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#!/usr/bin/Rscript
# Copyright (c) 2014,
# Mathias Kuhring, KuhringM@rki.de, Robert Koch Institute, Germany,
# All rights reserved. For details, please note the license.txt.
# surankco-prediction: prediction of scores and ranking of contigs using
# trained random forests (from surankco-training) and
# contig features (from surankco-feature)
# get script path
args <- commandArgs(trailingOnly = FALSE)
script.arg <- "--file="
script.name <- sub(script.arg, "", args[grep(script.arg, args)])
script.path <- dirname(script.name)
# testing/debugging
# args <- c("--features=data/adenoABC.features.txt", "-r", "surankco_RFs.RData")
# script.path <- getwd()
DEBUGGING <- FALSE
# sources and libraries
source(paste('/usr/lib/R/site-library/surankco', '/parameter.R', sep=""))
source(paste('/usr/lib/R/site-library/surankco', '/import.R', sep=""))
source(paste('/usr/lib/R/site-library/surankco', '/rf.R', sep=""))
source(paste('/usr/lib/R/site-library/surankco', '/voting.R', sep=""))
# ...
loadPackages(c("optparse","randomForest"), quietly=TRUE)
# parsing parameter
cat("prepare files\n")
parameters <- parseSurankcoPrediction()
if (DEBUGGING){
print(args)
print(parameters)
print(parameters$files.features)
print(parameters$files.rf)
}
# import feature files and RFs
cat("import features and RFs\n")
features <- read.table(file=parameters$files.features, sep="\t",
dec = ".", header=TRUE,
colClasses=get.colClasses(parameters$files.features, 3))
rf.loaded <- load(parameters$files.rf)
if (!all(c("rfs") %in% rf.loaded)){
print("error")
}
# prepare datacat
cat("prepare data\n")
features <- dataFilter(features)
metadata <- features[ ,1:3]
features <- features[ ,-c(1:3)]
# prediction
cat("predict scores\n")
prediction <- scorePrediction(rfs=rfs, input=features, type="response")
weighting <- scorePrediction(rfs=rfs, input=features, type="prob")
# voting and ranking
cat("vote and rank\n")
final.scores <- weightedVotingSum(scoreList=prediction, weightList=weighting)
results <- cbind(metadata, SurankcoContigScore=final.scores)
results <- results[order(results$SurankcoContigScore, decreasing=TRUE),]
# export rankings
cat("export ranking\n")
write.table(results, file=parameters$output.filename,
sep="\t", dec = ".", col.names=TRUE, row.names=FALSE)
# done
cat("surankco-prediction calculations done\n")
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