script to offset coordinates of from the annotation file to perform *upstream*/*downstream* analyses

diff --git a/testing/disp_annCoords-pmXXpb.R b/testing/disp_annCoords-pmXXpb.R
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+
+##########################################################################
+#
+# This script can be used for *upstream/downstream* analysis of reads in
+# ChIP-Seq data utilizing the RACS pipeline.
+# If upstream/downstream considerations have to be done when analyising
+# ChIP-Seq data, this script will allow the user to offset the annotation
+# file by an specif number of pair-bases.
+# Then the usual methods implemented in the RACS pipeline can be used as usual
+# to study the data in reference to the modified annotation file, effectively
+# resulting in the comparison of "wider"/"slimer" regions in relationship to the
+# original annotation file.
+# Another way to describe this in terms of a relative change of coordinates,
+# instead of changing the coordinates of the ChIP/INPUT files, the
+# corresponding anotation is file is coordinates-'shifted'.
+#
+# This script is part of
+#        RACS v1.0 (2018/2019) -- Open source tools for Rapid Analisys of ChIP-Seq data
+#
+#
+# Usage:
+#	Rscript modif_TT-pmXXpb.R  N  [refTable]
+#
+# where N is the number of pair-bases to shift the reference table
+# and 'refTable' is the filename of the annotation file, if this argument is
+# not specified the annotation file for the T.thermophila will be assumed.
+#
+###########
+
+
+usage <- function() {
+	cat("How to use this script: \n")
+	cat(" Rscript modif_TT-pmXXpb.R  N [refTable] \n \n")
+
+	cat(" where N is the number of pb to shift the ref. table \n")
+	cat(' "refTable" is the filename of the annotation file, if not specified we will assume the T.Thermophila one, ie. "T_thermophila_June2014.gff3"')
+	stop("please try again!")
+}
+
+error <- function(msg) {
+	cat(msg,'\n')
+	usage()
+}
+
+
+# read command line arguments
+args <- commandArgs(trailingOnly=T)
+NbrArgs <- length(args)
+
+if (NbrArgs < 1) error("This script requires at least one argument")
+if (NbrArgs > 2) error("This script uses upto 2 arguments!")
+
+# determine number of pb to offset the ranges...
+# 1st check that is a number indeed
+if (is.na(as.numeric(args[1]))) {
+	error("The first argument should be a possitive number representing the pb offset to apply to the ref. file!")
+} else {
+	pb <- as.numeric(args[1])
+
+	# check that is a positive number!
+	if (pb<0) error("The first argument should be a possitive number representing the pb offset to apply to the ref. file!")
+}
+
+cat("Offset: ",pb,'\n')
+
+# check that the second argument is an existent file
+if (file.exists(args[2])) {
+	refTable <- args[2]
+} else {
+	defRef <- "T_thermophila_June2014.gff3"
+	cat("Ref. file not specified or not found...",'\n')
+	cat(" assuming 'Tetrahymena Thermophila' ref. file: ",defRef,'\n')
+	refTable <- defRef
+}
+
+# read ref. file...
+cat(" . reading ref. table ", refTable, '\n')
+# check that ref.file exists...
+if (file.exists(refTable)) {
+	TT <- read.csv(refTable, sep='\t', header=F)
+} else {
+	error(paste(refTable,"NOT found!"))
+}
+
+
+
+###
+# offset regions...
+cat(" .. offsetting regions...",'\n')
+
+## "upstream"
+# take care of the limits at the beggining...
+# ie. check for cases where the beggining of the region is smaller than the offset...
+to1 <- TT$V4<=pb
+# set such cases to 1
+TT[to1,]$V4 <- 1
+# and the rest to the propper offset
+TT[!to1,]$V4 <- TT[!to1,]$V4-pb
+
+## "downstream"
+# define key for  the whole scaffold
+scfldID <- "supercontig"
+# obtain a new dataframe for each scaffold with begginings and *ends*
+scflds <- data.frame(TT[TT$V3==scfldID,]$V1, TT[TT$V3==scfldID,]$V4, TT[TT$V3==scfldID,]$V5)
+names(scflds) <- c("V1", "V4", "V5")
+# go over each entry...
+lowerLim <- 1
+upperLim <- dim(TT)[1]
+toEnd <- 0
+for (scfl in lowerLim:upperLim) {
+	# check that the record is not the scaffold information given by the 'scfldID' keyword, eg. "supercontig"
+	if (TT[scfl,]$V3 != scfldID) {
+		# look for the maximum of the scaffold
+		maxScfld <- scflds[scflds$V1 == TT[scfl,]$V1,]$V5
+		# assign either ending+pb OR max.scaffold to the ending of the region
+		#cat(maxScfld, TT[scfl,]$V5 , min(TT[scfl,]$V5+pb, maxScfld) )
+		#cat("\n")
+		TT[scfl,]$V5 <- min(TT[scfl,]$V5+pb, maxScfld)
+		if (TT[scfl,]$V5== maxScfld) toEnd <- toEnd+1
+	} else {
+		cat(" +--> at scaffold", as.character(TT$V1)[scfl], paste("(",scfl,"/",upperLim,")", sep=''), '\n')
+	}
+}
+###
+
+# some stats to print out
+cat("elements shifted to the beggining of the region ", length(to1), '\n')
+cat("elements topped at the end of the region: ", toEnd, '\n')
+
+# save file...
+outputFile <- paste(refTable,'__',pb,"pb", sep='')
+cat(" ... saving file into:",outputFile,'\n')
+write.table(TT,file=outputFile, sep='\t', quote=FALSE, col.names=FALSE, row.names=FALSE)
+
+
+#########