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1 # AIM: Test some IO features betweent Python/Galaxy and R
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2 #
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3 # Author: Christian Hundsrucker
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4 ###############################################################################
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5 #options(echo=FALSE) #non-interactive -> galaxy
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6 #options(echo=TRUE)
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7 #I/O
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8 #args: filename input
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9 cargs <- commandArgs(trailingOnly = TRUE)
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10 args.no<-length(cargs)-1 #last argument is output-file
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11 outputfile<-cargs[args.no+1]
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12
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13 #functions
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14 mapKV<-function(keyValue){
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15 if (length(keyValue)>2){
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16 stop("Wrong arguments used!")
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17 }
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18 if (length(keyValue)==2){
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19 value<-keyValue[2]
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20 names(value)<-keyValue[1]
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21 }else {
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22 value<-keyValue[1]
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23 names(value)<-""
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24 }
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25 return(value)
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26 }
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27
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28 KVargs<-strsplit(cargs[1:args.no],"([ \t])*=([ \t])*",fixed = FALSE, perl = FALSE, useBytes = FALSE)
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29 keyValues<-unlist(lapply(KVargs,mapKV))
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30
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31 output<-paste(names(keyValues),keyValues,sep=" -- ")
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32 output<-paste(output,"\n","current dir: ",getwd(),"\n",sep="")
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33 capture.output(print(output),file=outputfile,append=FALSE)
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