no hit to database
####################################################################
NTresults <- subset(addtopBlatHitData,V4<3000)
nonNTresults <- subset(addtopBlatHitData,V4>3000)
if (nrow(NTresults) > 0) {
NTresults$V13 <- "NT"
NTout <- NTresults[,c("id","V13")]
} else if (nrow(NTresults)==0) {
cat("No NT serotypes found","\n")
}
##########################################
## Extract serotypes for separate analyses
##########################################
sero6Results<-subset(nonNTresults, V1=="6A"|V1=="6B"|V1=="6Bii(6E)"|V1=="6F"|V1=="6G"|V1=="6C"|V1=="6D")
sero9Results<-subset(nonNTresults, V1=="9V"|V1=="9A")
sero7Results<-subset(nonNTresults, V1=="7A"|V1=="7F")
sero18Results<-subset(nonNTresults, V1=="18B"|V1=="18C")
sero33Results<-subset(nonNTresults, V1=="33A"|V1=="33F")
sero22Results<-subset(nonNTresults, V1=="22A"|V1=="22F")
sero11Results<-subset(nonNTresults, V1=="11A"|V1=="11D")
sero20Results<-subset(nonNTresults, V1=="20")
sero25Results<-subset(nonNTresults, V1=="25A"|V1=="25F")
###########################################################################
## Save remaining serotype predictions to own variable for saving out later
###########################################################################
resttoBlat <- nonNTresults[nonNTresults$V1!="6A"&nonNTresults$V1!="6B"&nonNTresults$V1!="6Bii(6E)"&nonNTresults$V1!="6F"&nonNTresults$V1!="6G"&nonNTresults$V1!="6C"&nonNTresults$V1!="6D"&nonNTresults$V1!="9V"&nonNTresults$V1!="9A"&nonNTresults$V1!="7A"&nonNTresults$V1!="7F"&nonNTresults$V1!="18B"&nonNTresults$V1!="18C"&nonNTresults$V1!="33A"&nonNTresults$V1!="33F"&nonNTresults$V1!="22A"&nonNTresults$V1!="22F"&nonNTresults$V1!="11A"&nonNTresults$V1!="11D"&nonNTresults$V1!="20"&nonNTresults$V1!="25A"&nonNTresults$V1!="25F",]
resttoBlatOut <- resttoBlat[,c("id","V1")]
#############################
## Serogroup 6 identification
#############################
if (nrow(sero6Results)>0) {
fasta6 <- sero6Results$filePath
fasta6ID <- sero6Results$id
id6 <- sero6Results[,c("id","filePath")]
tab6 <- paste(fasta6ID,".6all.tab",sep="")
n6 <- length(fasta6)
###############################
## Identify serotypes 6C and 6D
###############################
for (i in 1:n6) {
RunBlastall(BARef = assign6CDref, BAquerySeqs = fasta6[[i]], blastAllOut = tab6[[i]])
}
out6CDin <- dir(pattern=".6all.tab")
out6CDRead <- NULL
for (i in 1:length(out6CDin)) out6CDRead[[i]] <- read.delim(out6CDin[i],header=F, sep="\t")
sort6CDReadOut <- NULL
for (i in 1:length(out6CDRead)) sort6CDReadOut[[i]] <- out6CDRead[[i]][order(-out6CDRead[[i]]$V12),]
head6CDwciN <- NULL
for (i in 1:length(sort6CDReadOut)) head6CDwciN[[i]] <- sort6CDReadOut[[i]][1,]
head6CDwciNout <- file("6CD_head_out", open="a")
for (i in 1:length(head6CDwciN)) {
write.table(head6CDwciN[[i]],file=head6CDwciNout,sep="\t",row.names=FALSE,col.names=FALSE,quote=FALSE)
}
close(head6CDwciNout)
sero6CDresults <- read.delim("6CD_head_out",header=F,sep="\t")
addSero6CDdata <- cbind(id6,sero6CDresults)
assignOtherSero6 <- subset(addSero6CDdata, V4<500)
assignSero6CD <- subset(addSero6CDdata, V4>500)
if (nrow(assignSero6CD) > 0) {
checkSero6CD <- assignSero6CD$filePath
checkSero6CDid <- assignSero6CD$id
checkSero6CDTab <- paste(checkSero6CDid,".6CD.tab",sep="")
for (i in 1:length(checkSero6CD)) {
RunBlat(querySeqs = checkSero6CD[[i]], refNuc = assign6CEGref, blatOutput = checkSero6CDTab[[i]])
}
listSero6CDTab<-dir(pattern=".6CD.tab")
listSero6CDTabFasta <- paste(listSero6CDTab,".fasta",sep="")
for (i in 1:length(listSero6CDTab)) {
runMview(mviewIn = listSero6CDTab[[i]], mviewOut = listSero6CDTabFasta[[i]])
}
listSero6CDFasta <- dir(pattern=".6CD.tab.fasta")
system2("mkdir","6CD")
for (i in 1:length(listSero6CDFasta)) {
runSplitMultifasta(multifasta = listSero6CDFasta[[i]], outDir = "6CD")
}
system2("rm","6CD/wzy.fsa")
fsaSero6CDListT <- list.files("6CD",full.names=TRUE)
fsaSero6CDListF <- list.files("6CD",full.names=FALSE)
pepSero6CD <- paste(fsaSero6CDListF,".pep",sep="")
for (i in 1:length(fsaSero6CDListT)){
runTranseq(TranseqIn = fsaSero6CDListT[[i]], TranseqOut = pepSero6CD[[i]])
}
listSero6CDPep <- dir(pattern=".pep")
readlistSero6CDPep <- NULL
for (i in 1:length(listSero6CDPep)) {
readlistSero6CDPep[[i]] <-read.fasta(listSero6CDPep[[i]],seqtype="AA",set.attributes=FALSE)
}
wzy117 <- NULL
sero6CDOut<-NULL
for (i in 1:length(readlistSero6CDPep)){
wzy117[[i]] <- getFrag(readlistSero6CDPep[[i]],begin = 117, end=117)
}
for (i in 1:length(readlistSero6CDPep)){
sero6CDOut[[i]]<-cbind(listSero6CDPep[[i]],wzy117[[i]])
}
sero6CDOutWrite <- file("6CD_out",open="a")
for (i in 1:length(sero6CDOut)){
write.table(sero6CDOut[[i]],file=sero6CDOutWrite,sep="\t",row.names=FALSE,col.names=FALSE,quote=FALSE)
}
close(sero6CDOutWrite)
assignSero6CDin <- read.delim("6CD_out",header=F,sep="\t",colClasses="character")
for (i in 1:length(assignSero6CDin$V2)){
if (assignSero6CDin$V2[i]=="T")
{assignSero6CDin$V3[i]="6C"}
else if (assignSero6CDin$V2[i]=="I")
{assignSero6CDin$V3[i]="6D"}
}
addIDassignSero6CDin <- cbind(checkSero6CDid,assignSero6CDin)
assignSero6CDfinal <- addIDassignSero6CDin[,c("checkSero6CDid","V3")]
} else if (nrow(assignSero6CD)==0) {
cat("No serotypes 6C or 6D found","\n")
}
###############################
## Identify serotypes 6E and 6G
###############################
if (nrow(assignOtherSero6) > 0) {
checknotSero6CD <- assignOtherSero6$filePath
checknotSero6CDid <- assignOtherSero6$id
checknotSero6CDTab <- paste(checknotSero6CDid,".6AG.tab",sep="")
for (i in 1:length(checknotSero6CD)) {
RunBlat(querySeqs = checknotSero6CD[[i]], refNuc = assign6CEGref, blatOutput = checknotSero6CDTab[[i]])
}
listSero6AGTab<-dir(pattern=".6AG.tab")
listSero6AGTabFasta <- paste(listSero6AGTab,".fasta",sep="")
for (i in 1:length(listSero6AGTab)) {
runMview(mviewIn = listSero6AGTab[[i]], mviewOut = listSero6AGTabFasta[[i]])
}
listSero6AGFasta <- dir(pattern=".6AG.tab.fasta")
system2("mkdir","6AG")
for (i in 1:length(listSero6AGFasta)) {
runSplitMultifasta(multifasta = listSero6AGFasta[[i]], outDir = "6AG")
}
system2("rm","6AG/wzy.fsa")
fsaSero6AGListT <- list.files("6AG",full.names=TRUE)
fsaSero6AGListF <- list.files("6AG",full.names=FALSE)
pepSero6AG <- paste(fsaSero6AGListF,".6AG.pep",sep="")
for (i in 1:length(fsaSero6AGListT)){
runTranseq(TranseqIn = fsaSero6AGListT[[i]], TranseqOut = pepSero6AG[[i]])
}
listSero6AGpep <- dir(pattern=".6AG.pep")
readlistSero6AGpep <- NULL
for (i in 1:length(listSero6AGpep)) {
readlistSero6AGpep[[i]] <-read.fasta(listSero6AGpep[[i]],seqtype="AA",set.attributes=FALSE)
}
wzy220 <- NULL
wzy225 <- NULL
sero6AGOut<-NULL
for (i in 1:length(readlistSero6AGpep)){
wzy220[[i]] <- getFrag(readlistSero6AGpep[[i]],begin = 220, end=220)
}
for (i in 1:length(readlistSero6AGpep)){
wzy225[[i]] <- getFrag(readlistSero6AGpep[[i]],begin = 225, end=225)
}
sero6AGOut <- NULL
for (i in 1:length(listSero6AGpep)) {
sero6AGOut[[i]]<-cbind(listSero6AGpep[[i]],wzy220[[i]],wzy225[[i]])
}
sero6AGOutWrite <- file("6AG_out",open="a")
for (i in 1:length(sero6AGOut)){
write.table(sero6AGOut[[i]],file=sero6AGOutWrite,sep="\t",row.names=FALSE,col.names=FALSE,quote=FALSE)
}
close(sero6AGOutWrite)
assignSero6E <- read.delim("6AG_out",header=F,sep="\t",colClasses="character")
addIDassignSero6Ein <- cbind(checknotSero6CDid, checknotSero6CD, assignSero6E)
for (i in 1:length(addIDassignSero6Ein$V2)){
if (addIDassignSero6Ein$V2[i]=="T"&addIDassignSero6Ein$V3[i]=="Y")
{addIDassignSero6Ein$V4[i]="6Bii(6E)"}
else if (addIDassignSero6Ein$V2[i]=="S"&addIDassignSero6Ein$V3[i]=="Y")
{addIDassignSero6Ein$V4[i]="6A/F"}
else if (addIDassignSero6Ein$V2[i]=="A"&addIDassignSero6Ein$V3[i]=="Y")
{addIDassignSero6Ein$V4[i]="6B"}
else if (addIDassignSero6Ein$V2[i]=="S"&addIDassignSero6Ein$V3[i]=="D")
{addIDassignSero6Ein$V4[i]="6G"}
else if (addIDassignSero6Ein$V2[i]!="S"|addIDassignSero6Ein$V2[i]!="A"|addIDassignSero6Ein$V2[i]!="T")
{addIDassignSero6Ein$V4[i]="6unk"}
}
idSero6E <- subset(addIDassignSero6Ein,V4=="6Bii(6E)")
idSero6G <- subset(addIDassignSero6Ein,V4=="6G")
idSero6AFB <- subset(addIDassignSero6Ein,V4=="6A/F"|V4=="6B"|V4=="6unk")
assignSero6Efinal <- idSero6E[,c("checknotSero6CDid","V4")]
assignSero6Gfinal <- idSero6G[,c("checknotSero6CDid","V4")]
file6AFlist <- idSero6AFB[,c("checknotSero6CDid", "checknotSero6CD")]
##############
## Identify 6F
##############
if (nrow(file6AFlist) > 0) {
listSero6AFfasta <- paste(file6AFlist$checknotSero6CD)
listSero6AFfastaID <-paste(file6AFlist$checknotSero6CDid)
listSero6AFTab <- paste(file6AFlist$checknotSero6CDid,".6AF.tab",sep="")
for (i in 1:length(listSero6AFfasta)) {
RunBlat(querySeqs = listSero6AFfasta[[i]], refNuc = assign6Fref, blatOutput = listSero6AFTab[[i]])
}
listSero6AFtab<-dir(pattern=".6AF.tab")
listSero6AFtabFasta <- paste(listSero6AFtab,".fasta",sep="")
for (i in 1:length(listSero6AFtab)) {
runMview(mviewIn = listSero6AFtab[[i]], mviewOut = listSero6AFtabFasta[[i]])
}
listSero6AFfastaIn <- dir(pattern=".6AF.tab.fasta")
system2("mkdir","6AF")
for (i in 1:length(listSero6AFfastaIn)) {
runSplitMultifasta(multifasta = listSero6AFfastaIn[[i]], outDir = "6AF")
}
system2("rm","6AF/6A_wciNalpha.fsa")
fsaSero6AFlistT <- list.files("6AF",full.names=TRUE)
fsaSero6AFlistF <- list.files("6AF",full.names=FALSE)
pepSero6AF <- paste(fsaSero6AFlistF,".6AF.pep",sep="")
for (i in 1:length(fsaSero6AFlistT)){
runTranseq(TranseqIn = fsaSero6AFlistT[[i]], TranseqOut = pepSero6AF[[i]])
}
listpepSero6AF <- dir(pattern=".6AF.pep")
readListPepSero6AF <- NULL
for (i in 1:length(listpepSero6AF)) {
readListPepSero6AF[[i]] <- read.fasta(listpepSero6AF[[i]],seqtype="AA",set.attributes=FALSE)
}
wciN150 <- NULL
sero6AFout <- NULL
for (i in 1:length(readListPepSero6AF)){
wciN150[[i]] <- getFrag(readListPepSero6AF[[i]],begin=150,end=150)
}
for (i in 1:length(listpepSero6AF)){
sero6AFout[[i]]<-cbind(listpepSero6AF[[i]],wciN150[[i]])
}
sero6AFoutWrite <- file("6AF_out",open="a")
for (i in 1:length(sero6AFout)){
write.table(sero6AFout[[i]],file=sero6AFoutWrite,sep="\t",row.names=FALSE,col.names=FALSE,quote=FALSE)
}
close(sero6AFoutWrite)
assignSero6F <- read.delim("6AF_out",header=F,sep="\t",colClasses="character")
addIDassignSero6Fin <- cbind(listSero6AFfastaID, listSero6AFfasta, assignSero6F)
for (i in 1:length(addIDassignSero6Fin$V2)) {
if (addIDassignSero6Fin$V2[i]=="T")
{addIDassignSero6Fin$V3[i]="6F"}
else if (addIDassignSero6Fin$V2[i]!="T")
{addIDassignSero6Fin$V3[i]="6A/6B"}
}
assignSero6Fout <- subset(addIDassignSero6Fin,V3=="6F")
assignSero6Ffinal <- assignSero6Fout[,c("listSero6AFfastaID","V3")]
assignSero6ABout <- subset(addIDassignSero6Fin,V3=="6A/6B")
} else if (nrow(file6AFlist)==0) {
cat("No serotype 6F found","\n")
}
#####################
## Identify 6A and 6B
#####################
if (exists("assignSero6ABout") == TRUE) {
checkSero6AB <- paste(assignSero6ABout$listSero6AFfasta)
checkSero6ABid <- assignSero6ABout$listSero6AFfastaID
checkSero6ABtab <- paste(checkSero6ABid,".6AB.tab",sep="")
for (i in 1:length(checkSero6AB)) {
RunBlat(querySeqs = checkSero6AB[[i]], refNuc = assign6ABref, blatOutput = checkSero6ABtab[[i]])
}
listSero6ABtab<-dir(pattern=".6AB.tab")
listSero6ABtabFasta <- paste(listSero6ABtab,".fasta",sep="")
for (i in 1:length(listSero6ABtab)) {
runMview(mviewIn = listSero6ABtab[[i]], mviewOut = listSero6ABtabFasta[[i]])
}
listSero6ABfasta <- dir(pattern=".6AB.tab.fasta")
system2("mkdir","6AB")
for (i in 1:length(listSero6ABfasta)) {
runSplitMultifasta(multifasta = listSero6ABfasta[[i]], outDir = "6AB")
}
system2("rm","6AB/wciP.fsa")
fsaSero6ABlistT <- list.files("6AB",full.names=TRUE)
fsaSero6ABlistF <- list.files("6AB",full.names=FALSE)
pepSero6AB <- paste(fsaSero6ABlistF,".6AB.pep",sep="")
for (i in 1:length(fsaSero6ABlistT)){
runTranseq(TranseqIn = fsaSero6ABlistT[[i]], TranseqOut = pepSero6AB[[i]])
}
listSero6ABpep <- dir(pattern="6AB.pep")
readlistSero6ABpep <- NULL
for (i in 1:length(listSero6ABpep)) {
readlistSero6ABpep[[i]] <-read.fasta(listSero6ABpep[[i]],seqtype="AA",set.attributes=FALSE)
}
wciP195 <- NULL
outSero6AB<-NULL
for (i in 1:length(readlistSero6ABpep)){
wciP195[[i]] <- getFrag(readlistSero6ABpep[[i]],begin = 195, end=195)
}
for (i in 1:length(readlistSero6ABpep)){
outSero6AB[[i]]<-cbind(listSero6ABpep[[i]],wciP195[[i]])
}
outSero6ABwrite <- file("6AB_out",open="a")
for (i in 1:length(outSero6AB)){
write.table(outSero6AB[[i]], file = outSero6ABwrite, sep="\t", row.names=FALSE, col.names=FALSE, quote=FALSE)
}
close(outSero6ABwrite)
assignSero6AB <- read.delim("6AB_out",header=F,sep="\t",colClasses="character")
addIDassignSero6Ein <- cbind(checkSero6ABid, checkSero6AB, assignSero6AB)
for (i in 1:length(addIDassignSero6Ein$V2)) {
if (addIDassignSero6Ein$V2[i]=="S")
{addIDassignSero6Ein$V3[i]="6A"}
else if (addIDassignSero6Ein$V2[i]=="N")
{addIDassignSero6Ein$V3[i]="6B"}
else if (addIDassignSero6Ein$V2[i]!="N"|addIDassignSero6Ein$V2[i]!="S")
{addIDassignSero6Ein$V3[i]="6unk"}
}
assignSero6ABfinal <- addIDassignSero6Ein[,c("checkSero6ABid","V3")]
} else if (exists("assignSero6ABout") != TRUE) {
cat("No serotypes 6A or 6B found","\n")
}
} else if (nrow(assignOtherSero6)==0) {
cat("No serotypes 6A, 6B, 6Bii(6E), 6F or 6G found","\n")
}
} else if (nrow(sero6Results)==0) {
cat("No serotype 6 sequences found","\n")
}
###############################
## Identify serotypes 7A and 7F
###############################
if (nrow(sero7Results)>0) {
fasta7 <- sero7Results$filePath
fasta7ID <- sero7Results$id
tab7 <- paste(fasta7ID,".7all.tab",sep="")
n7 <- length(fasta7)
for (i in 1:n7) {
RunBlatBlast8(querySeqs = fasta7[[i]], refNuc = assign7AFref, blatOutput = tab7[[i]])
}
tabinSero7 <- dir(pattern=".7all.tab")
outSero7<-NULL
for (i in 1:length(tabinSero7)) outSero7[[i]] <- read.delim(tabinSero7[i],header=F,sep="\t")
sortoutSero7<-NULL
for (i in 1:length(tabinSero7)) sortoutSero7[[i]] <- outSero7[[i]][order(-outSero7[[i]]$V12),]
headSero7<-NULL
for (i in 1:length(tabinSero7)) headSero7[[i]] <- sortoutSero7[[i]][1,]
headSero7out <- file("7_head_out",open="a")
for (i in 1:length(tabinSero7)) {
write.table(headSero7[[i]],file=headSero7out,sep="\t",row.names=FALSE,col.names=FALSE,quote=FALSE)
}
close(headSero7out)
blatresSero7 <- read.delim("7_head_out",header=F,sep="\t")
for (i in 1:length(blatresSero7$V7)) {
if (blatresSero7$V4[i]>900)
{blatresSero7$V13[i]="7F"}
else if (blatresSero7$V4[i]<700)
{blatresSero7$V13[i]="7A"}
}
addSero7data <- cbind(fasta7ID,blatresSero7)
assignSero7final <- addSero7data[,c("fasta7ID","V13")]
} else if (nrow(sero7Results)==0) {
cat("No serotype 7 sequences found","\n")
}
###############################
## Identify serotypes 9A and 9V
###############################
if (nrow(sero9Results)>0) {
fasta9 <- sero9Results$filePath
fasta9ID <- sero9Results$id
tab9 <- paste(fasta9ID,".9all.tab", sep="")
n9 <- length(fasta9)
for (i in 1:n9) {
RunBlatBlast8(querySeqs = fasta9[[i]], refNuc = assign9AVref, blatOutput = tab9[[i]])
}
tabinSero9 <- dir(pattern=".9all.tab")
sero9out <- NULL
for (i in 1:length(tabinSero9)) sero9out[[i]] <- read.delim(tabinSero9[i],header=F,sep="\t")
sortSero9out <- NULL
for (i in 1:length(tabinSero9)) sortSero9out[[i]] <- sero9out[[i]][order(-sero9out[[i]]$V12),]
headSero9 <- NULL
for (i in 1:length(tabinSero9)) headSero9[[i]] <- sortSero9out[[i]][1,]
headSero9out <- file("9_head_out",open="a")
for (i in 1:length(tabinSero9)) {
write.table(headSero9[[i]],file=headSero9out,sep="\t",row.names=FALSE,col.names=FALSE,quote=FALSE)
}
close(headSero9out)
blatresSero9 <- read.delim("9_head_out",header=F,sep="\t")
for (i in 1:length(blatresSero9$V7)) {
if (blatresSero9$V4[i]>1000)
{blatresSero9$V13[i]="9V"}
else if (blatresSero9$V4[i]<900)
{blatresSero9$V13[i]="9A"}
}
addSero9data <- cbind(fasta9ID,blatresSero9)
assignSero9final <- addSero9data[,c("fasta9ID","V13")]
} else if (nrow(sero9Results)==0) {
cat("No serotype 9 sequences found","\n")
}
######################################
## Identify serotypes 11A, 11D and 11E
######################################
if (nrow(sero11Results)>0) {
fasta11 <- sero11Results$filePath
fasta11ID <- sero11Results$id
id11 <- sero11Results[,c("id","filePath")]
tab11 <- paste(fasta11ID,".11AD.tab",sep="")
n11 <- length(fasta11)
#################################
## Identify serotypes 11A and 11D
#################################
for (i in 1:n11) {
RunBlat(querySeqs = fasta11[[i]], refNuc = assign11ADref, blatOutput = tab11[[i]])
}
listSero11ADtab <- dir(pattern=".11AD.tab")
listSero11ADtabFasta <- paste(listSero11ADtab,".fasta",sep="")
for (i in 1:length(listSero11ADtab)) {
runMview(mviewIn = listSero11ADtab[[i]], mviewOut = listSero11ADtabFasta[[i]])
}
listSero11ADfasta <- dir(pattern=".11AD.tab.fasta")
system2("mkdir","11AD")
for (i in 1:length(listSero11ADfasta)) {
runSplitMultifasta(multifasta = listSero11ADfasta[[i]], outDir = "11AD")
}
system2("rm","11AD/11A_wcrL.fsa")
fsaSero11ADlistT <- list.files("11AD",full.names=TRUE)
fsaSero11ADlistF <- list.files("11AD",full.names=FALSE)
pepSero11AD <- paste(fsaSero11ADlistF,".11AD.pep",sep="")
for (i in 1:length(fsaSero11ADlistT)){
runTranseq(TranseqIn = fsaSero11ADlistT[[i]], TranseqOut = pepSero11AD[[i]])
}
listSero11ADpep <- dir(pattern=".11AD.pep")
readListSero11ADpep <- NULL
for (i in 1:length(listSero11ADpep)) {
readListSero11ADpep[[i]] <- read.fasta(listSero11ADpep[[i]],seqtype="AA",set.attributes=FALSE)
}
wcrL112 <- NULL
outSero11AD <- NULL
for (i in 1:length(readListSero11ADpep)){
wcrL112[[i]] <- getFrag(readListSero11ADpep[[i]],begin=112,end=112)
}
for (i in 1:length(listSero11ADpep)){
outSero11AD[[i]]<-cbind(listSero11ADpep[[i]],wcrL112[[i]])
}
outSero11ADwrite <- file("11AD_out",open="a")
for (i in 1:length(outSero11AD)){
write.table(outSero11AD[[i]],file=outSero11ADwrite,sep="\t",row.names=FALSE,col.names=FALSE,quote=FALSE)
}
close(outSero11ADwrite)
assignSero11D <- read.delim("11AD_out",header=F,sep="\t",colClasses="character")
addIDassignSero11Din <- cbind(id11, assignSero11D)
for (i in 1:length(addIDassignSero11Din$V2)) {
if (addIDassignSero11Din$V2[i]=="N")
{addIDassignSero11Din$V3[i]="11A"}
else if (addIDassignSero11Din$V2[i]=="S")
{addIDassignSero11Din$V3[i]="11D"}
}
idSero11D <- subset(addIDassignSero11Din,V3=="11D")
idSero11AE <- subset(addIDassignSero11Din,V3=="11A")
assignSero11Dfinal <- idSero11D[,c("id","V3")]
###############
## Identify 11E
###############
if (nrow(idSero11AE)>0) {
sero11AEfasta <- idSero11AE$filePath
sero11AEid <- idSero11AE$id
sero11AEtab <- paste(sero11AEid,".11AE.tab",sep="")
for (i in 1:length(sero11AEfasta)) {
RunBlatBlast8(querySeqs = sero11AEfasta[[i]], refNuc = assign11Eref, blatOutput = sero11AEtab[[i]])
}
tabinSero11AE <- dir(pattern=".11AE.tab")
Sero11AEout<-NULL
for (i in 1:length(tabinSero11AE)) Sero11AEout[[i]] <- read.delim(tabinSero11AE[i],header=F,sep="\t")
sortSero11AEout<-NULL
for (i in 1:length(tabinSero11AE)) sortSero11AEout[[i]] <- Sero11AEout[[i]][order(-Sero11AEout[[i]]$V12),]
headSero11AE<-NULL
for (i in 1:length(tabinSero11AE)) headSero11AE[[i]] <- sortSero11AEout[[i]][1,]
headSero11AEout <- file("11AE_head_out",open="a")
for (i in 1:length(tabinSero11AE)) {
write.table(headSero11AE[[i]],file=headSero11AEout,sep="\t",row.names=FALSE,col.names=FALSE,quote=FALSE)
}
close(headSero11AEout)
blatresSero11AE <- read.delim("11AE_head_out",header=F,sep="\t")
addSero11AEdata <- cbind(sero11AEid, blatresSero11AE)
for (i in 1:length(addSero11AEdata$V7)) {
if (addSero11AEdata$V4[i]>1000)
{addSero11AEdata$V13[i]="11A"}
else if (addSero11AEdata$V4[i]<900)
{addSero11AEdata$V13[i]="11E"}
}
assignSero11AEfinal <- addSero11AEdata[,c("sero11AEid","V13")]
} else if (nrow(idSero11AE)==0) {
cat("No serotype 11A/E found","\n")
}
} else if (nrow(sero11Results)==0) {
cat("No serotype 11 sequences found","\n")
}
#################################
## Identify serotypes 18B and 18C
#################################
if (nrow(sero18Results)>0) {
fasta18 <- sero18Results$filePath
fasta18ID <- sero18Results$id
tab18 <- paste(fasta18ID,".18all.tab",sep="")
n18 <- length(fasta18)
for (i in 1:n18) {
RunBlatBlast8(querySeqs = fasta18[[i]], refNuc = assign18BCref, blatOutput = tab18[[i]])
}
tabinSero18 <- dir(pattern=".18all.tab")
sero18out<-NULL
for (i in 1:length(tabinSero18)) sero18out[[i]] <- read.delim(tabinSero18[i],header=F,sep="\t")
sortSero18out<-NULL
for (i in 1:length(tabinSero18)) sortSero18out[[i]] <- sero18out[[i]][order(-sero18out[[i]]$V12),]
headSero18<-NULL
for (i in 1:length(tabinSero18)) headSero18[[i]] <- sortSero18out[[i]][1,]
headSero18out <- file("18_head_out",open="a")
for (i in 1:length(tabinSero18)) {
write.table(headSero18[[i]],file=headSero18out,sep="\t",row.names=FALSE,col.names=FALSE,quote=FALSE)
}
close(headSero18out)
blatresSero18 <- read.delim("18_head_out",header=F,sep="\t")
for (i in 1:length(blatresSero18$V7)) {
if (blatresSero18$V4[i]>900)
{blatresSero18$V13[i]="18C"}
else if (blatresSero18$V4[i]<900)
{blatresSero18$V13[i]="18B"}
}