Nothing
checkSpeciesTable <-
function(checkMQ){
if(length(checkMQ)> 0){
# dbLib <- list.files(checkMQ,recursive = T,pattern = "databases.xml",full.name = T)[1]
# try(dbLib <- readLines(dbLib),silent = T)
species.path <- list.files(path.package("mqqc"),pattern = "MQQCspecies.txt",full.name = T,recursive = T)
file.rename(species.path,species.path2 <- paste(dirname(species.path),"MQQCspecies.txt",sep = "/"))
species <- read.csv(species.path2,sep = "\t")
sp <- species$Fasta
sp <- sp[!is.na(sp)]
sp <- sapply(as.character(sp),file.exists)
# colBad <- c()
# for(i in 1:length(species$Fasta)){
# test.grep <- grep(paste("filename=\"",basename(as.character(species$Fasta[i])),"\"",sep =""),dbLib,fixed = T)
# hm <- gsub(" ","",dbLib[test.grep])
#
#
# if(length(test.grep) == 0|!file.exists(as.character(species$Fasta[i]))){
# colBad <- c(colBad,i)
# }
#
# }
if(any(!sp)){
tkFix <- tkmessageBox(type = "yesnocancel",icon = "question",message = "Could not resolve paths to fasta files. Fix paths?")
if(tclvalue(tkFix) == "no"){ fix(species)
write.table(species,file =paste(path.package("mqqc"),"data/MQQCspecies.txt",sep = "/"),quote = F, row.names = F,sep = "\t")
}
if(tclvalue(tkFix) == "yes"){
try(speciesTK(species[!sp,]))
if(exists("mqqcSpeciesSet",envir = .GlobalEnv)){
species$Fasta[!sp] <- .GlobalEnv$mqqcSpeciesSet
write.table(species,file =paste(path.package("mqqc"),"data/MQQCspecies.txt",sep = "/"),quote = F, row.names = F,sep = "\t")
}
}
}
}
}
#checkSpeciesTable()
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