diff export_to_fastq/export_to_fastq_past.R @ 0:97792524cc9c default tip

Migrated tool version 0.1 from old tool shed archive to new tool shed repository

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/export_to_fastq/export_to_fastq_past.R	Tue Jun 07 17:21:49 2011 -0400
@@ -0,0 +1,49 @@
+my.args <- commandArgs(trailingOnly = TRUE)
+# ----- Check input and output directories -----
+if(!file.exists(my.args[1])){ 
+   stop("The provided project directory does not exist!")
+}
+inputDirectory=my.args[1] #Directory where input data are. (e.g export or fastq ...)
+
+output_file = my.args[3]
+
+threshold=as.numeric(my.args[2]) #threshold for nFilter
+
+#print(my.args)
+
+library(ShortRead)
+#source('/home/galaxy/galaxy_dev/tools/EMBL_tools/HTS_helper_src_for_export_to_fastq.R')
+
+####Solution temporaire, chastityFilter sera dans le RNASeq package 
+chastityFilter <- function(.name="Illumina Chastity Filter") 
+{
+  srFilter(function(x){
+    if(any(rownames(varMetadata(alignData(x))) == "filtering")){
+      keep<-alignData(x)$filtering=="Y"
+    } else {
+      warning(paste("The '",.name,"' filter is only valid for Illumina reads.",sep=""))
+      keep<-rep(TRUE,length(x))
+    }
+    return(keep)
+  },name=.name)
+}
+
+"summarize.by.transcripts" <- function(sample,annotation){
+  
+  transcripts <- do.call(rbind,lapply(names(sample),function(chr,sample,annotation){
+    counts<-stats:::aggregate(sample[[chr]],list(transcript=annotation[chr]$transcript),sum)
+  },sample,annotation))
+
+  colnames(transcripts)[2] <- "counts"
+  
+  return(transcripts)
+}
+###
+
+#----- FILTER ----
+filter<- compose(chastityFilter(),nFilter(threshold=threshold))
+
+#----- ALIGN ----
+# call the readAligned function with this filter
+aln<-readAligned(inputDirectory, type='SolexaExport',filter=filter, withAll=TRUE )
+writeFastq(aln,file=output_file,mode='a')